RetrogeneDB ID: retro_nleu_1164

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397283.1:5185454..5186288(-)
• Located in intron of: ENSNLEG00000012055

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSNLEG00000007131
• Aliases: None
• Description: None

Sequence

>retro_nleu_1164
TCTGACCATCCAGGGGAAAGTACACTTTTTTTGAGAAAATATCAAATGAGTGTGCAAGAAAAGAGGAGGAGCTCTCACCT
ATATTACATACCTCCATGGCATCTTGATAGAAAATACACCTCGTGTTATACCATATTGCTAGATAACAGCACAGTCGGCC
AGCCTGATCTTAGACACACATTAGAAAGTGTGACTTGGGCAATATATTACAACATAAAGCACAGATACACAAATAGATCT
CTGGATATTTTTTGACAAGCCAATACATCCACTTTCACAAGAGAAGATTCCAGGGAAATCCTTCGAGCATGATCCCAAAC
GCAACTGTACTTTCAGATATTTCTGTACTCTTTTTCAAGTCATAAAACTAACAGCTCCATGTGCAATCGTAGCTTTGGTG
TACATCGAACGACTTTTAACTATGGTAACATCGCTCTTTGTCCTACTAATAGGAAAAAGATTGTCCTCGGAGCCATGCTT
CTTGCCTCCAAGGTTTGGAGAAATCGTGGTCTGTAGAGTGTGGATGACAGCCAGAATCCCAAGGACATTGCAGTTGAGAA
CATGAGCAAGATGGAGAAGTGTTTTTTGGAGCTACTGGAGTTTAATATTCATGTGTCTGCCAGTGTTTATGCAAGATATT
ACTTCGACCTGCGTGCCTTGGCAAATGACCGTGACCTGTATTTTCTATTTAGTTTTCTTCACAAAGATAAAGCACAGAAA
CTGGAGGCTGTGCCATGGCCATGTGAATACAAAGACTTGCATCAACATGCCGCTGCTATGACAAGGGCTATCAGCATGAA
TTTCATTGGTATTTGGTGCACTAATGCCATCTTA

Alignment

ORF - retro_nleu_1164 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.01 %
• Parental protein coverage: 91.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SDHPRASTIFLSKSQTDVREKRKSNHLNHVSPGQLTKKYSSCSTIFLDDSTVSQPNLRTTVKCVTLAIYY
          SDHP..ST.FL.K.Q..V.EKR.S.HL....P..L..KY.SC.TI.LD.STV.QP.LR.T...VT.AIYY
Retrocopy SDHPGESTLFLRKYQMSVQEKRRSSHLYYIPPWHLDRKYTSCYTILLDNSTVGQPDLRHTLESVTWAIYY

Parental  HIKNRDANRSLDIF-DERSHPLTREKVPEEYFKHDPEHKFIYRFVRTLFSAAQLTAECAIVTLVYLERLL
          .IK.R..NRSLDIF.D...HPL..EK.P...F.HDP......R...TLF....LTA.CAIV.LVY.ERLL
Retrocopy NIKHRYTNRSLDIF>DKPIHPLSQEKIPGKSFEHDPKRNCTFRYFCTLFQVIKLTAPCAIVALVYIERLL

Parental  T-YAEIDICPTNWKRIVLGAILLASKVWDDQAVWNVDYCQILKDITVEDMNEMERHFLELLQFNINVPAS
          T.Y..I..CPTN.K.IVLGA.LLASKVW.......VD..Q..KDI.VE.M..ME..FLELL.FNI.V.AS
Retrocopy T<YGNIALCPTNRKKIVLGAMLLASKVWRNRGL*SVDDSQNPKDIAVENMSKMEKCFLELLEFNIHVSAS

Parental  VYAKYYFDLRSLADDNNLNFLFAPLSKERAQNLEAISRLCEDKDLCR--AAMRRSFSADNFIGIQRSKAI
          VYA.YYFDLR.LA.D..L.FLF..L.K..AQ.LEA....CE.KDL....AAM.R..S..NFIGI....AI
Retrocopy VYARYYFDLRALANDRDLYFLFSFLHKDKAQKLEAVPWPCEYKDLHQHAAAMTRAISM-NFIGIWCTNAI

Parental  L
          L
Retrocopy L

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_1164 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002901	1 retrocopy	retro_cjac_569,
Homo sapiens	ENSG00000163249	3 retrocopies	retro_hsap_1629, retro_hsap_1984, retro_hsap_4845,
Macaca mulatta	ENSMMUG00000020211	1 retrocopy	retro_mmul_2587,
Mus musculus	ENSMUSG00000070871	1 retrocopy	retro_mmus_3072,
Nomascus leucogenys	ENSNLEG00000007131	3 retrocopies	retro_nleu_1164 , retro_nleu_2902, retro_nleu_430,
Pongo abelii	ENSPPYG00000013118	3 retrocopies	retro_pabe_1345, retro_pabe_3766, retro_pabe_76,