RetrogeneDB ID: retro_nleu_2743

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397416.1:2614760..2615855(-)
• Located in intron of: ENSNLEG00000001029

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR12
• Ensembl ID: ENSNLEG00000007018
• Aliases: None
• Description: None

Sequence

>retro_nleu_2743
ATGGCTCAGCTGCAAACAAGCTTCTACACTGATCACAAGAAATAGGCCATCGATGATGTTCCCTTCTCAATCCCTGCTGT
CTCTGAAAGTGTTGACCTTAGTAACATCATCAATTAATTACTAAAGGGCAGAAATGAGTTCCACAAATATATGGAGTCTG
ATTTCCTTATTAAGGGTCAGTTTCTGCGAATGCCCTTGGTCAAACACATGGAACGGGAGAACACCTCATCAGAAGAGGTT
GTGGAAAGAGAATACGCGGAGAAGTATACTGCACCCCAACCAGAATGATGTGTCCACGATGACTGGACCAGTTCAGTGTA
AGGGACAGAGGTATGGATCTTGACTGGTTCTTGTGTCGTAACTTCTCGAATCCGGTCCTTGGAAGGAAAGTCAACATTGA
CAATTGTGGGACATATGGATGTTATAAAAGATGTGGCCTGGGTGATAAAGACAGTTTGTGTTATTACTGAGTGCCTCTAC
GGATCAGACTATTCTCTTATGGGAGTGGAATGTCGAGAGAAACAAAGTGAAAACCCTATACTGCTGCACAAGTGTAGATT
CTACAGCTATTGATAGCTCAGGAACTAAATTTTGCAGTGGCTCCTGGGATAAGATGATAAGGATCTGGTCTACTGTCCCT
ACAGAAGAAGATGAAATGGAGGAATCCACAAATTGACCAAGAAAGAAACAGAAAACAGAGCAGCTGGGACTAACAAGGAC
TCCCATAGTGACCCTCTCTGGCCACAAGGAAGCAATCTCCTCAGTGCTGTGGTAAGATGCTGAAGAAATCTGCAGTGTAT
CTTGGGACCATAAAATTAGTGTGTGGAATGTCGTGTTTGGCAATCTTAAGTCAACTTTACAGGAAATAAAGTGTTTAATT
GTATTTCCTATTCTCCACTTTGTAAATGTTTAGCATCTGGAAGCCCAGATAGGCATATCAGACTGTGGGATCCCCAAACT
AAAGACGGTTCTTTCATGTTGCCATCCCTAATGTCACATACAGGTTGGGAGACATCAGTAAAACTGTCTCCTACCCATGA
AGCACAGCTGATTTCAGGATCCTTATATACCACTGTCAAGCTGTGGGATTCAAGA

Alignment

ORF - retro_nleu_2743 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.46 %
• Parental protein coverage: 88.18 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAQLQTRFYTDNKKYAVDDVPFSIPAASEIADLSNIINKLLKDKNEFHKHVEFDFLIKGQFLRMPLDKHM
          MAQLQT.FYTD.KK.A.DDVPFSIPA.SE..DLSNIIN.LLK..NEFHK..E.DFLIKGQFLRMPL.KHM
Retrocopy MAQLQTSFYTDHKK*AIDDVPFSIPAVSESVDLSNIIN*LLKGRNEFHKYMESDFLIKGQFLRMPLVKHM

Parental  ELENISSEEVVEIEYVEKYTAPQPEQCMFHDDWISSIKGAEEWILTGSYDKTSRIWSLEGKSIMTIVGHT
          E.EN.SSEEVVE.EY.EKYTAPQPE.C..HDDW.SS..G.E.WILTGS...TSRI.SLEGKS..TIVGH.
Retrocopy ERENTSSEEVVEREYAEKYTAPQPE*CV-HDDWTSSV*GTEVWILTGSCVVTSRIRSLEGKSTLTIVGHM

Parental  DVVKDVAWV-KKDSLSC-LLLSASMDQTILLWEWNVERNKVKALHCCRGHAGSVDSIAVDGSGTKFCSGS
          DV.KDVAWV..KDSL.C.LLLSAS.DQTILLWEWNVERNKVK.L.CC.....SVDS.A.D.SGTKFCSGS
Retrocopy DVIKDVAWV<DKDSL-C<LLLSASTDQTILLWEWNVERNKVKTLYCCT----SVDSTAIDSSGTKFCSGS

Parental  WDKMLKIWSTVPTDEEDETEESTNRPRKKQKTEQLGLTRTPIVTLSGHMEAVSSVLWSEAEEICSASWDH
          WDKM..IWSTVPT.EEDE.EESTN.PRKKQKTEQLGLTRTPIVTLSGH.EA.SSVLW..AEEICS.SWDH
Retrocopy WDKMIRIWSTVPT-EEDEMEESTN*PRKKQKTEQLGLTRTPIVTLSGHKEAISSVLW*DAEEICSVSWDH

Parental  TIRVWDVESGSLKSTL-TGNKVFNCISYSPLCKRLASGSTDRHIRLWDPRTKDGSLVSLSLTSHTGWVTS
          .I.VW.V..G.LKSTL.TGNKVFNCISYSPLCK.LASGS.DRHIRLWDP.TKDGS....SL.SHTGW.TS
Retrocopy KISVWNVVFGNLKSTL<TGNKVFNCISYSPLCKCLASGSPDRHIRLWDPQTKDGSFMLPSLMSHTGWETS

Parental  VKWSPTHEQQLISGSLDNIVKLWDTR
          VK.SPTHE.QLISGSL...VKLWD.R
Retrocopy VKLSPTHEAQLISGSLYTTVKLWDSR

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_2743 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012519	1 retrocopy	retro_cfam_1759,
Choloepus hoffmanni	ENSCHOG00000013851	1 retrocopy	retro_chof_118,
Callithrix jacchus	ENSCJAG00000005171	1 retrocopy	retro_cjac_2690,
Cavia porcellus	ENSCPOG00000008824	1 retrocopy	retro_cpor_1107,
Homo sapiens	ENSG00000138442	1 retrocopy	retro_hsap_1615,
Gorilla gorilla	ENSGGOG00000026073	1 retrocopy	retro_ggor_1222,
Loxodonta africana	ENSLAFG00000011955	1 retrocopy	retro_lafr_1102,
Mus musculus	ENSMUSG00000026019	3 retrocopies	retro_mmus_1394, retro_mmus_2649, retro_mmus_2897,
Nomascus leucogenys	ENSNLEG00000007018	1 retrocopy	retro_nleu_2743 ,
Pongo abelii	ENSPPYG00000013089	1 retrocopy	retro_pabe_1327,
Pan troglodytes	ENSPTRG00000012823	1 retrocopy	retro_ptro_1083,
Tursiops truncatus	ENSTTRG00000001231	1 retrocopy	retro_ttru_1380,