RetrogeneDB ID: retro_nleu_408

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397264.1:3954302..3955063(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A1
• Ensembl ID: ENSNLEG00000005215
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1 [Source:HGNC Symbol;Acc:10979]

Sequence

>retro_nleu_408
CAGCTGGACTAGCCCTTGCACCCGCCACGGTACCAGAGCATCGGGGACTGCGTGTGGCAGACAGTCCGCAGCTATGGCGT
CCTGGGCCTGTACCGCGGTCTCAGCTCCCTGCTCTAGGGCTCCATCCCTAAGGCGGCCGCCAGCTTCGGAATGTTCTAGT
TCCTCAGCAACCACAGGCGGGATTCCCAGGGATGGCTGGACAGCAAACGCGGGCTGCTGTGCTGCCCGGGCGCTGGAGTG
GCTGAGGCCGTGGTGATCGTGTGCCCCATGGAGACCATCAAGGTGAGGTTCATCCACGACCAGACCTCCCCAAACCCCAA
GTACAGAGGATTCTTCCACGGGTTAGGAAGATTGTGCGGGAACAAGGGCCGAAGGGGATGTATCAGAGCCTCACGGCCAC
CGCACTGAAACAGGGCTGGAACCAGGCCATCCGCTTCTTCGTCATGACATTCCCTGCACAACTGGTACCGAGGGGACAAC
CCCAACAAGCCCATGAACCCGCTGATCATTGGGGTCTTCGGAGCCATCGTGTGCACAGCCAGCGTCTTTGGAAACACTCC
TCTGGACGTGATTAAGACCCACACGTAGGGCCTGGAGGAGCACAAATACCAGAACTCGATGGACTGCGGCTGGCAGATCC
TGAGGAAGGAGGAGCTCAAGGCATTATACAAGGGCATTGTCCCGCGCTGGGCCAGGTCAGCCTGGATGTGGCCATAGTGT
TTATCATCTATGATGAGGTGGTGAAGCTGCTCAACAAAGTG

Alignment

ORF - retro_nleu_408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.1 %
• Parental protein coverage: 97.69 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QLDERSHPPRYRGIGDCVRQTVRSHGVLGLYRGLSSLLYGSIPKAAVRFGMFEFLSNHMRDAQGRLDSTR
          QLD...HPPRY..IGDCV.QTVRS.GVLGLYRGLSSLL.GSIPKAA..FGMF.FLSNH.RD.QG.LDS.R
Retrocopy QLD*PLHPPRYQSIGDCVWQTVRSYGVLGLYRGLSSLL*GSIPKAAASFGMF*FLSNHRRDSQGWLDSKR

Parental  GLLCGLGAGVAEAVVVVCPMETIKVKFIHDQTSPNPKYRGFFHG-VREIVREQGLKGTYQGLTATVLKQG
          GLLC..GAGVAEAVV.VCPMETIKV.FIHDQTSPNPKYRGFFHG.VR.IVREQG.KG.YQ.LTAT.LKQG
Retrocopy GLLCCPGAGVAEAVVIVCPMETIKVRFIHDQTSPNPKYRGFFHG<VRKIVREQGPKGMYQSLTATALKQG

Parental  SNQAIRFFVMT-SLRNWYRGDNPNKPMNPLITGVFGAIAGAASVFGNTPLDVIKTRMQGLEAHKYRNTWD
          .NQAIRFFVMT.SL.NWYRGDNPNKPMNPLI.GVFGAI...ASVFGNTPLDVIKT...GLE.HKY.N..D
Retrocopy WNQAIRFFVMT>SLHNWYRGDNPNKPMNPLIIGVFGAIVCTASVFGNTPLDVIKTHT*GLEEHKYQNSMD

Parental  CGLQILRKEGLKAFYKGTVPR-LGRVCLDVAIVFIIYDEVVKLLNKV
          CG.QILRKE.LKA.YKG.VPR.LG.V.LDVAIVFIIYDEVVKLLNKV
Retrocopy CGWQILRKEELKALYKGIVPR<LGQVSLDVAIVFIIYDEVVKLLNKV

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_408 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 8 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100075	2 retrocopies	retro_hsap_1632, retro_hsap_804,
Gorilla gorilla	ENSGGOG00000006198	2 retrocopies	retro_ggor_1230, retro_ggor_661,
Macaca mulatta	ENSMMUG00000005431	4 retrocopies	retro_mmul_1077, retro_mmul_1556, retro_mmul_1683, retro_mmul_485,
Nomascus leucogenys	ENSNLEG00000005215	2 retrocopies	retro_nleu_2866, retro_nleu_408 ,
Ochotona princeps	ENSOPRG00000011649	1 retrocopy	retro_opri_1053,
Pongo abelii	ENSPPYG00000029785	9 retrocopies	retro_pabe_1346, retro_pabe_1414, retro_pabe_1529, retro_pabe_1671, retro_pabe_3125, retro_pabe_3217, retro_pabe_334, retro_pabe_3564, retro_pabe_719,
Pan troglodytes	ENSPTRG00000014057	3 retrocopies	retro_ptro_1139, retro_ptro_1364, retro_ptro_560,
Tursiops truncatus	ENSTTRG00000006845	1 retrocopy	retro_ttru_228,