RetrogeneDB ID: retro_nleu_423

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397264.1:33203319..33204065(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTCH1
• Ensembl ID: ENSNLEG00000010899
• Aliases: None
• Description: None

Sequence

>retro_nleu_423
ATGGATGGCAAGACAGGGCTGTTCCGAGGTCTGAGCCCCCAACTGATGTGACTCCTCTCCTTTGTAACCGGGGGCAGCAT
GAAGAAGGTTTTCCCTCCAGATGAAATCAAGCAGGTTTCCAATAAGGATGGATATGAAGACTTCTCTGAAGCAAGCAGTG
AAGGAGACCTCCTAGGGGATGATGATGCAGTGTGTGTCCTGTATGTTGGCCCACCTCCTGCATGCCATCTTGATGTGCTG
CATGGTCTAATTTGTGGGATGGGAGGTCAAGTACAGTGGTGGGCTGAGCTCCACTGGGAAGATTTTCAAAGAGGAAGGGC
CGCTGGGATTCTTTGTTGGCTTGATCCCTCATGTCCCGGGTGAAGTAGTTTTCTTGTGAGGCTATAACCTGCTGGCCCAC
TTTATCAATGCCTACCTGGTGGATGACAGCGTGAGTGACACCTAGGGGGGGCTGAGAAATGACCAGAATCGGGGTTCCCA
GTTAGGCCAGGCCCTGGCCATCCGGAGCTACACCAAGTTTGTGATGGAGATCGCAGTGAGCATGCTGACCTACCCTTTCC
TGCCAGTTGGCAGCCTCATGGCTGTGAACAACTGCAGGCCGCAGGCTGGGCTCTCACCTTACTCCCTGGTGTTCAAATCC
TGGATTTACTGCTGTTAAGTACCTGAGTGTGCAGGGCCAGCTCTTCTGAGGCTCCAGCCTGCTTGCTTTTCCACAAGTGT
CATCAGGATCATGCTTTGGCCTGGAG

Alignment

ORF - retro_nleu_423 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.08 %
• Parental protein coverage: 63.75 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VDGKIGLFRGLSPRLMSNALSTVTRGSMKKVFPPDEIEQVSNKD-DMKTSLKKVVKETSYEMMMQCVSRM
          .DGK.GLFRGLSP.LM...LS.VT.GSMKKVFPPDEI.QVSNKD.DMKTSLK..VKETS..MMMQCVS.M
Retrocopy MDGKTGLFRGLSPQLM*-LLSFVTGGSMKKVFPPDEIKQVSNKD>DMKTSLKQAVKETS*GMMMQCVSCM

Parental  LAHPLHVISMRCMVQFVGREAKYSGVLSSIGKIFKEEGLLGFFVGLIPHLLGDVVFLWGCNLLAHFINAY
          LAH.LH.I.M.CMV.FVG.E.KYSG.LSS.GKIFKEEG.LGFFVGLIPH..G.VVFL.G.NLLAHFINAY
Retrocopy LAHLLHAILMCCMV*FVGWEVKYSGGLSSTGKIFKEEGPLGFFVGLIPHVPGEVVFL*GYNLLAHFINAY

Parental  LVDDSVSDTPGGLGNDQNPGSQFSQALAIRSYTKFVMGIAVSMLTYPFLLVGDLMAVNNCGLQAGLPPYS
          LVDDSVSDT.GGL.NDQN.GSQ..QALAIRSYTKFVM.IAVSMLTYPFL.VG.LMAVNNC..QAGL.PYS
Retrocopy LVDDSVSDT*GGLRNDQNRGSQLGQALAIRSYTKFVMEIAVSMLTYPFLPVGSLMAVNNCRPQAGLSPYS

Parental  PVFKSWIHCW-KYLSVQGQLFRGSSLL-FRRVSSGSCFALE
          .VFKSWI.C..KYLSVQGQLF.GSSLL.F..VSSGSCF.LE
Retrocopy LVFKSWIYCC>KYLSVQGQLF*GSSLLAFPQVSSGSCFGLE

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_423 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000137409	2 retrocopies	retro_hsap_3671, retro_hsap_856,
Gorilla gorilla	ENSGGOG00000003908	1 retrocopy	retro_ggor_2481,
Macaca mulatta	ENSMMUG00000021976	1 retrocopy	retro_mmul_1060,
Nomascus leucogenys	ENSNLEG00000010899	1 retrocopy	retro_nleu_423 ,
Nomascus leucogenys	ENSNLEG00000014704	2 retrocopies	retro_nleu_1335, retro_nleu_913,
Pongo abelii	ENSPPYG00000016557	2 retrocopies	retro_pabe_3011, retro_pabe_691,
Pan troglodytes	ENSPTRG00000018115	1 retrocopy	retro_ptro_2490,
Tarsius syrichta	ENSTSYG00000014777	1 retrocopy	retro_tsyr_488,
Tursiops truncatus	ENSTTRG00000001966	2 retrocopies	retro_ttru_1101, retro_ttru_563,