RetrogeneDB ID: retro_nleu_1638

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397302.1:15578469..15579448(+)
• Located in intron of: ENSNLEG00000009133

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A14
• Ensembl ID: ENSNLEG00000015318
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier, brain), member 14 [Source:HGNC Symbol;Acc:10984]

Sequence

>retro_nleu_1638
TTTCTATGCTTCCGGGTTGGCACTGCAGTGGCATTTTTGACTGTGGGAGCCTCAGTTTCCCAGTCGTCTGATGAGCCTGA
GCAGCAGCAGAAGAGGACCACTGTAAGCCTTGAGATGTCTCGTCTGAACTGGAAACCCTTTGTACATGACGCCTTGCCTC
TATCATTGCTGAGTTTGGAACTTTCCCCATGGACCTTGCCAAAACGCGACTTCAGGCAGGTTCAAGGCCAAAGCATTGAT
GTCCGTTTCAAAGAAACAAAATATAGACGGATGTTTCATGCTTTGTTTTGGATCTATAAAGAGGAAGGTGTATTGGCTCT
GTATTCAGGAATTGCTCCTGCTTTGCGAAGACAAGCATCATATGGCACCATTAAAACTGGGATTTACCAAAGCTTGAAGC
AATTATTTGTAGAACGTTTAGAAGATGAAACTCTTTTAACTAACATGATCTATGGGGTAGTGTCAGGAGTGATATTTTCC
ACTATAGCCAATCCCACCGATGTTCTAAAGATTTGAATGCAGGCTCAAGGAAGTTTGTTCCAAGGGAGCATGATTGGCAG
CTTCATTGATACATACCAACAGGAAGGCACCAGGGGTCTGTGGAGGGGTGTGGTACCAACTGCTCAGCATGCTGCCATCG
TTGTGGGAGTAGAGCTACCAGTCTATGATTTTACTAAGAAGCACTTAATATTGTCAGGAATGATGGAAGACACAACTTTA
ACTCACTTTGTTTCCAGCTTTACGTGTGGTTTGGCTGGGGCTCTTGCCTCTAATCCAGGTGATGTGGCAGGCACTCGCAT
GATGAACCACAGGGCAATTGTGGGATATGTGGATCTCTATAAGGGCACTTTGGATGGTGTTTTAAAGATGTGGAAACATG
AGGGCTTTTTTGTACTCTAAAGGATTTTGGCCAAACTGGCTTTGGCTTGAACCCTGGAACATCATTCTTTAAATTACATA
TGAGTAGCTCAAGAGGCTT

Alignment

ORF - retro_nleu_1638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.87 %
• Parental protein coverage: 94.77 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FQCFRVGAAVAFPTVGASASQSSDEPEQHQKSTTVSHEMSGLNWKPFVYGGL-ASIVAEFGTF-PVDLTK
          F.CFRVG.AVAF.TVGAS.SQSSDEPEQ.QK.TTVS.EMS.LNWKPFV...L.ASI.AEFGTF.P..L.K
Retrocopy FLCFRVGTAVAFLTVGASVSQSSDEPEQQQKRTTVSLEMSRLNWKPFVHDAL<ASIIAEFGTF>PWTLPK

Parental  TRL-QVQGQSIDARFKEIKYRGMFHALFRICKEEGVLALYSGIAPALLRQASYGTIKIGIYQSLKRLFVE
          ....QVQGQSID.RFKE.KYR.MFHALF.I.KEEGVLALYSGIAPAL.RQASYGTIK.GIYQSLK.LFVE
Retrocopy RDFRQVQGQSIDVRFKETKYRRMFHALFWIYKEEGVLALYSGIAPALRRQASYGTIKTGIYQSLKQLFVE

Parental  RLEDETLLINMICGVVSGVISSTIANPTDVLKIRMQAQGSLFQGSMIGSFIDIYQQEGTRGLWRGVVPTA
          RLEDETLL.NMI.GVVSGVI.STIANPTDVLKI.MQAQGSLFQGSMIGSFID.YQQEGTRGLWRGVVPTA
Retrocopy RLEDETLLTNMIYGVVSGVIFSTIANPTDVLKI*MQAQGSLFQGSMIGSFIDTYQQEGTRGLWRGVVPTA

Parental  QRAAIVVGVELPVYDITKKHLILSGMMGDTILTHFVSSFTCGLAGALASNPVDVVRTRMMNQRAIVGHVD
          Q.AAIVVGVELPVYD.TKKHLILSGMM.DT.LTHFVSSFTCGLAGALASNP.DV..TRMMN.RAIVG.VD
Retrocopy QHAAIVVGVELPVYDFTKKHLILSGMMEDTTLTHFVSSFTCGLAGALASNPGDVAGTRMMNHRAIVGYVD

Parental  LYKGTVDGILKMWKHEGFFAL-YKGFWPNWLRLGP-WNIIFFITYEQLKRL
          LYKGT.DG.LKMWKHEGFF.L..K.F......L.P.WNII..ITYE.LKRL
Retrocopy LYKGTLDGVLKMWKHEGFFVL<LKDFGQTGFGLNP<WNIIL*ITYE*LKRL

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_1638 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016263	1 retrocopy	retro_btau_1362,
Canis familiaris	ENSCAFG00000018766	1 retrocopy	retro_cfam_1359,
Callithrix jacchus	ENSCJAG00000002456	1 retrocopy	retro_cjac_2257,
Homo sapiens	ENSG00000102078	1 retrocopy	retro_hsap_2954,
Macaca mulatta	ENSMMUG00000008386	1 retrocopy	retro_mmul_1943,
Nomascus leucogenys	ENSNLEG00000015318	1 retrocopy	retro_nleu_1638 ,
Pongo abelii	ENSPPYG00000020715	2 retrocopies	retro_pabe_2450, retro_pabe_3595,
Pan troglodytes	ENSPTRG00000022268	1 retrocopy	retro_ptro_2048,
Tursiops truncatus	ENSTTRG00000016206	2 retrocopies	retro_ttru_1159, retro_ttru_1570,