RetrogeneDB ID: retro_ggor_2176

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:63033475..63034507(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF6
• Ensembl ID: ENSGGOG00000009808
• Aliases: None
• Description: None

Sequence

>retro_ggor_2176
ATGCCGCGCGTCTACATAGGACGCCTAAGCTACAACGTCCAGGAGAAGGCCATCCAGCGCTTTTTCGGTGGCTATGGCCG
CCTCCTCGAAGTAGACCTCAAAAATGGCTACGGCTTCGTGGAGTTCGAGGACTCCCGCGACGCCGACGACGCCCTTTTAC
GAGCTGAACGGCGAGGAGCTCTGCGGCGAGCGCGTGATCGTAGAGCTCGCCCGGGGCCCGCGTCGCAATCGCGACGGCTA
CAGCTACGGAAGCCGCCGTGGTGGAGGTGGATACAGCAGTCGGAGACATCTGGCAGAGACAAATACGGACCACCTGTTCG
TACAGAATACAGGCTTATTGTAGAAAATCTTTCTAGTCTGTGCAGTTGGCGAGATTTAAAGGATTTTATGCGACAAGCAG
GTTAAGTAACCTGTGCGGATGCCCACAAGGAAGGAACAAATGAGGGTGTAATTGAGTTTCGCTCCTACTCTGACATGAAG
CGTGCTTTGGACAAACTGGATGGCACAGAAATAAATGGCAGAAATATTAGGCTTATTGAAGATAAGCCACGCACAAGCCA
TAGGCGATCTTACTCTGGAAGCAGATCCAGGTCTCGATCTAGAAGATGGTCACGAAGTAGGAGTCACAGGAGCAGCCACA
GTAGATCTGGAAGTGTCTCAAAAAGTCGCTCCCGTTCCAGGTCGCGGAGCAAAGGTCGATCACGTTCTCGATCAGAAGGC
AGGAAATCTAGATCAAAGAGCAAATCTAAGCCCAAGTCTGATCGGGGCTCCCATTCACATTCTCGAAGCAGATCTAAGGA
TGAGTATGAGAAATATCGAAGCAGGTCTCGGTCCGGATCCCCCAAAGAAAATGGAAAGGGTGATACAAAGTCAAAATCCA
GATCAAGGAGCCAGTCCCGTTCCAATTCGCCGCTACCTGGTCCACACTGAAAGGCCCGTTCTGCGTCCCCTCCACCAAAA
AGAGCTACTTCAAGATCCCGTTCTAGATCTCGCTCAAAGTCAAGATCAAGGTCCAGGTCGAGTTCCAGGGAT

Alignment

ORF - retro_ggor_2176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.91 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPRVYIGRLSYNVREKDIQRFFSGYGRLLEVDLKNGYGFVEFEDSRDADDAV-YELNGKELCGERVIVEH
          MPRVYIGRLSYNV.EK.IQRFF.GYGRLLEVDLKNGYGFVEFEDSRDADDA..YELNG.ELCGERVIVE.
Retrocopy MPRVYIGRLSYNVQEKAIQRFFGGYGRLLEVDLKNGYGFVEFEDSRDADDAL>YELNGEELCGERVIVEL

Parental  ARGPRRDRDGYSYGSRSGGGGYSSRR-TSGRDKYGPPVRTEYRLIVENLSSRCSWQDLKDFMRQAGEVTY
          ARGPRR.RDGYSYGSR.GGGGYSSRR.TSGRDKYGPPVRTEYRLIVENLSS.CSW.DLKDFMRQAG.VT.
Retrocopy ARGPRRNRDGYSYGSRRGGGGYSSRR<TSGRDKYGPPVRTEYRLIVENLSSLCSWRDLKDFMRQAG*VTC

Parental  ADAHKERTNEGVIEFRSYSDMKRALDKLDGTEINGRNIRLIEDKPRTSHRRSYSGSRSRSRSRRRSRSRS
          ADAHKE.TNEGVIEFRSYSDMKRALDKLDGTEINGRNIRLIEDKPRTSHRRSYSGSRSRSRSRR.SRSRS
Retrocopy ADAHKEGTNEGVIEFRSYSDMKRALDKLDGTEINGRNIRLIEDKPRTSHRRSYSGSRSRSRSRRWSRSRS

Parental  RRSSRSRSRSISKSRSRSRSRSKGRSRSRSKGRKSRSKSKSKPKSDRGSHSHSRSRSKDEYEKSRSRSRS
          .RSS.SRS.S.SKSRSRSRSRSKGRSRSRS.GRKSRSKSKSKPKSDRGSHSHSRSRSKDEYEK.RSRSRS
Retrocopy HRSSHSRSGSVSKSRSRSRSRSKGRSRSRSEGRKSRSKSKSKPKSDRGSHSHSRSRSKDEYEKYRSRSRS

Parental  RSPKENGKGDIKSKSRSRSQSRSNSPLPVPPSKARSVSPPPKRATSRSRSRSRSKSRSRSRSSSRD
          .SPKENGKGD.KSKSRSRSQSRSNSPLP.P..KARS.SPPPKRATSRSRSRSRSKSRSRSRSSSRD
Retrocopy GSPKENGKGDTKSKSRSRSQSRSNSPLPGPH*KARSASPPPKRATSRSRSRSRSKSRSRSRSSSRD

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	1.29 RPM	43.21 RPM
SRP007412_cerebellum	2.01 RPM	48.34 RPM
SRP007412_heart	0.72 RPM	21.01 RPM
SRP007412_kidney	4.33 RPM	103.86 RPM
SRP007412_liver	3.01 RPM	81.72 RPM
SRP007412_testis	7.46 RPM	105.15 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2176 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1809
Pan troglodytes	retro_ptro_3057
Pongo abelii	retro_pabe_1483

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002061	1 retrocopy	retro_acar_191,
Canis familiaris	ENSCAFG00000009289	1 retrocopy	retro_cfam_392,
Echinops telfairi	ENSETEG00000006221	1 retrocopy	retro_etel_1261,
Homo sapiens	ENSG00000124193	1 retrocopy	retro_hsap_1809,
Gorilla gorilla	ENSGGOG00000009808	1 retrocopy	retro_ggor_2176 ,
Gorilla gorilla	ENSGGOG00000017186	5 retrocopies	retro_ggor_1654, retro_ggor_1706, retro_ggor_2030, retro_ggor_2746, retro_ggor_630,
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,
Rattus norvegicus	ENSRNOG00000006380	1 retrocopy	retro_rnor_1752,
Tupaia belangeri	ENSTBEG00000013448	1 retrocopy	retro_tbel_383,
Tursiops truncatus	ENSTTRG00000015410	2 retrocopies	retro_ttru_1786, retro_ttru_1787,