RetrogeneDB ID: retro_nleu_1518

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397297.1:12264984..12265819(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARMC1
• Ensembl ID: ENSNLEG00000003916
• Aliases: None
• Description: Armadillo repeat-containing protein 1 [Source:UniProtKB/TrEMBL;Acc:G1QUX6]

Sequence

>retro_nleu_1518
ATGAATTCTTCCACCTCCACCATGAGTGAAGAGTCTGATACTCTATCAGTAGTTAACCAGTTACAGGATATAGCAGCAGA
TCCATTAAACAGAAGAGCCATTGTCCAGGATCAGGGATGTCTGCCTGGCCTTATTTTATTTATGGACCACCCCAACCCTC
CAGTCGTCCATTCGGCTTTGCTTGCTCTTTGATACTTGGGAGAATACCGTGCAAACAGAGAAAAGATGAAAGGAGAACTG
ATGTTGAGCCTACAAAATGTTATACAGAAAACTGCAACTCTAGGAGAAACAAAACTTCTGGCCTCTGAAATCTATGACAT
ACTTCAGTCCTCCAATAAGGCAGATGGTGATAGTTGCAGTGAAATGAATTCATATTGAAGGAAAGCTCAGTTTTTTCTGG
GAACTACAAACAAACGTGCCAAAACAGTGGTTTTGCATATAGACGGCCATGATGATACGTCTTCAAGAAATCTATGTGAA
GAGGCTTTGTTAAAAATTAAAGGTGTTATTAGCTTTACTTTTCAAATGGCTGTTCAAAGGTGTGGTGTGAATCCATTCAG
ATTTGAAAGCTGAGGCTTTGGCATCAGCGAGAGCATCAACCAAGGTTATGAAAGCTTAGTAAGTTGTGAAAAGTGAAAGT
GGAGAAGAGATGCTGGTCCCATTCCAAGACCTTCCTGTGGTAGAACAGAACACAGAGCTACCTGACTACCTGTCTGAAGA
TGATAGTACCACAAAGAAACAGGACAAAGTGGTGTCCTGGGTCAGCTCACACCCAGTGGGTGGAACTAGCTGGCTGAGCA
CAGTGGCAAACTTTTTATCCAGATCGTTTTATTGG

Alignment

ORF - retro_nleu_1518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNSSTSTMSEEPDALSVVNQLRDLAADPLNRRAIVQDQGCLPGLILFMDHPNPPVVHSALLALRYLAECR
          MNSSTSTMSEE.D.LSVVNQL.D.AADPLNRRAIVQDQGCLPGLILFMDHPNPPVVHSALLAL.YL.E.R
Retrocopy MNSSTSTMSEESDTLSVVNQLQDIAADPLNRRAIVQDQGCLPGLILFMDHPNPPVVHSALLAL*YLGEYR

Parental  ANREKMKGELGMMLSLQNVIQKTTTPGETKLLASEIYDILQSSNMADGDSFNEMNSRRRKAQFFLGTTNK
          ANREKMKGEL..MLSLQNVIQKT.T.GETKLLASEIYDILQSSN.ADGDS..EMNS..RKAQFFLGTTNK
Retrocopy ANREKMKGEL--MLSLQNVIQKTATLGETKLLASEIYDILQSSNKADGDSCSEMNSY*RKAQFFLGTTNK

Parental  RAKTVVLHIDGLDDTSRRNLCEEALLKI-KGVISFTFQMAVQRCVVRIRSDLKAEALASAIASTKVMKAQ
          RAKTVVLHIDG.DDTS.RNLCEEALLKI.K......F.......VV.I.SDLKAEALASA.ASTKVMKA.
Retrocopy RAKTVVLHIDGHDDTSSRNLCEEALLKI>KVLLALLFKWLFKG-VV*IHSDLKAEALASARASTKVMKA*

Parental  QVVKSESGEEMLVPFQDTPVEVEQNTELPDYLPEDESPTKEQDKAVSRVGSHPEGGASWLSTAANFLSRS
          .VVKSESGEEMLVPFQD.PV.VEQNTELPDYL.ED.S.TK.QDK.VS.V.SHP.GG.SWLST.ANFLSRS
Retrocopy *VVKSESGEEMLVPFQDLPV-VEQNTELPDYLSEDDSTTKKQDKVVSWVSSHPVGGTSWLSTVANFLSRS

Parental  FYW
          FYW
Retrocopy FYW

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_1518 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015901	1 retrocopy	retro_btau_1447,
Homo sapiens	ENSG00000104442	1 retrocopy	retro_hsap_3100,
Gorilla gorilla	ENSGGOG00000022803	1 retrocopy	retro_ggor_2129,
Myotis lucifugus	ENSMLUG00000014037	1 retrocopy	retro_mluc_2058,
Nomascus leucogenys	ENSNLEG00000003916	1 retrocopy	retro_nleu_1518 ,
Oryctolagus cuniculus	ENSOCUG00000000392	2 retrocopies	retro_ocun_1437, retro_ocun_782,
Pongo abelii	ENSPPYG00000018630	1 retrocopy	retro_pabe_2474,
Pan troglodytes	ENSPTRG00000020298	1 retrocopy	retro_ptro_2096,
Sus scrofa	ENSSSCG00000006220	1 retrocopy	retro_sscr_1027,