RetrogeneDB ID: retro_nleu_1267

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397286.1:22036018..22037499(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UHRF1
• Ensembl ID: ENSNLEG00000013406
• Aliases: None
• Description: None

Sequence

>retro_nleu_1267
CCATCCTGCAAGCACTGCAAGGACGACATGAATAGACTCTGTTGGATCTGCGCCTGCCACCTGTGTGAGGGCCAGTAAGA
CCCCAACAAGCAGCTCATGTGTGACGAATGTGACATGGCCTTCCACATCTACTGCCTGTGCCCCTCCCTCAGCAGCACTC
CCAGCTAGTACAAGTGGTACTGCCCGAGTGCCGGAATGACACCAGCAAGGTAGTGCTGGCAGGAGAGAGGCTGAGAGAGA
GCAAGAAGAAGGCGAAGATGGCCTCGGCCACGTTGTCCTTGAAGCGGGACTGGGGCAAGGGCATTGCGTGTGTGGGCCTC
ACCAAGGAGTGCACCATCGTCCCGTCCAACCACTACGGACCCATCCCAGGGATCCCCGTGGGCACCATGTGGCGGTTCTG
AGTCCAGGTCAGCGAGTCTGGGGCTCATCGGCCCCACGTGGCTGGCATTCACGGCCGGAGCAATGACGGGTCGTACTCCC
TGGTCCTGGACAGGGGCTACAAGGACGATGTGGACCAGGAGAATTTTTTCAGATACACAGATAGTGATGGTTGAGATCTT
TTTGCAACAAGAGGACCGCGGAACAGTCTTGTGATCAGAAACTCACCAACACCAACAGGGCGCTGGCTCTCAGGTGCTTT
ACTCTCTTTAATGACCAAGAAGGGGCTGAGGCCAAGGACTGGCAGTCGGGAATGCCTGTCAGGGTGGTGCCCAACGTCAA
GGGTGGTAAGAACAGAAAGTACGCCCCCGCCAAGGGCAACTGCTACGACCGCATCTAGCAGGTGGTGAAGTAGTGGCCCG
AGAAGTGGAAGTCCAGGTTTCTCCTGCGGCGCTACCTCCTGCAGAGGGACGATGACGAGCCTGGCCCCTGGACGAAGGAG
GAGAAGGAATGGATCAAGAAGCTGGGGCTGACTATGCAGTATCCAGAAGGCCACCTGGAAGCCCTGGCCAACCGAGAGCG
GGAGAAGGAGAATTAGCAAGAGAGAGGAGGAGGAGGAGCAGGAGGAGGGCTTCGCGGGCCCCAGGGAAAGCAAGGGAAAG
TGGAAGCAGAAGCAGGCAGGAGGTGGCCTGAGCAGGGCCGCCTCCCCTCGCTGGACATCCAAGAAAACTAAAGTGGAGCC
CTACAACCTCACAGCCCAGCAGAGCGGCCTCATCAGAAAGGACAAGAGCAACGCCCAACTGTGGAATGAGGTCCTGGCGT
TGCTCAAGGGCCGGCCAGCGAGGAGCAGCCCGTTTCAGATGTTCCTGAGTAAAGTGGAGGAGATGCTCCAGTGTATCTGC
TATCAGGAGCTGGTGTTCCGGCCCATTGCAACTGTGTGCCAGCACAAGGTATGCAAGGACTGCCTGGACAAATCCTTCTG
GGCACAGGTGTTCAGCTGCCCCGCCTGCCGCTCTGACCTGGGCTGGAGCTATGCCATGCAGGTGAACCAGCCCCTGCAGA
CGGTCCTCAACCAGTTCTTGCCTGGCTACGGCAATGGCCGG

Alignment

ORF - retro_nleu_1267 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.1 %
• Parental protein coverage: 72.58 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLNPPLSSVPSEDEWYCP-ECRNDAS
          PSCKHCKDD.NRLC..CACHLC.G..DP.KQLMCDECDMAFHIYCL.P.LSS.PS...WYCP.ECRND.S
Retrocopy PSCKHCKDDMNRLCWICACHLCEGQ*DPNKQLMCDECDMAFHIYCLCPSLSSTPS*YKWYCP<ECRNDTS

Parental  EVVLAGERLRESKKKAKMASATSSSQRDWGKGSPCCGYQLECSGAVSAHYNLPLPPSPVAGRWSFSAAVS
          .VVLAGERLRESKKKAKMASAT.S..RDWGKG..C.G...EC....S.HY..P.P..PV...W.F...VS
Retrocopy KVVLAGERLRESKKKAKMASATLSLKRDWGKGIACVGLTKECTIVPSNHYG-PIPGIPVGTMWRF*VQVS

Parental  ESGVHRPHVAGIHGRSNDGAYSLVLAGGYKDDVDHGNFFTYTGSGGRDLSG-NKRTAEQSCDQKLTNTNR
          ESG.HRPHVAGIHGRSNDG.YSLVL..GYKDDVD..NFF.YT.S.G.DL...NKRTAEQSCDQKLTNTNR
Retrocopy ESGAHRPHVAGIHGRSNDGSYSLVLDRGYKDDVDQENFFRYTDSDG*DLFA<NKRTAEQSCDQKLTNTNR

Parental  ALALNCFAPINDQEGAEAKDWRSGKPVRVVRNVKGGKNSKYAPAEGNRYDGIYKVVKYWPEKGKSGFLVW
          ALAL.CF...NDQEGAEAKDW.SG.PVRVV.NVKGGKN.KYAPA.GN.YD.I..VVK.WPEK.KS.FL..
Retrocopy ALALRCFTLFNDQEGAEAKDWQSGMPVRVVPNVKGGKNRKYAPAKGNCYDRI*QVVK*WPEKWKSRFLLR

Parental  RYLLRRDDDEPGPWTKEGKDRTKKLGLTMQYPEGYLEALANREREKENSKREEEEQQEGGFASPRTGKGK
          RYLL.RDDDEPGPWTKE.K...KKLGLTMQYPEG.LEALANRE....................P....GK
Retrocopy RYLLQRDDDEPGPWTKEEKEWIKKLGLTMQYPEGHLEALANREXXXXXXXXXXXXXXXXXLRGPQGKQGK

Parental  -WKRKSAGGGPSRAGSPRRTSKKTKVEPYSLTAQQSSLIREDKSNAKLWNEVLASLKDRPASGSPFQLFL
          .WK.K.AGGG.SRA.SPR.TSKKTKVEPY.LTAQQS.LIR.DKSNA.LWNEVLA.LK.RPA..SPFQ.FL
Retrocopy >WKQKQAGGGLSRAASPRWTSKKTKVEPYNLTAQQSGLIRKDKSNAQLWNEVLALLKGRPARSSPFQMFL

Parental  SKVEETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGRSYAMQVNQPLQTVLNQL
          SKVEE..QCIC.QELVFRPI.TVCQH.VCKDCLD.SF.AQVFSCPACR.DLG.SYAMQVNQPLQTVLNQ.
Retrocopy SKVEEMLQCICYQELVFRPIATVCQHKVCKDCLDKSFWAQVFSCPACRSDLGWSYAMQVNQPLQTVLNQF

Parental  FPGYGNGR
          .PGYGNGR
Retrocopy LPGYGNGR

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_1267 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000001228	1 retrocopy	retro_mmus_3696,
Nomascus leucogenys	ENSNLEG00000009135	1 retrocopy	retro_nleu_1985,
Nomascus leucogenys	ENSNLEG00000013406	1 retrocopy	retro_nleu_1267 ,