RetrogeneDB ID: retro_nleu_286

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397262.1:40464498..40465456(-)
• Located in intron of: ENSNLEG00000007213

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMARCE1
• Ensembl ID: ENSNLEG00000001957
• Aliases: None
• Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109]

Sequence

>retro_nleu_286
ATGCCCAGCACACCAAGGTTTGTGGGATACAGTCCATACAGTCATCTCACCTACAACAACTACAGGCTGGGAAGGAACCC
GGGTGCCAACAGCCAGGTCATGGCATCCTCTGGTACTACGATTCCAAAACCTCCAAAGCCACCAGATAAGCTGCTGATGC
CCTACATGAGGTACAGCTGAAAGGTCTGGGACCAAGTAAAGGCTTCCAACCCTGACCTAAAGTTGTGGGAGACTGGCGAG
ATTATTGGTGGCATGTGGTGAGATCTCACTGATGAAGAAAAACAAGAATATTTAAATGGATACGAAGCAGAAAGATAGAG
TACAATGAATTTATGAAGGCCTATCGTAATTCCCCCACGTACCTAAATGCAAAGAATCGTGCAGAAGCTGCTTTAGAGGA
AGAAAGTTGACAGAGACAGTCTTGCATGGAGAAAGGAGAACCACACATGAGCATTCAGCTTTGCTGAACATCCAGATGAT
TATGGTAATGGGTTTTCAGTGAAGCATACAGCCACTGACTGTTTCCAGAGAAACCACCACCTCTTCAGTGAAATCCTTAG
TGAGAGTGTGGTGCCAGACGTTCGGTCAGTTGTTGCAACAGCTAGAATGCAGGTCCTTAAACGACAGGTCCAGTCCTTAA
TGGTTCATCAGCGAAAACTAGAAGCTGAACTTCTTCAAATAGAGGAGGAGAAGAGGAAATTCCTAGAAAGCACAGATTCA
CTTAACAATGAACTTAAAAGGTTGTGCGGTCTGACAGTAGAAGTGGATATGGAGAAAGTTGCAGCTGAGATTGCACAGGC
AGAGGAACAGACCAGCAAAAAAGCAGGAGGAAAGGGAGAAGGAGGCAGCAGAGCAAGCTGAGTGCAGTCAGAGCAGCATT
ATTCCTGAGGAAGAACAAGCACCAAACAAAGGTGAGGAGAAGAAAGACGATGAGAACATTCCAGTGGAGACAGAGGAG

Alignment

ORF - retro_nleu_286 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.89 %
• Parental protein coverage: 94.49 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPSTPGFVGYNPYSHLAYNNYRLGGNPGTNSRVTASSGITIPKPPKPPDKPLMPYMRYSRKVWDQVKASN
          MPSTP.FVGY.PYSHL.YNNYRLG.NPG.NS.V.ASSG.TIPKPPKPPDK.LMPYMRYS.KVWDQVKASN
Retrocopy MPSTPRFVGYSPYSHLTYNNYRLGRNPGANSQVMASSGTTIPKPPKPPDKLLMPYMRYS*KVWDQVKASN

Parental  PDLKLWEIGKIIGGMWRDLTDEEKQEYLNEYEAE-KIEYNESMKAYHNSPAYLAYINAKSRAEAALEEES
          PDLKLWE.G.IIGGMW.DLTDEEKQEYLN.YEAE.KIEYNE.MKAY.NSP.YL...NAK.RAEAALEEES
Retrocopy PDLKLWETGEIIGGMW*DLTDEEKQEYLNGYEAE<KIEYNEFMKAYRNSPTYL---NAKNRAEAALEEES

Parental  RQRQSRMEKGEPYMSIQP-AEDPDDYDDGFSMKHTATARFQRNHRLISEILSESVVPDVRSVVTTARMQV
          .QRQS.MEKGEP.MSIQ..AE.PDDY..GFS.KHTAT..FQRNH.L.SEILSESVVPDVRSVV.TARMQV
Retrocopy *QRQSCMEKGEPHMSIQL>AEHPDDYGNGFSVKHTATDCFQRNHHLFSEILSESVVPDVRSVVATARMQV

Parental  LKRQVQSLMVHQRKLEAELLQIEERHQEKKRKFLESTDSFNNELKRLCGLKVEVDMEKIAAEIAQAEEQA
          LKRQVQSLMVHQRKLEAELLQIEE.....KRKFLESTDS.NNELKRLCGL.VEVDMEK.AAEIAQAEEQ.
Retrocopy LKRQVQSLMVHQRKLEAELLQIEE----EKRKFLESTDSLNNELKRLCGLTVEVDMEKVAAEIAQAEEQT

Parental  -RKRQEEREKEAAEQAERSQSSIVPEEEQAANKGEEKKDDENIPMETEK
          ..K.QEEREKEAAEQAE.SQSSI.PEEEQA.NKGEEKKDDENIP.ETE.
Retrocopy >AKKQEEREKEAAEQAECSQSSIIPEEEQAPNKGEEKKDDENIPVETEE

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_286 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 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013573	4 retrocopies	retro_cjac_1107, retro_cjac_2109, retro_cjac_50, retro_cjac_854,
Homo sapiens	ENSG00000073584	5 retrocopies	retro_hsap_1195, retro_hsap_1304, retro_hsap_3623, retro_hsap_3947, retro_hsap_922,
Gorilla gorilla	ENSGGOG00000011803	2 retrocopies	retro_ggor_1020, retro_ggor_931,
Microcebus murinus	ENSMICG00000009821	4 retrocopies	retro_mmur_1408, retro_mmur_1592, retro_mmur_608, retro_mmur_928,
Myotis lucifugus	ENSMLUG00000004609	1 retrocopy	retro_mluc_1209,
Macaca mulatta	ENSMMUG00000004005	3 retrocopies	retro_mmul_1284, retro_mmul_2159, retro_mmul_2286,
Mustela putorius furo	ENSMPUG00000014660	4 retrocopies	retro_mputfur_1411, retro_mputfur_1482, retro_mputfur_1499, retro_mputfur_739,
Mus musculus	ENSMUSG00000037935	5 retrocopies	retro_mmus_1111, retro_mmus_1127, retro_mmus_2437, retro_mmus_2618, retro_mmus_3194,
Nomascus leucogenys	ENSNLEG00000001957	4 retrocopies	retro_nleu_1060, retro_nleu_2051, retro_nleu_2083, retro_nleu_286 ,
Oryctolagus cuniculus	ENSOCUG00000008981	1 retrocopy	retro_ocun_59,
Otolemur garnettii	ENSOGAG00000001652	7 retrocopies	retro_ogar_1734, retro_ogar_2059, retro_ogar_3199, retro_ogar_402, retro_ogar_454, retro_ogar_682, retro_ogar_760,
Ochotona princeps	ENSOPRG00000000985	1 retrocopy	retro_opri_731,
Pongo abelii	ENSPPYG00000008456	4 retrocopies	retro_pabe_2973, retro_pabe_3251, retro_pabe_794, retro_pabe_994,
Pan troglodytes	ENSPTRG00000022902	5 retrocopies	retro_ptro_2451, retro_ptro_2678, retro_ptro_3039, retro_ptro_639, retro_ptro_894,
Pteropus vampyrus	ENSPVAG00000011355	1 retrocopy	retro_pvam_237,
Rattus norvegicus	ENSRNOG00000010676	7 retrocopies	retro_rnor_1278, retro_rnor_1311, retro_rnor_1456, retro_rnor_1507, retro_rnor_1599, retro_rnor_2383, retro_rnor_2593,
Tupaia belangeri	ENSTBEG00000000770	10 retrocopies	retro_tbel_1246, retro_tbel_1554, retro_tbel_2208, retro_tbel_2955, retro_tbel_4035, retro_tbel_4629, retro_tbel_4656, retro_tbel_658, retro_tbel_821, retro_tbel_844,