RetrogeneDB ID: retro_nleu_227

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397261.1:54260241..54260783(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSNLEG00000014137
• Aliases: None
• Description: None

Sequence

>retro_nleu_227
ATGGGGAATATCTTTTACCAACCTCTTTAAGGGCATTTTTGGCAAAAAAGAAACGCTTGTCCTCATGGTGGGTCTGGATG
CTGCAGGCAAGATGATGATTCTGTATGAGCTGAAGCTGGTTGAGATTGTGACCACTGTTCCCATCACAGGCTTCAATGCA
GACACATGGAGTCTAGGAACATCAGCTTCACTGTGTGGGACATGGCAGGCCAGCACAAGATCTGGCCTCTGTGGTGCCAC
TACTTCCAGAACACATAAGGCCTGATCTTTATGGAGGACGGTAGTGACAGAGAGCACATGAATAAGGCCCACGAGGAGCT
CATGAGGATATTGGCTGAGGATGAGCTCTGGAATGCGGTCCCCCTGGTGTTCCCAACAAGTAGGCCCTCCTCAACGCCAT
GAGCACCACTGAGATCACAGACAAGCTGGGGCTGCATTCCCTGCTCCACAGGAACTGGTACATTCAGGCCACCTGTGGCA
CCTGTGGTGACCAGCTCCATGAAGGACTGGACTGGCTGTCCAGTCAGCTCCAGAACTAGAAG

Alignment

ORF - retro_nleu_227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGNIF-ANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVET-VEYKNISFTVWDV
          MGNIF..NLFKG.FGKKE...LMVGLDAAGK..ILY.LKL.EIVTT.P..GFN..T..E..NISFTVWD.
Retrocopy MGNIF>TNLFKGIFGKKETLVLMVGLDAAGKMMILYELKLVEIVTTVPITGFNADT<MESRNISFTVWDM

Parental  GGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVF-ANKQDLPNAMNAA
          .GQ.KI.PLW.HYFQNT.GLIF..D..DRE..N.A.EELMR.LAEDEL..AV.LVF..NK..L.NAM...
Retrocopy AGQHKIWPLWCHYFQNT*GLIFMEDGSDREHMNKAHEELMRILAEDELWNAVPLVF<PNK*ALLNAMSTT

Parental  EITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK
          EITDKLGLHSL.HRNWYIQATC.T.GD.L.EGLDWLS.QL.N.K
Retrocopy EITDKLGLHSLLHRNWYIQATCGTCGDQLHEGLDWLSSQLQN*K

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_227 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 17 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000004509	1 retrocopy	retro_apla_4,
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Macaca mulatta	ENSMMUG00000002792	3 retrocopies	retro_mmul_237, retro_mmul_541, retro_mmul_810,
Nomascus leucogenys	ENSNLEG00000007270	3 retrocopies	retro_nleu_2106, retro_nleu_2703, retro_nleu_2704,
Nomascus leucogenys	ENSNLEG00000014137	3 retrocopies	retro_nleu_210, retro_nleu_227 , retro_nleu_2929,
Nomascus leucogenys	ENSNLEG00000017859	2 retrocopies	retro_nleu_1348, retro_nleu_94,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Ochotona princeps	ENSOPRG00000015063	2 retrocopies	retro_opri_317, retro_opri_759,
Procavia capensis	ENSPCAG00000014202	2 retrocopies	retro_pcap_15, retro_pcap_23,
Pteropus vampyrus	ENSPVAG00000007383	1 retrocopy	retro_pvam_1324,
Rattus norvegicus	ENSRNOG00000030591	3 retrocopies	retro_rnor_1268, retro_rnor_1348, retro_rnor_1950,
Sus scrofa	ENSSSCG00000013992	2 retrocopies	retro_sscr_429, retro_sscr_82,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,