RetrogeneDB ID: retro_nleu_2388

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397350.1:5472532..5473711(+)
• Located in intron of: ENSNLEG00000011225

Retrocopy information

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

Parental gene information

• Parental gene symbol: LARP4
• Ensembl ID: ENSNLEG00000017798
• Aliases: None
• Description: La ribonucleoprotein domain family, member 4 [Source:HGNC Symbol;Acc:24320]

Sequence

>retro_nleu_2388
AATGCAGAGCTCTCAGAAGATATATGTAAAGAATATGAAGTAATGTGTTCTTCATCTTGTGAAACCACAAGAAATACTAC
AGGCATTGAAGAATCAACTGATGGGATGATTTTAGGACCAGATCTGAGTTACTAAATATATGATGTTTCTGGAGAAAGCA
ATTCAGCAATTTCTACAGAAGACCTAAAAGAATGTCTAAAGAAACAATTAGAATTCTGTTTTTCATGAGAAAATTTGTCA
AAGGATCTTTACTTGATATCTCAAATGGATAGTGATCAGTTCATCCCAATTTGGACAGTTGTTAACATGGAAGAAATAAA
AAAATTGACCACAGACCCTGATGTAATTCTTGAAGTGTTAAGATCTTCTCCCATGGTACAAATTGATGAGAAGGGTAAAA
AGTGAGACCAAGTCATAAGCGTTGTATTGTGATTCTTAGAGAGATTCCTGAAACAACACCAATAGGGGAAGTGAAAGTTT
TGTTCAAATTGAAAACTGCCCCAAAGTGATAAGCTGTGAGTTTGCACACAGTAGCAGCTGGTATATCACTTTCCAGTCAG
ACACAGATGCACAACAGGCTTTTAAATCCTTAAGAGAAGAAGTTAAAACATTTCAGGGCAAGCCAATTATGGCAAGGATA
AAAGCCATCAATACATTTTTTGCTAAGAATTGTTACTGATTAATGGATTCTAGTATCTGTAGTCAGCCCATTCAAACTCA
AGCACAGTATGCCTCCCCAGTCTTCATGCAGCCTGTATATAATCCTCACCAGCAATTCTCAGTCTATAGTATTATTCCAC
AGTCTTGGTCTCCAAATCCTACACCTTACTTTGAAACACCACTGGCCCACTTTGCCAATGGTAGTTTTGTGAATGGCTTT
AATTCACCAGGATCTTATAAAACAAATGCTGCTGCTGTGAATATGGGTCGATCATTCCAAAAAAAAAATCTGAAGCCTCA
TTTTAGGTCATCCAGTGGTTCAGAACACTCAACAGAGGACTCTGTATCATTGGGGGATGGACAGTTGAACAGATGTAGTT
CAAAAAATTTTTCAACTGAAAGCATAATCCTACAGTAACTGGGGATTAGGAGCAAACTTAACTTCAAAAGGAGACTTCCA
CTTTGCAGATGGAACAGAATGGGGACTATGGTAGGGGCAGGAGAACTCTTTTCAGAGGT

Alignment

ORF - retro_nleu_2388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.2 %
• Parental protein coverage: 57.33 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NAELSEDICKEYEVMYSSSCETTRNTTGIEESTDGMILGPEDLSYQIYDVSGESNSAVSTEDLKECLKKQ
          NAELSEDICKEYEVM.SSSCETTRNTTGIEESTDGMILGP.DLSY.IYDVSGESNSA.STEDLKECLKKQ
Retrocopy NAELSEDICKEYEVMCSSSCETTRNTTGIEESTDGMILGP-DLSY*IYDVSGESNSAISTEDLKECLKKQ

Parental  LEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLILEVLRSSPMVQVDEKGEK-VRPS
          LEFCFS.ENLSKDLYLISQMDSDQFIPIWTV.NMEEIKKLTTDPD.ILEVLRSSPMVQ.DEKG.K.VRPS
Retrocopy LEFCFS*ENLSKDLYLISQMDSDQFIPIWTVVNMEEIKKLTTDPDVILEVLRSSPMVQIDEKGKK<VRPS

Parental  HKRCIVILREIPETTPIEEVKALFKS-ENCPKVISCEFAHNSNWYITFQSDTDAQQAFKYLREEVKTFQG
          HKRCIVILREIPETTPI.EVK.LFK..ENCPKVISCEFAH.S.WYITFQSDTDAQQAFK.LREEVKTFQG
Retrocopy HKRCIVILREIPETTPIGEVKVLFKL<ENCPKVISCEFAHSSSWYITFQSDTDAQQAFKSLREEVKTFQG

Parental  KPIMARIKAINTFFAKNGYRLMDSSIYSQPIQTQAQYASPVFMQPVYNPHQQYSVYSFVPQSWSPNPTPY
          KPIMARIKAINTFFAKN.Y.LMDSSI.SQPIQTQAQYASPVFMQPVYNPHQQ.SVYS..PQSWSPNPTPY
Retrocopy KPIMARIKAINTFFAKNCY*LMDSSICSQPIQTQAQYASPVFMQPVYNPHQQFSVYSIIPQSWSPNPTPY

Parental  FETPLAPFPNGSFVNGFNSPGSYKTNAAAMNMGRPFQKNRVKPHFRSSSGSEHSTEGSVSLGDGQLNRSS
          FETPLA.F.NGSFVNGFNSPGSYKTNAAA.NMGR.F.....KPHFRSSSGSEHSTE.SVSLGDGQLNR.S
Retrocopy FETPLAHFANGSFVNGFNSPGSYKTNAAAVNMGRSFXXXXLKPHFRSSSGSEHSTEDSVSLGDGQLNRCS

Parental  SRNFPTE-RHNPTVTGHQEQTYLQKEISTLQMEQNGDYSRGRRTLFRG
          S.NF.TE..HNPTVTG..EQT.LQKE.STLQMEQNGDY.RGRRTLFRG
Retrocopy SKNFSTE<KHNPTVTGD*EQT*LQKETSTLQMEQNGDYGRGRRTLFRG

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_2388 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000161813	1 retrocopy	retro_hsap_1483,
Myotis lucifugus	ENSMLUG00000012513	1 retrocopy	retro_mluc_1180,
Macaca mulatta	ENSMMUG00000008172	1 retrocopy	retro_mmul_2129,
Mus musculus	ENSMUSG00000023025	1 retrocopy	retro_mmus_3568,
Nomascus leucogenys	ENSNLEG00000017798	1 retrocopy	retro_nleu_2388 ,
Pan troglodytes	ENSPTRG00000004935	1 retrocopy	retro_ptro_1003,
Rattus norvegicus	ENSRNOG00000049091	1 retrocopy	retro_rnor_644,