RetrogeneDB ID: retro_pabe_1483

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:16976882..16977913(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF6
• Ensembl ID: ENSPPYG00000011019
• Aliases: None
• Description: splicing factor, arginine/serine-rich 6 [Source:RefSeq peptide;Acc:NP_001182497]

Sequence

>retro_pabe_1483
ATGCTACGCGTCTACATAGGACGCCTGAGCTACAACGTCCAGGAGAAGGCCATCCAGTGCTTTTTCAGTGGCTATGGCTG
CCTCCTCGAAGTAGACCTCAAAAATGGCTACGGCTTGGTGGAGTTCGAGGACTCCCGTGACGCCAACGAAGCCGTTTACG
AGCTGAACTGCAAGGAGCTCTGCGGCGAGCCTCTGATGGTAGAGCACGCCCGGGCCCGCGTCGCAATCGCGACGGCTACA
GCTACGGAAGCAGCCGTGGTGGAGGTGGACACAGCAGTGGGAGAACATCTAGCAGAGACAAATACGGACCACCTGTTCAT
ACAGAATACAGGCTTATTGTAGAAAATCTTTCTAGTCTGTGCAGTTGGCAAGATTTAAAGGATTTTATGCGACAAGCAGG
TGAAGTAACCTGTGCGGATGCCCACAAGGAAGGAACAAATGAGGGTGTAATTGAGTTTCACTCCTACTCTGACATGAAGC
GTGCTTTGGACAAACTGGATGGCACAGAAATAAATGGCAGAAATATTAGGCTTATTGAAGATAAGCCACGCACAAGCCAT
AGGCGATCTTACTCTGGAAGCAGATCCAGGTCTCGATCTAGAAGATGGTCACGAAGTAGGAGTCGCAGCAACAGCCGCAG
TAGATCTCGAAGTATCTCAAAAAGTCGCTCCAGTTCCAGGTCGCGGAGCAGAGGTCGATCACGTTCTCGATCAAAAGGCA
GGAAATCTAGATCAAAGAGCAAATCTAAGCCCAAGTCTGATCGGGGTTCCCATTCACATTCTCGAAGCAGATCTAAGGAT
GAGTATGAGAAATCTCGAAGCAGGTCTCGGTCCCGATCCCCCAAAGAAAATGGAAAGGGTGCTATAAAGTCAAAATCCAG
ATCAAGGAGCGAGTCCTGTTCCAATTCGCCGCTACTTGGTCCACCCTCAAAGGCCCGTTCTGTGTCCCCTCCACCAAAAA
GAGCTACTTCAAGATCCCACTCTAGTTCTCACTCAAAGTCCAGATCAAGGTCCAGGTCGAGTTCCAGAGAT

Alignment

ORF - retro_pabe_1483 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPRVYIGRLSYNVREKDIQRFFSGYGRLLEVDLKNGYGFVEFEDSRDADDAVYELNGKELCGERVIVEHA
          M.RVYIGRLSYNV.EK.IQ.FFSGYG.LLEVDLKNGYG.VEFEDSRDA..AVYELN.KELCGE...VEHA
Retrocopy MLRVYIGRLSYNVQEKAIQCFFSGYGCLLEVDLKNGYGLVEFEDSRDANEAVYELNCKELCGEPLMVEHA

Parental  R-GPRRDRDGYSYGSRSGGGGYSSRRTSGRDKYGPPVRTEYRLIVENLSSRCSWQDLKDFMRQAGEVTYA
          R.GPRR.RDGYSYGS..GGGG.SS.RTS.RDKYGPPV.TEYRLIVENLSS.CSWQDLKDFMRQAGEVT.A
Retrocopy R<GPRRNRDGYSYGSSRGGGGHSSGRTSSRDKYGPPVHTEYRLIVENLSSLCSWQDLKDFMRQAGEVTCA

Parental  DAHKERTNEGVIEFRSYSDMKRALDKLDGTEINGRNIRLIEDKPRTSHRRSYSGSRSRSRSRRRSRSRSR
          DAHKE.TNEGVIEF.SYSDMKRALDKLDGTEINGRNIRLIEDKPRTSHRRSYSGSRSRSRSRR.SRSRSR
Retrocopy DAHKEGTNEGVIEFHSYSDMKRALDKLDGTEINGRNIRLIEDKPRTSHRRSYSGSRSRSRSRRWSRSRSR

Parental  RSSRSRSRSISKSRSRSRSRSKGRSRSRSKGRKSRSKSKSKPKSDRGSHSHSRSRSKDEYEKSRSRSRSR
          ..SRSRSRSISKSRS.SRSRS.GRSRSRSKGRKSRSKSKSKPKSDRGSHSHSRSRSKDEYEKSRSRSRSR
Retrocopy SNSRSRSRSISKSRSSSRSRSRGRSRSRSKGRKSRSKSKSKPKSDRGSHSHSRSRSKDEYEKSRSRSRSR

Parental  SPKENGKGDIKSKSRSRSQSRSNSPLPVPPSKARSVSPPPKRATSRSRSRSRSKSRSRSRSSSRD
          SPKENGKG.IKSKSRSRS.S.SNSPL..PPSKARSVSPPPKRATSRS.S.S.SKSRSRSRSSSRD
Retrocopy SPKENGKGAIKSKSRSRSESCSNSPLLGPPSKARSVSPPPKRATSRSHSSSHSKSRSRSRSSSRD

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	0.33 RPM	49.71 RPM
SRP007412_cerebellum	0.49 RPM	118.44 RPM
SRP007412_heart	0.06 RPM	44.40 RPM
SRP007412_kidney	0.27 RPM	121.25 RPM
SRP007412_liver	0.12 RPM	119.35 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1483 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1483 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1483 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1809
Pan troglodytes	retro_ptro_3057
Gorilla gorilla	retro_ggor_2176

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 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	ENSPPYG00000005031	1 retrocopy	retro_pabe_119,
Pongo abelii	ENSPPYG00000011019	1 retrocopy	retro_pabe_1483 ,
Pan troglodytes	ENSPTRG00000013506	1 retrocopy	retro_ptro_3057,
Rattus norvegicus	ENSRNOG00000006380	1 retrocopy	retro_rnor_1752,
Tursiops truncatus	ENSTTRG00000015410	2 retrocopies	retro_ttru_1786, retro_ttru_1787,