RetrogeneDB ID: retro_nleu_2326

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397343.1:7337103..7338192(-)
• Located in intron of: ENSNLEG00000011592

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACCSL
• Ensembl ID: ENSNLEG00000017966
• Aliases: None
• Description: None

Sequence

>retro_nleu_2326
ATGAGTCATCAGTCAGACACCCTTCCTGTGCCCTCTGGCCAGATGAGAGGCCAGGTCCTCAGAGACCAGAGCATCTATAC
CCAGCTGTTAAGATGATGCTGCACTTGCGGCAGACCATGAGGGAGTACTTTGTGCAGCTGATGAGCAGGCAGGGCCTGCC
GCTGGAAGAATGGAGGCACACTCAGGCCATCTGTGAGCATGAAGCCCTTCTGGGTCGCTTAATGTGCCAGATGATCCATA
GTCTAGGGCCATGAGTGGCCTGGAGCTCCAAGTGCCTCTTCCTTCCCAGGACTCCAGGGGTAATGTCAGATATGGGCAGG
GGGCCCAACTGTCAAGGCAGCCTGATCCAGTTCCCCAACTGAGTGATTGTGAAGCTGCCTTCATCAGCCGTGACCTATCC
AACTGTGGGATTGACATCTGTGTTTTCTATTAGTCGAGCTTCCAGGACTACAATGCCTACCAAAAAGACAAATATCATAA
GGACAAGAACACCTTGGGCTTCGTTAACCTTGGCACCAGTGAGAACAAGCTCTGCATAGATCTGATGACTGAAAGATTGC
AATAAAGTGACATGGACTGCACTGAGGACATCTTGCTGCAGTACCCGGATTGGAGAGGGCACCCGTTCCTGCAAGAAGAA
GTGGCCCGGTTCCTGACCTACTAGTGTAAGGCACCTGCCCGACTTGATCCAGAAAATGTGGTTGTTCTAAATGGCCGCTG
CTCTGTCTTCTCTGCACTGGCCATGGTTCTGTGTGATCCAGGCTAGGCCTTCCTGGTCCTTGCTCCCTTCTATAGTGGCT
TTGACTTTAGCTCCTGCCTATACATGAAGGTTGAGTTGATTCCTGTCCACCTGGAGAGTGAGATCACTGTTACAAACACC
CATCCTTTCCACCTCACTATGGACAAGTTAGAGGAAGCCCTGCTTGAAGCTAGGCTTGAGGGGAAAAAGGTCCGAGGCCT
TGTGCTAATCAACCCTCAGACTCCTCTGGGTGACATCTGCTCCTCAGACTCGCGACGGAATACCTGGAATTTGCCAAGAG
GTATAACCTACATGTGATCGTAGATGAGATTTACATGCTGTCTGTGTTT

Alignment

ORF - retro_nleu_2326 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.71 %
• Parental protein coverage: 64.12 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSHRSDTLPVPSGQRRGQIPRDHSICTQLL-EITLHLQQAMTEHFVQLTSRQGLSLEERRHTEAICEHEA
          MSH.SDTLPVPSGQ.RGQ..RD.SI.TQLL....LHL.Q.M.E.FVQL.SRQGL.LEE.RHT.AICEHEA
Retrocopy MSHQSDTLPVPSGQMRGQVLRDQSIYTQLL<KMMLHLRQTMREYFVQLMSRQGLPLEEWRHTQAICEHEA

Parental  LLSRLICRMINLL-QSGAASGLELQVPLPSEDSRGDVRYGQRAQLSGQPDPVPQLSDCEAAFVSRDLSHR
          LL.RL.C.MI..L........L....P..S.DSRG.VRYGQ.AQLS.QPDPVPQLSDCEAAF.SRDLS..
Retrocopy LLGRLMCQMIHSL<RAMSGLELQVPLP--SQDSRGNVRYGQGAQLSRQPDPVPQLSDCEAAFISRDLSNC

Parental  GIDISVFYQSSFQDYNAYQKDKYHKDKNTLGFINLGTSENKLCMDLMTERLQESDMNCIEDTLLQYPDWR
          GIDI.VFY.SSFQDYNAYQKDKYHKDKNTLGF.NLGTSENKLC.DLMTERLQ.SDM.C.ED.LLQYPDWR
Retrocopy GIDICVFY*SSFQDYNAYQKDKYHKDKNTLGFVNLGTSENKLCIDLMTERLQ*SDMDCTEDILLQYPDWR

Parental  GQPFLREEVARFLTYYCRAPTRLDPENVVVLNGCCSVFSALAMVLCDPGEAFLVPAPFYGGFAFSSRLYA
          G.PFL.EEVARFLTY.C.AP.RLDPENVVVLNG.CSVFSALAMVLCDPG.AFLV.APFY.GF.FSS.LY.
Retrocopy GHPFLQEEVARFLTY*CKAPARLDPENVVVLNGRCSVFSALAMVLCDPG*AFLVLAPFYSGFDFSSCLYM

Parental  KVQLIPVHLESEV---NGAPSLLSMPR-QWTVLGTLKGGKKVRGFVIINPQNPLGDIYSPDS-LMKYLE-
          KV.LIPVHLESE....N..P..L.M.......L.....GKKVRG.V.INPQ.PLGDI.S.DS....YLE.
Retrocopy KVELIPVHLESEITVTNTHPFHLTMDKLEEALLEARLEGKKVRGLVLINPQTPLGDICSSDS<ATEYLEF

Parental  AKRYNLHVIIDEIYMLSVF
          AKRYNLHVI.DEIYMLSVF
Retrocopy AKRYNLHVIVDEIYMLSVF

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_2326 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 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011384	1 retrocopy	retro_cjac_100,
Dipodomys ordii	ENSDORG00000005058	1 retrocopy	retro_dord_340,
Equus caballus	ENSECAG00000011908	1 retrocopy	retro_ecab_575,
Echinops telfairi	ENSETEG00000009026	2 retrocopies	retro_etel_1006, retro_etel_204,
Homo sapiens	ENSG00000205126	1 retrocopy	retro_hsap_3553,
Myotis lucifugus	ENSMLUG00000005151	1 retrocopy	retro_mluc_1235,
Nomascus leucogenys	ENSNLEG00000017966	1 retrocopy	retro_nleu_2326 ,
Ochotona princeps	ENSOPRG00000002097	1 retrocopy	retro_opri_526,
Ochotona princeps	ENSOPRG00000006805	7 retrocopies	retro_opri_1064, retro_opri_1151, retro_opri_251, retro_opri_252, retro_opri_398, retro_opri_399, retro_opri_808,
Pongo abelii	ENSPPYG00000003340	1 retrocopy	retro_pabe_2934,
Pan troglodytes	ENSPTRG00000028662	1 retrocopy	retro_ptro_2414,
Tupaia belangeri	ENSTBEG00000016623	1 retrocopy	retro_tbel_3677,
Tursiops truncatus	ENSTTRG00000002727	1 retrocopy	retro_ttru_1321,