RetrogeneDB ID: retro_ptro_3057

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL392652.1:772046..773053(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF6
• Ensembl ID: ENSPTRG00000013506
• Aliases: None
• Description: serine/arginine-rich splicing factor 6 [Source:HGNC Symbol;Acc:10788]

Sequence

>retro_ptro_3057
ATGCCGCGCGTCTACATAGGACGCCTGAGCTACAACGTCCAGGAGAAGGCCATCCAGCGCTTTTTCAGTGGCTATGGCCG
CCTCCTCGAAGTAGACCTCAAAAATGGCTACGGCTTCGTGGAGTTCGAGGACTCCCGCGACACCGACGACGCCCTTTACG
AGCTGAACGGCGAGGAGCTCTGCGGCGAGCGCGTGATCGTAGAGCACGCCCGGGGCCCGCGTCGCAATCGCGACGGCTAC
AGCTACGGAAGCCGCCGTGGTGGAGGTGGATACAGCAGTCGGAGACATCTGGCAGAGACAAATACGGACCACCTGTTTGT
ACAGAATACAGGCTTATTGTAGAAAATCTTTCTAGTCTGTGCAGTTGGCAAGATTTAAAGGATTTTATGCGACAAGCAGG
TTAAGTAACCTGTGCGGATGCCCACAAGGAAGGAACAAATGAGGGTGTAATTGAGTTTCGCTCCTACTCTGACATGAAGC
GTGCTTTGGACAAACTGGATGGCACAGAAATAAATGGCAGAAATATTAGGCTTATTGAAGATAAGCCACGCACAAGCCAT
AGGCGATCTTACTCTGGAAGCAGATCCAGCTCTCGATCTAGAAGATGGTCACGAAGTAGGAGTCGCAGGAGCAGCCGCAG
TAGATCTCGAAGTGTCTCAAAAAGTCGCTCCCGTTCCAGGTCGCGGAGCAAAGGTCGATCACGTTCTCGATCAAAAGGCA
GGAAATCTAGATCAAAGAGCAAATCTAAGCCCAAGTCTGATCGGGGCTCCCATTCACATTCTCGAAGCAGATCTAAGGAT
GAGTATGAGAAATATCGAAGCAGGTCTCGGTCCGGATCCCCCAAAGGAAATGGAAAGGGTGATACAAAGTCAAAATCCAG
ATCAAGGAGCCAGTCCCGTTCCAATTCGCCGCTACCTGGTCCACCCTGAAAGGCCCGTTCTGTGTCCCCTCCACCAAAAA
GAGCTACTTCAAGATCCCGTTCTAGATCTCGCTCAAAGTCAAGATCA

Alignment

ORF - retro_ptro_3057 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.1 %
• Parental protein coverage: 97.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPLEEIGRLSYNVREKDIQRFFSG-SRLLEVGLKKGYGFVEFEDSRDADDAVYELNGKELCGERVIVEHA
          MP...IGRLSYNV.EK.IQRFFSG..RLLEV.LK.GYGFVEFEDSRD.DDA.YELNG.ELCGERVIVEHA
Retrocopy MPRVYIGRLSYNVQEKAIQRFFSGYGRLLEVDLKNGYGFVEFEDSRDTDDALYELNGEELCGERVIVEHA

Parental  RGPRRDRDGYSYGSRSGGGGYSSRR-TSGRDKYGPPVRTEYRLIVENLSSRCSWQDLKDFMRQAGEVTYA
          RGPRR.RDGYSYGSR.GGGGYSSRR.TSGRDKYGPPV.TEYRLIVENLSS.CSWQDLKDFMRQAG.VT.A
Retrocopy RGPRRNRDGYSYGSRRGGGGYSSRR<TSGRDKYGPPVCTEYRLIVENLSSLCSWQDLKDFMRQAG*VTCA

Parental  DAHKERTNEGVIEFRSYSDMKRALDKLDGTEINGRNIRLIEDKPRTSHRRSYSGSRSRSRSRRRSRSRSR
          DAHKE.TNEGVIEFRSYSDMKRALDKLDGTEINGRNIRLIEDKPRTSHRRSYSGSRS.SRSRR.SRSRSR
Retrocopy DAHKEGTNEGVIEFRSYSDMKRALDKLDGTEINGRNIRLIEDKPRTSHRRSYSGSRSSSRSRRWSRSRSR

Parental  RSSRSRSRSISKSRSRSRSRSKGRSRSRSKGRKSRSKSKSKPKSDRGSHSHSRSRSKDEYEKSRSRSRSR
          RSSRSRSRS.SKSRSRSRSRSKGRSRSRSKGRKSRSKSKSKPKSDRGSHSHSRSRSKDEYEK.RSRSRS.
Retrocopy RSSRSRSRSVSKSRSRSRSRSKGRSRSRSKGRKSRSKSKSKPKSDRGSHSHSRSRSKDEYEKYRSRSRSG

Parental  SPKENGKGDIKSKSRSRSQSRSNSPLPVPPSKAHSVSPPPKRATSRSRSRSRSKSRS
          SPK.NGKGD.KSKSRSRSQSRSNSPLP.PP.KA.SVSPPPKRATSRSRSRSRSKSRS
Retrocopy SPKGNGKGDTKSKSRSRSQSRSNSPLPGPP*KARSVSPPPKRATSRSRSRSRSKSRS

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	1.75 RPM	28.90 RPM
SRP007412_cerebellum	0.86 RPM	43.34 RPM
SRP007412_heart	0.15 RPM	20.40 RPM
SRP007412_kidney	1.86 RPM	56.78 RPM
SRP007412_liver	0.98 RPM	39.18 RPM
SRP007412_testis	0.21 RPM	53.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3057 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3057 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3057 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1809
Gorilla gorilla	retro_ggor_2176
Pongo abelii	retro_pabe_1483

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002061	1 retrocopy	retro_acar_191,
Echinops telfairi	ENSETEG00000006221	1 retrocopy	retro_etel_1261,
Homo sapiens	ENSG00000124193	1 retrocopy	retro_hsap_1809,
Gorilla gorilla	ENSGGOG00000009808	1 retrocopy	retro_ggor_2176,
Monodelphis domestica	ENSMODG00000003107	1 retrocopy	retro_mdom_697,
Nomascus leucogenys	ENSNLEG00000006524	1 retrocopy	retro_nleu_1294,
Oryctolagus cuniculus	ENSOCUG00000009785	1 retrocopy	retro_ocun_312,
Pongo abelii	ENSPPYG00000011019	1 retrocopy	retro_pabe_1483,
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,
Rattus norvegicus	ENSRNOG00000006380	1 retrocopy	retro_rnor_1752,
Tursiops truncatus	ENSTTRG00000015410	2 retrocopies	retro_ttru_1786, retro_ttru_1787,