RetrogeneDB ID: retro_nleu_1231

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397285.1:18016991..18017834(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATAD1
• Ensembl ID: ENSNLEG00000012135
• Aliases: None
• Description: None

Sequence

>retro_nleu_1231
GTAGACTATCTTAATATGCATGTTACTTGGAAGTGATATAGCAGGTTTAGATGAGGTCCTTATGGATCTGAAAGACACAG
TCATCTTACCTATCAAAAAGAAACATTTGTTTGAGAATTCCAGGCTTCTGCAGCCTCCAAAAGGTGTTCTTCTCTATGGG
CCCCCCCAGGCTGTGGTAAAACGTTGATTGCCAAGGCCACAGCCAAAGAAGCAGGCTGTCGATTTATTAACCTTGAGCCT
TGGACACTGACTAATAAGTGGTAGGGAGAATCTCAAACATTGGCAGCTGCTGTCTTCTCCCTTGTCATAAAGCTACAACT
GTCCATCATCATTATAGATGAAATAGACTCCTTTCTACGAAACCGTTCAAGTTCTGACCATGAAGCTACAGCCATGATGA
AAGCTCAGTTTATGAATCTCTGGGATGGATTGGATACTGATCACAGCTGCCAGGTCATAGTAATGGGAGCTACCATTCAT
CCTCAGGACCTTGACACGGCTATAATGAGAAGAATCCCTACAAGATTTCATATCAACCAGCCTGCTTTAAAACAGAGAGA
AGCAATCCTGAAACTCATCTTGAAAAATGAAAATGTGGACAGGCATGTAGACTGCTAGAAGTTGCCCAGGAAACTGATGC
GTTTTCAGGAAGGGACCTAAAAGCGATGTGTTGAGATGCTGCTCTCCTCTGTGTTAGAGAATGTTAATTCTACATCAGAA
GAAAGCCATGATGAAGATGAAATTCGGCCTGTTCAACAGCAGGACCTGCATCGGGCAATTGAAAAGATTAAGAAATCAAA
GGATGCAGCATTTCAGAATGTTTTAACACAAGTTTGTTTAGAT

Alignment

ORF - retro_nleu_1231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.37 %
• Parental protein coverage: 77.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VDPLNMHVTW-SDIAGLDDVITDLKDTVILPI-KKKHLFENSRLLQPPKGVL-LYGPPGCGKTLIAKATA
          VD.LNMHVTW.SDIAGLD.V..DLKDTVILPI.KK........L..P....L.L..PPGCGKTLIAKATA
Retrocopy VDYLNMHVTW>SDIAGLDEVLMDLKDTVILPIKKKHLFENSRLLQPPKGVLL<LWAPPGCGKTLIAKATA

Parental  KEAGCRFINLQPSTLTDKWYGESQKLAAAVFSLAIKLQPSIIFIDEIDSFLRNRSSSDHEATAMMKAQFM
          KEAGCRFINL.P.TLT.KW.GESQ.LAAAVFSL.IKLQ.SII.IDEIDSFLRNRSSSDHEATAMMKAQFM
Retrocopy KEAGCRFINLEPWTLTNKW*GESQTLAAAVFSLVIKLQLSIIIIDEIDSFLRNRSSSDHEATAMMKAQFM

Parental  SLWDGLDTDHSCQVIVMGATNRPQDLDSAIMRRMPTRFHINQPGFKQREAILKLILKNENVDRHVD-LLE
          .LWDGLDTDHSCQVIVMGAT..PQDLD.AIMRR.PTRFHINQP..KQREAILKLILKNENVDRHVD.LLE
Retrocopy NLWDGLDTDHSCQVIVMGATIHPQDLDTAIMRRIPTRFHINQPALKQREAILKLILKNENVDRHVD<LLE

Parental  VAQETDGFSGSDLKEMCRDAALLCVRE-YVNSTSEESHDEDEIRPVQQQDLHRAIEKMKKSKDAAFQNVL
          VAQETD.FSG.DLK.MC.DAALLCVRE.......E.......IRPVQQQDLHRAIEK.KKSKDAAFQNVL
Retrocopy VAQETDAFSGRDLKAMC*DAALLCVRE>VNSTSEESHDEDE-IRPVQQQDLHRAIEKIKKSKDAAFQNVL

Parental  THVCLD
          T.VCLD
Retrocopy TQVCLD

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_1231 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005296	1 retrocopy	retro_cjac_1101,
Homo sapiens	ENSG00000138138	1 retrocopy	retro_hsap_1900,
Gorilla gorilla	ENSGGOG00000026651	1 retrocopy	retro_ggor_1393,
Macaca mulatta	ENSMMUG00000006414	1 retrocopy	retro_mmul_608,
Nomascus leucogenys	ENSNLEG00000012135	1 retrocopy	retro_nleu_1231 ,
Oryctolagus cuniculus	ENSOCUG00000012082	1 retrocopy	retro_ocun_1634,
Pan troglodytes	ENSPTRG00000002717	1 retrocopy	retro_ptro_1255,
Pteropus vampyrus	ENSPVAG00000014020	1 retrocopy	retro_pvam_1080,
Rattus norvegicus	ENSRNOG00000010861	1 retrocopy	retro_rnor_2752,
Ictidomys tridecemlineatus	ENSSTOG00000006563	1 retrocopy	retro_itri_309,