RetrogeneDB ID: retro_ptro_1628

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:106604871..106605351(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF3
• Ensembl ID: ENSPTRG00000018106
• Aliases: None
• Description: None

Sequence

>retro_ptro_1628
ATGCATCGTGATTCCTGTCCATTGGACTGTAAGGTTTATGTAGGCAATCTTGGAAACAATGGCAACAAGACCGAACTGGA
ACGGGCTTTTGGCTAGTATGGACCACTCCAAAGTGTGTGGGTTGCTAGAAACCCTCGCGGCTTTGCTTTTGTTGAATTTG
AAGATCCCCGAGATGCAGCTGATGTGGTCTGAGAACTAGATGGAAGAACACTATGTGGCCGCTGTGTAAGAGTGGAACTG
TCGAATGGTGATAAAAGAAGTAGAAATCGTAGCCCACCTCCCTCTTGGGGTCATCGTCCTTGAGATGATTGTCATAGGAG
GAGTCTTCCACCTCGCCGCAGATCTCCACGAAGAAGCCTCTCTCGCAGCCGGAGCAGGTCCCTTTCTAGAGATAGGAGAA
GAGAGAGATCTCTGTCTCGGGAGAGAAATCACAAGCCGTCCAGATCCTTCTCTAGGTCTCGTAGCCGATCTAGGTCAAAT

Alignment

ORF - retro_ptro_1628 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.06 %
• Parental protein coverage: 98.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT
          MHRDSCPLDCKVYVGNLGNNGNKTELERAFG.YGPL.SVWVARNP.GFAFVEFEDPRDAAD.V.ELDGRT
Retrocopy MHRDSCPLDCKVYVGNLGNNGNKTELERAFG*YGPLQSVWVARNPRGFAFVEFEDPRDAADVV*ELDGRT

Parental  LCGCRVRVELSNGEKRSRNRGPPPSWGRRPRDDYRRRSPPPRRRSPRRRSFSRSRSRSLSRDRRRERSLS
          LCG..VRVELSNG.KRSRNR.PPPSWG.RP.DD..RRS.PPRRRSP.RRS.SRSRSRSLSRDRRRERSLS
Retrocopy LCGRCVRVELSNGDKRSRNRSPPPSWGHRP*DDCHRRSLPPRRRSP-RRSLSRSRSRSLSRDRRRERSLS

Parental  RERNHKPSRSFSRSRSRSRSN
          RERNHKPSRSFSRSRSRSRSN
Retrocopy RERNHKPSRSFSRSRSRSRSN

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	0.07 RPM	29.10 RPM
SRP007412_cerebellum	0.04 RPM	100.77 RPM
SRP007412_heart	0.06 RPM	63.28 RPM
SRP007412_kidney	0.03 RPM	62.35 RPM
SRP007412_liver	0.16 RPM	71.98 RPM
SRP007412_testis	0.00 RPM	147.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1628 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1628 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1628 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2299

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016062	5 retrocopies	retro_cjac_1035, retro_cjac_1969, retro_cjac_2006, retro_cjac_620, retro_cjac_746,
Dasypus novemcinctus	ENSDNOG00000000421	9 retrocopies	retro_dnov_1326, retro_dnov_1513, retro_dnov_1702, retro_dnov_1951, retro_dnov_2153, retro_dnov_2328, retro_dnov_2491, retro_dnov_569, retro_dnov_784,
Equus caballus	ENSECAG00000018741	2 retrocopies	retro_ecab_178, retro_ecab_961,
Gorilla gorilla	ENSGGOG00000017186	5 retrocopies	retro_ggor_1654, retro_ggor_1706, retro_ggor_2030, retro_ggor_2746, retro_ggor_630,
Loxodonta africana	ENSLAFG00000018193	2 retrocopies	retro_lafr_1219, retro_lafr_80,
Myotis lucifugus	ENSMLUG00000010671	6 retrocopies	retro_mluc_1205, retro_mluc_1312, retro_mluc_1554, retro_mluc_2283, retro_mluc_278, retro_mluc_51,
Mus musculus	ENSMUSG00000071172	9 retrocopies	retro_mmus_100, retro_mmus_1347, retro_mmus_1749, retro_mmus_2294, retro_mmus_2337, retro_mmus_2433, retro_mmus_2654, retro_mmus_2933, retro_mmus_3629,
Oryctolagus cuniculus	ENSOCUG00000006684	3 retrocopies	retro_ocun_415, retro_ocun_772, retro_ocun_970,
Otolemur garnettii	ENSOGAG00000000502	6 retrocopies	retro_ogar_1850, retro_ogar_1959, retro_ogar_2131, retro_ogar_2783, retro_ogar_597, retro_ogar_803,
Pan troglodytes	ENSPTRG00000013506	1 retrocopy	retro_ptro_3057,
Pan troglodytes	ENSPTRG00000018106	4 retrocopies	retro_ptro_1566, retro_ptro_1628 , retro_ptro_2776, retro_ptro_533,
Sus scrofa	ENSSSCG00000001564	1 retrocopy	retro_sscr_1038,
Ictidomys tridecemlineatus	ENSSTOG00000014280	5 retrocopies	retro_itri_123, retro_itri_502, retro_itri_664, retro_itri_857, retro_itri_901,