Ciclev10004015m, PAC:20786149 (mRNA) Citrus clementina

Transcript Overview


Name	Ciclev10004015m
Unique Name	PAC:20786149
Type	mRNA
Organism	Citrus clementina (Clementine)
Sequence length	1770

Analyses

This mRNA is derived from or has results from the following analyses


Analysis Name	Date Performed
Citrus clementina genome v1.0 (JGI)	2012-12-20
InterProScan analysis of Citrus clementina v1.0 transcripts	2012-12-17
C. clementina v1.0 CDS	2018-06-06

Orthologs

Syntenic blocks


Syntentic block	Assembly	Species
cccsR166	Citrus sinensis genome v1.1 (JGI)	Citrus sinensis
ccptR090	Poncirus trifoliata genome v1.3.1 (JGI)	Poncirus trifoliata
ccclpR134	Citrus limon L. Burm f. genome v1.0 - Primary	Citrus limon
ccclaR135	Citrus limon L. Burm f. genome v1.0 - Alternative	Citrus limon
cccsiR120	Citrus sinensis Valencia genome v1.0 (HZAU)	Citrus sinensis
ccdvaR079	Citrus sinensis cv. Valencia DVS_A genome v1.0	Citrus sinensis
ccdvbR067	Citrus sinensis cv. Valencia DVS_B genome v1.0	Citrus sinensis
ccfhsR124	Fortunella hindsii S3y-45 genome v2.0	Fortunella hindsii
cccsnR167	Citrus sinensis cv. Newhall v1.0 genome	Citrus sinensis
cccsnR173	Citrus sinensis cv. Newhall v1.0 genome	Citrus sinensis
ccminR217	Citrus inodora CRC3784 genome v1.0	Citrus inodora
ccminR275	Citrus inodora CRC3784 genome v1.0	Citrus inodora
ccccrR161	Citrus australasica CRC3672 genome v1	Citrus australasica
ccccrR190	Citrus australasica CRC3672 genome v1	Citrus australasica
cccsgR097	Citrus sinensis cv. Gannanzao v1.0 genome	Citrus sinensis
ccmpjR127	Murraya paniculata cv. JLX genome v1.0	Murraya paniculata
cccigR100	Citropsis gilletiana cv. CGI genome v1.0	Citropsis gilletiana
cccsjR161	Citrus sinensis cv. Jinhong genome v1.0	Citrus sinensis
cccsjR180	Citrus sinensis cv. Jinhong genome v1.0	Citrus sinensis
ccneiR084	Citrus sinensis cv. Neixiu genome v1.0	Citrus sinensis
cccraR147	Citrus australasica cv. Rainbow genome v1.0	Citrus australasica
cccraR154	Citrus australasica cv. Rainbow genome v1.0	Citrus australasica
cccchR090	Citrus changshanensis cv. Huyou genome v1.0	Citrus changshanensis
ccciuR150	Citrus inodora genome v1.0 (UQ)	Citrus inodora
ccciuR172	Citrus inodora genome v1.0 (UQ)	Citrus inodora
cccrcR103	Citrus reticulata 'Chachi' cv. Dazhongyoushen genome v1.0	Citrus reticulata
cccstR091	Citrus sinensis cv. Newhall T2T v2.0 genome	Citrus sinensis
cccrmR138	Citrus reticulata cv. Murcott genome v1.0	Citrus reticulata
cccrmR149	Citrus reticulata cv. Murcott genome v1.0	Citrus reticulata
cccriR144	Citrus reticulata cv. IRM2 genome v1.0	Citrus reticulata
cccriR166	Citrus reticulata cv. IRM2 genome v1.0	Citrus reticulata

Orthologs


Gene/Transcript	Assembly	Species
orange1.1g046422m.v1.1	Citrus sinensis genome v1.1 (JGI)	Citrus sinensis
gene-KPL70_014353-mRNA1	Citrus sinensis cv. Valencia DVS_A genome v1.0	Citrus sinensis

Relationships

This mRNA is a part of the following gene feature(s):


Feature Name	Unique Name	Species	Type
Ciclev10004015m.g	Ciclev10004015m.g	Citrus clementina	gene

The following CDS feature(s) are a part of this mRNA:


Feature Name	Unique Name	Species	Type
PAC:20786149.CDS.1	PAC:20786149.CDS.1	Citrus clementina	CDS
PAC:20786149.CDS.2	PAC:20786149.CDS.2	Citrus clementina	CDS
PAC:20786149.CDS.3	PAC:20786149.CDS.3	Citrus clementina	CDS
PAC:20786149.CDS.4	PAC:20786149.CDS.4	Citrus clementina	CDS
PAC:20786149.CDS.5	PAC:20786149.CDS.5	Citrus clementina	CDS

The following polypeptide feature(s) derives from this mRNA:


Feature Name	Unique Name	Species	Type
PAC:20786149	PAC:20786149	Citrus clementina	polypeptide

Homology

[Close]

BLAST of Ciclev10004015m vs. DB:SwissProt
Match: ZMYM1_HUMAN (Zinc finger MYM-type protein 1 OS=Homo sapiens OX=9606 GN=ZMYM1 PE=1 SV=1)

HSP 1 Score: 76.6406 bits (187), Expect = 4.966e-14
Identity = 49/194 (25.26%), Postives = 101/194 (52.06%), Query Frame = 1

Query:  280 LRGHDESVNSLNRQNFMELIKLLAT-MNEEI-----NEVVLENASKNAQYIAPKIQNELLNILANKVQHKI-------RALDESHKKKMAIILRYVDCDG---FIRERFFEVVNVDDIKASTLKNEICNVLARYNLLVENLRGQGHDGASNMSREWNGLQFLFLNDCPFVYYVHCFTHRLQLVLVAVSKKVHDI 813
            LRG+D+SV+S+N+ NF+EL+++ A    EE      ++V   N+++    I   I+ E+L  + N++             ++ + K++++I +RY         I+ERF   V+ +++  + L   I   L +  + ++ + GQ +D  +N+  ++N +   F  + P   Y+HC+ H L L ++   K+V ++
Sbjct:  571 LRGNDQSVSSVNKGNFLELLEMRAKDKGEETFRLMNSQVDFYNSTQIQSDIIEIIKTEMLQDIVNEINDSSAFSIICDETINSAMKEQLSICVRYPQKSSKAILIKERFLGFVDTEEMTGTHLHRTIKTYLQQIGVDMDKIHGQAYDSTTNLKIKFNKIAAEFKKEEPRALYIHCYAHFLDLSIIRFCKEVKEL 764

The following BLAST results are available for this feature:

BLAST of Ciclev10004015m vs. DB:SwissProt

BLAST of Ciclev10004015m vs. DB:SwissProt
Analysis Date: 2018-06-06 (C. clementina v1.0 CDS)
Total hits: 1

Position :

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Match Name	E-value	Identity	Description
ZMYM1_HUMAN	4.966e-14	25.26	Zinc finger MYM-type protein 1 OS=Homo sapiens OX=...	[more]

InterPro

Analysis Name: InterProScan analysis of Citrus clementina v1.0 transcripts
Date Performed: 2012-12-17

Position :

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x 1


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR012337	Ribonuclease H-like domain	SUPERFAMILY	53098	Ribonuclease H-like	coord: 155..319 score: 3.2
IPR025398	Domain of unknown function DUF4371	PFAM	PF14291	DUF4371	coord: 94..235 score: 1.6
None	No IPR available	PANTHER	PTHR11697	FAMILY NOT NAMED	coord: 95..319 score: 2.4
None	No IPR available	PANTHER	PTHR11697:SF9	ZINC FINGER PROTEIN 237	coord: 95..319 score: 2.4

Sequences

The following sequences are available for this feature:

mRNA sequence
protein sequence
mRNA from alignment at scaffold_5:20772451..20774220+
coding sequence from alignment at scaffold_5:20772451..20774220+

mRNA sequence

>PAC:20786149 ID=PAC:20786149; Name=Ciclev10004015m; organism=Citrus clementina; type=mRNA; length=1770bp
ATGTCCCACAAATCAAAGCCAAGAAAAATTCTCCTTTCATTCTTTGCCAA
AGTAGATGGTGGTCAATCATCAAATGAGGTAAGTTCTCCATGCAATATCG
ATGCCTGCTCAAGTTCTCCTACTTCTCAAAGAGCTAAATTTGAGAAAGTC
AATATTTCATTGACTATTGAAACCCCTTATTTAGAACGTGATCCTGGATT
ACGTATGATAATCAAAACTTATCACATTGATAGACAGGAAGATGTGCGGA
TGGCGTACATAGATATGAGACCATTTCAACTCGAGCCACAAAAGTACCCA
TTGACTAAACATGGTATGTAAAATCGACAATTTTAATTGTCTTGGTCCTT
AAAATTTCCTTAGCTTGAGTATTCCATATTAAAAGACAAAACATTTTTTT
TCGTACTTTCTTTTTTATGATACATTAATTAAGTATGATGCATTTATTGT
TGATGGTTGTAAACATTGGAAATATGTTTCTTGTGGCAAAAAATGTCATT
TTACTCTACATGAACAGAGTCATAATTCTTTTCCCAATGCTGCCATGGTA
AAATGGAGCAATTTAAAGGATCCATCTAGACATATTGATAAAAGAATGAA
TGCATACTCTTCACAACAAGTTTTAGAGAATAGATTGCGGTTAAAAACCT
CAATAATAGCTATCTAGTGGTTAGCGTAATAAGCTTGTGCTTTTAGAGGT
CATGATGAGTCGGTTAATTCTCTTAATCGTCAAAATTTTATGGAATTAAT
CAAGTTATTAGCAACGATGAATGAGGAGATTAATGAAGTTGTGTTAGAGA
ATGCTTCTAAGAATGCCCAATACATAGCACCTAAGATTCAAAACGAGTTA
TTGAATATTCTTGCTAATAAAGTGCAACACAAAATTCGGGTGGAAATTAG
GGATGCTAAATTTTGTATTTTTGTTGATTAGGCACTTGATGAATCTCACA
AAAAGAAAATGGCTATTATTTTGAGATATGTTGATTGTGATGGGTTTATT
AGAGAACGTTTCTTTGAAGTTGTGAATGTTGATGACATAAAGGCCTCAAC
TCTAAAAAATGAGATATGTAATGTTCTTGCTCGGTATAATCTTTTAGTTG
AAAATTTAAGAGGTCAAGGGCATGATGGTGCTAGTAATATGTCGAGAGAG
TGGAATGGATTACAATTTTTATTTCTTAATGATTGTCCATTTGTCTATTA
TGTACATTGCTTTACTCATCGACTACAACTTGTATTAGTTGCAGTATCTA
AAAAAGTGCATGATGTATGGTTATTTTTTTACTAAGTTGAGTTCTATTGT
CAACTTTGTTAATGATTCTTTCAAACGTTATTCTAAATTAAAAGCTGCTA
AAGAAAAAGAAATTATAGGATTGATAGCTTCAAAGGAGCTTGAGACTAGT
ACAAGCGCTAATCAAGTCCAAACTTTACAAAGGCCTGGAGATACTCGTTG
GAGCTTATATTTTACTTCAGTTAGTAGGCTTATTAAGATGTTTAGTGCAA
CCCCTGAAGTTTTAAGAAAGATGTTTGATGATGGATCTAGTCCAGATTTG
TGTGGAGAAGCTAAAGGTGCGTATAGAGAGATGAAATCCTTTGAGTTTGT
GTTTATTTTGCTTTCGTTAGATAGAGCTCTTGGAATATCTAATATTCTTT
GCCAACCACTACAAAACAAAATCTTTAGACATCTTAAATGCTTTGAATAC
TCGTTGGAGCTTATATTTTACTTCAGTTAGTAGGCTTATTAAGATGTTTA
GTGCAACCTTGAAGTTTTAA

protein sequence of PAC:20786149

>PAC:20786149 ID=PAC:20786149; Name=PAC:20786149; organism=Citrus clementina; type=polypeptide; length=320bp
MSHKSKPRKILLSFFAKVDGGQSSNEYDAFIVDGCKHWKYVSCGKKCHFT
LHEQSHNSFPNAAMVKWSNLKDPSRHIDKRMNAYSSQQVLENRLRGHDES
VNSLNRQNFMELIKLLATMNEEINEVVLENASKNAQYIAPKIQNELLNIL
ANKVQHKIRALDESHKKKMAIILRYVDCDGFIRERFFEVVNVDDIKASTL
KNEICNVLARYNLLVENLRGQGHDGASNMSREWNGLQFLFLNDCPFVYYV
HCFTHRLQLVLVAVSKKVHDIELLEYLIFFANHYKTKSLDILNALNTRWS
LYFTSVSRLIKMFSATLKF*

mRNA from alignment at scaffold_5:20772451..20774220+

Legend: CDS

Hold the cursor over a type above to highlight its positions in the sequence below.

> ID=; Name=; organism= ; type=; length=1770bp; location=Sequence derived from: scaffold_5:20772451..20774220+ (Citrus clementina
ATGTCCCACAAATCAAAGCCAAGAAAAATTCTCCTTTCATTCTTTGCCAA
AGTAGATGGTGGTCAATCATCAAATGAGGTAAGTTCTCCATGCAATATCG
ATGCCTGCTCAAGTTCTCCTACTTCTCAAAGAGCTAAATTTGAGAAAGTC
AATATTTCATTGACTATTGAAACCCCTTATTTAGAACGTGATCCTGGATT
ACGTATGATAATCAAAACTTATCACATTGATAGACAGGAAGATGTGCGGA
TGGCGTACATAGATATGAGACCATTTCAACTCGAGCCACAAAAGTACCCA
TTGACTAAACATGGTATGTAAAATCGACAATTTTAATTGTCTTGGTCCTT
AAAATTTCCTTAGCTTGAGTATTCCATATTAAAAGACAAAACATTTTTTT
TCGTACTTTCTTTTTTATGATACATTAATTAAGTATGATGCATTTATTGT
TGATGGTTGTAAACATTGGAAATATGTTTCTTGTGGCAAAAAATGTCATT
TTACTCTACATGAACAGAGTCATAATTCTTTTCCCAATGCTGCCATGGTA
AAATGGAGCAATTTAAAGGATCCATCTAGACATATTGATAAAAGAATGAA
TGCATACTCTTCACAACAAGTTTTAGAGAATAGATTGCGGTTAAAAACCT
CAATAATAGCTATCTAGTGGTTAGCGTAATAAGCTTGTGCTTTTAGAGGT
CATGATGAGTCGGTTAATTCTCTTAATCGTCAAAATTTTATGGAATTAAT
CAAGTTATTAGCAACGATGAATGAGGAGATTAATGAAGTTGTGTTAGAGA
ATGCTTCTAAGAATGCCCAATACATAGCACCTAAGATTCAAAACGAGTTA
TTGAATATTCTTGCTAATAAAGTGCAACACAAAATTCGGGTGGAAATTAG
GGATGCTAAATTTTGTATTTTTGTTGATTAGGCACTTGATGAATCTCACA
AAAAGAAAATGGCTATTATTTTGAGATATGTTGATTGTGATGGGTTTATT
AGAGAACGTTTCTTTGAAGTTGTGAATGTTGATGACATAAAGGCCTCAAC
TCTAAAAAATGAGATATGTAATGTTCTTGCTCGGTATAATCTTTTAGTTG
AAAATTTAAGAGGTCAAGGGCATGATGGTGCTAGTAATATGTCGAGAGAG
TGGAATGGATTACAATTTTTATTTCTTAATGATTGTCCATTTGTCTATTA
TGTACATTGCTTTACTCATCGACTACAACTTGTATTAGTTGCAGTATCTA
AAAAAGTGCATGATGTATGGTTATTTTTTTACTAAGTTGAGTTCTATTGT
CAACTTTGTTAATGATTCTTTCAAACGTTATTCTAAATTAAAAGCTGCTA
AAGAAAAAGAAATTATAGGATTGATAGCTTCAAAGGAGCTTGAGACTAGT
ACAAGCGCTAATCAAGTCCAAACTTTACAAAGGCCTGGAGATACTCGTTG
GAGCTTATATTTTACTTCAGTTAGTAGGCTTATTAAGATGTTTAGTGCAA
CCCCTGAAGTTTTAAGAAAGATGTTTGATGATGGATCTAGTCCAGATTTG
TGTGGAGAAGCTAAAGGTGCGTATAGAGAGATGAAATCCTTTGAGTTTGT
GTTTATTTTGCTTTCGTTAGATAGAGCTCTTGGAATATCTAATATTCTTT
GCCAACCACTACAAAACAAAATCTTTAGACATCTTAAATGCTTTGAATAC
TCGTTGGAGCTTATATTTTACTTCAGTTAGTAGGCTTATTAAGATGTTTA
GTGCAACCTTGAAGTTTTAA

Coding sequence (CDS) from alignment at scaffold_5:20772451..20774220+

>PAC:20786149 ID=PAC:20786149; Name=Ciclev10004015m; organism=Citrus clementina; type=CDS; length=960bp; location=Sequence derived from: scaffold_5:20772451..20774220+ (Citrus clementina
ATGTCCCACAAATCAAAGCCAAGAAAAATTCTCCTTTCATTCTTTGCCAA
AGTAGATGGTGGTCAATCATCAAATGAGTATGATGCATTTATTGTTGATG
GTTGTAAACATTGGAAATATGTTTCTTGTGGCAAAAAATGTCATTTTACT
CTACATGAACAGAGTCATAATTCTTTTCCCAATGCTGCCATGGTAAAATG
GAGCAATTTAAAGGATCCATCTAGACATATTGATAAAAGAATGAATGCAT
ACTCTTCACAACAAGTTTTAGAGAATAGATTGCGAGGTCATGATGAGTCG
GTTAATTCTCTTAATCGTCAAAATTTTATGGAATTAATCAAGTTATTAGC
AACGATGAATGAGGAGATTAATGAAGTTGTGTTAGAGAATGCTTCTAAGA
ATGCCCAATACATAGCACCTAAGATTCAAAACGAGTTATTGAATATTCTT
GCTAATAAAGTGCAACACAAAATTCGGGCACTTGATGAATCTCACAAAAA
GAAAATGGCTATTATTTTGAGATATGTTGATTGTGATGGGTTTATTAGAG
AACGTTTCTTTGAAGTTGTGAATGTTGATGACATAAAGGCCTCAACTCTA
AAAAATGAGATATGTAATGTTCTTGCTCGGTATAATCTTTTAGTTGAAAA
TTTAAGAGGTCAAGGGCATGATGGTGCTAGTAATATGTCGAGAGAGTGGA
ATGGATTACAATTTTTATTTCTTAATGATTGTCCATTTGTCTATTATGTA
CATTGCTTTACTCATCGACTACAACTTGTATTAGTTGCAGTATCTAAAAA
AGTGCATGATATAGAGCTCTTGGAATATCTAATATTCTTTGCCAACCACT
ACAAAACAAAATCTTTAGACATCTTAAATGCTTTGAATACTCGTTGGAGC
TTATATTTTACTTCAGTTAGTAGGCTTATTAAGATGTTTAGTGCAACCTT
GAAGTTTTAA

Annotated Terms

The following terms have been associated with this mRNA:

Vocabulary: **INTERPRO**
Term	Definition
IPR012337	RNaseH-like_sf
IPR025398	DUF4371

Vocabulary: **Molecular Function**
Term	Definition
GO:0003676	nucleic acid binding