RetrogeneDB ID: retro_nleu_1294

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397288.1:3971879..3972906(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF6
• Ensembl ID: ENSNLEG00000006524
• Aliases: None
• Description: None

Sequence

>retro_nleu_1294
ATGCCGCGCCTCTACATAGGACGCCTGAGCTACGACGTCCAGGAGAAAGCCATCCAGCGCTTTTTCAGTGGCTATGGCCT
CCTCGAAGTAGACCTCAAAAATGGCTACGGCTTCGTGGAGTTCGAGGACTCCCGCGACGCCAACGACGCCGTTTACGAGC
TGAACTGCAAGGAGCTCTGCAGCGAGCGCATAATCATAGAGCACGCCGGGGGCCTGCGTCGCCATCGCGACGGCTACAGC
TAGGGAAGCCGCAGTGGTGGAGGTGGATACAGCAATTGGAGAACATCTGGCAAAGACAAATACGGACCACCTGTTCGTAC
AGAATACAGGCTTACTGTAGAAAATCTTTCTAGTCTGTGCAGTTGGCAAGATTTAAAGGATTTTATGCGACAAGCAGGTG
AAGTAACCTATGCGGATGCCCACAAGGAAGGAACAGATGAGGGTGTAATTGAGTTTCGCTCCTACTCTGACATGAAGCGT
GCTTTGGACAAACTGGATGGCACAGAAATAAATGGCAGAAGTATTAGGCTTATTGAAGATAAGCCACGCACAAGCCATAG
GCGATCTTACTCTGGAAGCAGATCCAGATCTCGATCTAGAAGATGGTCATGAAGTAAGAGTCGCAGGAGCAGCCTCAGCA
GATCTCGAAGTATCTCAAAAAGTCGCTCCCGTTCCAGGTCGCGGAGCAAAGGTCGATCACCTTCTCGATCAAAAGGCAGG
AAATATAGATCAAAGAGCAAATCTAACCCAAGTCTGATCGGGGCTCCCATTCACATTCTCGAAGCAGATCTAAGGATGAG
TATGAGAAATCTCGAAGCAGGTCTCGGTCCCGATCCCCCAAAGAAAATGGAAAGGGTCATATAAAGTCAAAATCCAGATC
AAGGAGCCAGTCCCGTTCCAATTCGCCGCTACCTGGTCACCCTCAAAGGCCCGTTCTGTGTCCCCTCCACCAAAAAGAGC
CACTTCAAGATCCCGTTCTAGATCTCGCTCAAAGTCAAGATCAAGGTCCAGGTCGAGTTCCAGAGAT

Alignment

ORF - retro_nleu_1294 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPRVYIGRLSYNVREKDIQRFFSGYGRLLEVDLKNGYGFVEFEDSRDADDAVYELNGKELCGERVIVEHA
          MPR.YIGRLSY.V.EK.IQRFFSGYG.LLEVDLKNGYGFVEFEDSRDA.DAVYELN.KELC.ER.I.EHA
Retrocopy MPRLYIGRLSYDVQEKAIQRFFSGYG-LLEVDLKNGYGFVEFEDSRDANDAVYELNCKELCSERIIIEHA

Parental  RGPRRDRDGYSYGSRSGGGGYSSRRTSGRDKYGPPVRTEYRLIVENLSSRCSWQDLKDFMRQAGEVTYAD
          .G.RR.RDGYS.GSRSGGGGYS..RTSG.DKYGPPVRTEYRL.VENLSS.CSWQDLKDFMRQAGEVTYAD
Retrocopy GGLRRHRDGYS*GSRSGGGGYSNWRTSGKDKYGPPVRTEYRLTVENLSSLCSWQDLKDFMRQAGEVTYAD

Parental  AHKERTNEGVIEFRSYSDMKRALDKLDGTEINGRNIRLIEDKPRTSHRRSYSGSRSRSRSRRRSRSRSRR
          AHKE.T.EGVIEFRSYSDMKRALDKLDGTEINGR.IRLIEDKPRTSHRRSYSGSRSRSRSRR.S.S.SRR
Retrocopy AHKEGTDEGVIEFRSYSDMKRALDKLDGTEINGRSIRLIEDKPRTSHRRSYSGSRSRSRSRRWS*SKSRR

Parental  SSRSRSRSISKSRSRSRSRSKGRSRSRSKGRKSRSKSKSK-PKSDRGSHSHSRSRSKDEYEKSRSRSRSR
          SS.SRSRSISKSRSRSRSRSKGRS.SRSKGRK.RSKSKS..PKSDRGSHSHSRSRSKDEYEKSRSRSRSR
Retrocopy SSLSRSRSISKSRSRSRSRSKGRSPSRSKGRKYRSKSKSN<PKSDRGSHSHSRSRSKDEYEKSRSRSRSR

Parental  SPKENGKGDIKSKSRSRSQSRSNSPLP-VPPSKARSVSPPPKRATSRSRSRSRSKSRSRSRSSSRD
          SPKENGKG.IKSKSRSRSQSRSNSPLP...PSKARSVSPPPKRATSRSRSRSRSKSRSRSRSSSRD
Retrocopy SPKENGKGHIKSKSRSRSQSRSNSPLP<WSPSKARSVSPPPKRATSRSRSRSRSKSRSRSRSSSRD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_1294 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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 ,
Nomascus leucogenys	ENSNLEG00000015661	1 retrocopy	retro_nleu_1931,
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,
Tursiops truncatus	ENSTTRG00000015410	2 retrocopies	retro_ttru_1786, retro_ttru_1787,