RetrogeneDB ID: retro_ptro_2727

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:11707944..11708430(-)
• Located in intron of: ENSPTRG00000020012

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLTA
• Ensembl ID: ENSPTRG00000020930
• Aliases: None
• Description: clathrin, light chain A [Source:HGNC Symbol;Acc:2090]

Sequence

>retro_ptro_2727
ATGGCTGAGCAAGATCCATTCGGTGTCCCTGCTGGCACCCCTGGGGATCCTGTCCTGGGGAACGGAGTGGCTGGCGCCAG
TGAAGAAGACCCAGCTGCGGCCTTCTTGGCACAGCAAGAGAGCAAGACTACGGGTATCAAGAACAACAAGGTCGCCTTCG
ACATCCTGGATGGTGTCACCCCCAGGCCCCAGCCACAAGGTGAACAGCTGGGAGTCCAGATGCTGTTGACGGAGTGATGA
TGGTGACTACTACCAGGAAAGTAATGGTCCAAGAGACAATTATGCAGCTATTTCACAAGTGGATCAATTCCAATCCAGCC
TGAAAATATATGCAGATGGAAAGAAGAGAAAATGGAATGCTTAGAAGCCCTTGCTGCTTATTCTCAGAAGCAAGAAGCAG
AGTGGAAAGAAAAAGTGATAAATGAGCTAGAAGAATGGCGTGCAAGACGAGCAGCTACAGAAAAGAAAGGCAAACTACAG
GGCAGA

Alignment

ORF - retro_ptro_2727 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.07 %
• Parental protein coverage: 65.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAELDPFGAPAGAPGGPALGNGLAGAGEEDPAAAFLAQQESEIAGIENDE-AFAILDGGTPGPQPHGE-P
          MAE.DPFG.PAG.PG.P.LGNG.AGA.EEDPAAAFLAQQES...GI.N...AF.ILDG.TP.PQP.GE..
Retrocopy MAEQDPFGVPAGTPGDPVLGNGVAGASEEDPAAAFLAQQESKTTGIKNNKVAFDILDGVTPRPQPQGE<T

Parental  PGGPDAVDGVM-NGEYYQESNGPTDSYAAISQVDRLQS-EPESIRKWREEQMERLEALDANSRKQEAEWK
          .G.PDAVDGVM..G.YYQESNGP.D.YAAISQVD..QS..PE.I..W.EE.ME.LEAL.A.S.KQEAEWK
Retrocopy AGSPDAVDGVM<DGDYYQESNGPRDNYAAISQVDQFQS<QPENICRWKEEKMECLEALAAYSQKQEAEWK

Parental  EKAIKELEEWHARQDEQLQKTKANNR
          EK.I.ELEEW.AR......K.K...R
Retrocopy EKVINELEEWRARRAATEKKGKLQGR

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	0.00 RPM	98.35 RPM
SRP007412_cerebellum	0.04 RPM	104.50 RPM
SRP007412_heart	0.00 RPM	21.19 RPM
SRP007412_kidney	0.00 RPM	98.85 RPM
SRP007412_liver	0.00 RPM	72.67 RPM
SRP007412_testis	0.00 RPM	87.05 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2727 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2727 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2727 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4022

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001137	1 retrocopy	retro_btau_327,
Homo sapiens	ENSG00000122705	2 retrocopies	retro_hsap_4022, retro_hsap_955,
Macropus eugenii	ENSMEUG00000010858	1 retrocopy	retro_meug_480,
Macaca mulatta	ENSMMUG00000006132	2 retrocopies	retro_mmul_2319, retro_mmul_785,
Monodelphis domestica	ENSMODG00000002610	1 retrocopy	retro_mdom_1148,
Nomascus leucogenys	ENSNLEG00000003874	1 retrocopy	retro_nleu_659,
Pongo abelii	ENSPPYG00000019069	1 retrocopy	retro_pabe_3300,
Pan troglodytes	ENSPTRG00000020930	1 retrocopy	retro_ptro_2727 ,