RetrogeneDB ID: retro_ptro_2604

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:22204755..22205937(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CLK2
• Ensembl ID: ENSPTRG00000001419
• Aliases: None
• Description: None

Sequence

>retro_ptro_2604
AGTAGTAGTGACCGGACACGACGGCGCCGGCGAGAGGACAGCTACCATGTCCGGAGGAGGTGCAGCCGGACATTTAGCCG
CTCGTCTTCGCAGCACAGCAGCCGGAAAGCCAAGAGTGTAGAGGACGACGCTGAGGGCCACCTCATCTACCACGTCGGGG
ACTGGCTACAAGAGCGATATGAAATCGTCAGCACCTTAGGAAAGGGGACCTTCGGCCGAGTTGTACAATGTGTTGACCAT
CGCAGGGGTGGGGCTCGAGTTGCCCTGAAGATCATTAAGAATGTGGAGAAGTATAAGGAAGCAGCTCGACTTGAGATCAA
CGTGCTGGAGAAAATCAACGAGAAAGACCCTGGCAAGAACCTCTGTGTCCAGATGTTTGACTGGTTCGACTACCATGGCC
ACATGTGTATCTCCTTGGAGCTTCTGGGCCTTAGCACCTTCGATTTCCTCAAAGACAACAACCACCTGCCCTACCCCATC
CACCAAGTGCACCACATGGCCTTCCAGCTGTGTCAGGCTGTCAAGTTCCTCCATGATAACAAGCTGACACATACAGACCT
CAAGCCTGAAAATATTCTGTTTGTGGATTCAGACTATGAGCTCACCTACAACCTAGAGAAGAAGCGACATGAGCGCAGTG
TGAAGAGCACAGCTGTGCGGGTGGGAGACTTTGGCAGTGCCACCTTTGACCATGAGCACCATAGGACCATTGTCTCCACT
CGCCATTACCGAGCACCAGAAGTCATCCTTGAGTTGGGCTGGTCACAGCCTTGTGATGTGTGGAGTATAGGCTGCATCAT
CTTTGAGTACTACGTGGGCTTCACCCTCTTCCAGACCCATGACAACAGACAGCATCTAGCCACGATGGAAAGGATCTTGG
GTCCTATCCCTTCCCGGATGATCCGAAAGACAAGAAAACAGAAATATTTTTACCGGGGTCGCCTGGATTGGGATGAGAAC
ACATCAGCTGGGCGCTATGTTCGTGAGAACTGCAAACCGCTGCGGCAGTATCTGACCTCAGAGGCAGAGGAAGACCACCA
GCTCTTCGATCTGATTGAAAGCATGCTAGAGTATGAACCAGCTCAGCGGCTGACCTTGGGTGAAGCCCTTCAGCATCCTT
TCTTCGCCCGCCTTTGGGCTGAGCCACCCAACAAGTTGTGGGACTCCAGTCAGGATATCAGT

Alignment

ORF - retro_ptro_2604 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.15 %
• Parental protein coverage: 78.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NSSYRSQRSSRR-KHRRRRRRSRTFSRSSSQHSSRRAKSVEDDAEGHLIYHVGDWLQERYEIVSTLGEGT
          .SS.R..R..R......RRR.SRTFSRSSSQHSSR.AKSVEDDAEGHLIYHVGDWLQERYEIVSTLG.GT
Retrocopy SSSDRTRRRRREDSYHVRRRCSRTFSRSSSQHSSRKAKSVEDDAEGHLIYHVGDWLQERYEIVSTLGKGT

Parental  FGRVVQCVDHRRGGARVALKIIKNVEKYKEAARLEINVLEKINEKDPDNKNLCVQMFDWFDYHGHMCISF
          FGRVVQCVDHRRGGARVALKIIKNVEKYKEAARLEINVLEKINEKDP..KNLCVQMFDWFDYHGHMCIS.
Retrocopy FGRVVQCVDHRRGGARVALKIIKNVEKYKEAARLEINVLEKINEKDP-GKNLCVQMFDWFDYHGHMCISL

Parental  ELLGLSTFDFLKDNNYLPYPIHQVRHMAFQLCQAVKFLHDNKLTHTDLKPENILFVNSDYELTYNLEKKR
          ELLGLSTFDFLKDNN.LPYPIHQV.HMAFQLCQAVKFLHDNKLTHTDLKPENILFV.SDYELTYNLEKKR
Retrocopy ELLGLSTFDFLKDNNHLPYPIHQVHHMAFQLCQAVKFLHDNKLTHTDLKPENILFVDSDYELTYNLEKKR

Parental  DERSVKSTAVRVVDFGSATFDHEHHSTIVSTRHYRAPEVILELGWSQPCDVWSIGCIIFEYYVGFTLFQT
          .ERSVKSTAVRV.DFGSATFDHEHH.TIVSTRHYRAPEVILELGWSQPCDVWSIGCIIFEYYVGFTLFQT
Retrocopy HERSVKSTAVRVGDFGSATFDHEHHRTIVSTRHYRAPEVILELGWSQPCDVWSIGCIIFEYYVGFTLFQT

Parental  HDNREHLAMMERILGPIPSRMIRKTRKQKYFYRGRLDWDENTSAGRYVRENCKPLRRYLTSEAEEHHQLF
          HDNR.HLA.MERILGPIPSRMIRKTRKQKYFYRGRLDWDENTSAGRYVRENCKPLR.YLTSEAEE.HQLF
Retrocopy HDNRQHLATMERILGPIPSRMIRKTRKQKYFYRGRLDWDENTSAGRYVRENCKPLRQYLTSEAEEDHQLF

Parental  DLIESMLEYEPAKRLTLGEALQHPFFARLRAEPPNKLWDSSRDIS
          DLIESMLEYEPA.RLTLGEALQHPFFARL.AEPPNKLWDSS.DIS
Retrocopy DLIESMLEYEPAQRLTLGEALQHPFFARLWAEPPNKLWDSSQDIS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.13 RPM	25.10 RPM
SRP007412_cerebellum	0.07 RPM	33.27 RPM
SRP007412_heart	0.06 RPM	9.85 RPM
SRP007412_kidney	0.03 RPM	38.31 RPM
SRP007412_liver	0.03 RPM	25.40 RPM
SRP007412_testis	40.47 RPM	23.29 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2604 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2604 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2604 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3827

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000176444	1 retrocopy	retro_hsap_3827,
Gorilla gorilla	ENSGGOG00000009438	1 retrocopy	retro_ggor_2575,
Nomascus leucogenys	ENSNLEG00000012062	2 retrocopies	retro_nleu_2126, retro_nleu_3112,
Pan troglodytes	ENSPTRG00000001419	1 retrocopy	retro_ptro_2604 ,
Pan troglodytes	ENSPTRG00000007278	1 retrocopy	retro_ptro_405,
Pan troglodytes	ENSPTRG00000017683	1 retrocopy	retro_ptro_2859,
Tupaia belangeri	ENSTBEG00000000216	2 retrocopies	retro_tbel_4081, retro_tbel_4274,