RetrogeneDB ID: retro_nleu_31

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397393.1:2998629..3000504(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000018191
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: UBQLN1
• Ensembl ID: ENSNLEG00000003306
• Aliases: None
• Description: None

Sequence

>retro_nleu_31
ATGGCTGAGAATGGCGAGAGCAGCGGCCCCCCGCGCCCCTCCCGCGGCCCTGCTGCGGCCCAAGGCTCGGCTGCTGCCCC
AGCTGAGCCTAAAATCATCAAAGTCACTGTGAAGACTCCCAAAGAGAAAGAGGAGTTCGCGGTGCCTGAAAACAGCTCGG
TTCAGCAGTTTAAGGAAGCGATTTCGAAACGCTTCAAATCCCAAACCGATCAGCTAGTGCTGATTTTTGCCGGAAAAATC
TTAAAAGATCAAGATACCTTGATCCAGCATGGCATCCATGATGGGCTGACTGTTCACCTTGTCATCAAAAGCCAGAACCG
ACCTCAGGGCCAGTCCACGCAGCCTAGCAATGCCGCGGGAACTAACACTACCTCGGCGTCGACTCCCAGGAGTAACTCCA
CACCTATTTCCACAAATAGCAACCCGTTTGGGTTGGGGAGCCTGGGAGGACTTGCAGGCCTTAGCAGCCTGGGCTTGAGC
TCGACCAACTTCTCTGAGCTCCAGAGCCAGATGCAGCAGCAGCTTATGGCCAGCCCTGAGATGATGATACAAATAATGGA
AAATCCCTTTGTTCAGAGCATGCTTTCGAATCCCGATCTGATGAGGCAGCTCATTATGGCTAATCCACAGATGCAGCAAT
TGATTCAGAGAAACCCAGAAATCAGTCACCTGCTCAACAACCCAGATATAATGAGGCAGACACTCGAAATTGCCAGGAAT
CCAGCCATGATGCAAGAGATGATGAGAAATCAAGACCTGGCTCTGAGCAATCTAGAAAGCATCCCAGGTGGCTATAATGC
TTTACGGCGCATGTACACTGACATTCAAGAGCCGATGCTGAATGCCGCACAAGAGCAGTTTGGGGGTAATCCATTTGCCT
CCGTGGGGAGTAGTTCCTCCTCTGGGGAAGGTACGCAGCCTTCCCGCACAGAAAATCGCGATCCACTACCCAATCCATGG
GCACCACCGCCAGCTACCCAGAGTTCTGCAACTACCAGCACGACCACGAGCACTGGTAGTGGGTCTGGCAACAGTTCCAG
CAATGCTACTGGGAACACCGTTGCTGCCGCTAATTATGTCGCCAGCATCTTTAGTACCCCAGGCATGCAGAGCCTGCTGC
AACAGATAACTGAAAACCCCCAGCTGATTCAGAATATGCTGTCGGCGCCCTACATGAGAAGCATGATGCAGTCGCTGAGC
CAGAATCCAGATTTGGCTGCACAGATGATGCTGAATAGCCCGCTGTTTACTGCAAATCCTCAGCTGCAGGAGCAGATGCG
GCCACAGCTCCCAGCCTTCCTGCAGCAGATGCAGAATCCAGACACACTATCAGCCATGTCAAATCCAAGAGCAATGCAGG
CTTTAATGCAGATCCAGCAGGGGCTACAGACATTAGCCACTGAAGCACCTGGCCTGATTCCAAGCTTCACTCCAGGTGTG
GGGGTGGGGGTGCTGGGAACCGCTATAGGCCCTGTAGGCCCAGTCACCCCCATAGGCCCCATAGGCCCTATAGTCCCTTT
TACCCCCATAGGCCCCATTGGGCCCATAGGACCCACTGGCCCTGCAGGCCCCCCTGGCTCCACCGGCTCTGGTGGCCCCA
CTGGGCCTACTGTGTCCAGCGCTGCACCTAGTGAAAACACGAGTCCTACATCAGAATCTGGACCCAACCAGCAGTTCATT
CAGCAAATGGTGCAGGCCCTGGCTGGAGCAAATGCTCCACAGCTGCCGAATCCAGAAGTCAGATTTCAGCAACAACTGGA
ACAGCTCAACGCAATGGGGTTCTTAAACCGTGAAGCAAACTTGCAGGCCCTAATAGCAACAGGAGGCGACATCAATGCAG
CCATTGAAAGGCTGCTGGGCTCCCAGCCATCGTAA

Alignment

ORF - retro_nleu_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.28 %
• Parental protein coverage: 85.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAESGESGGPPGSQDSAAGAEGAGAPAAAASAEPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFK
          MAE.GES.GPP......A.A.G.....AAA.AEPKI.KVTVKTPKEKEEFAVPENSSVQQFKE.ISKRFK
Retrocopy MAENGESSGPPRPSRGPAAAQGS----AAAPAEPKIIKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFK

Parental  SHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNRPQDHSAQQTNTAGSNVTMSSTPNSNSTSG
          S.TDQLVLIFAGKILKDQDTL.QHGIHDGLTVHLVIK.QNRPQ..S.Q..N.AG.N.T..STP.SNST..
Retrocopy SQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKSQNRPQGQSTQPSNAAGTNTTSASTPRSNSTPI

Parental  SATSNPFGLGGLGGLAGLSSLGLNTTNFSELQSQMQRQLLSNPEMMVQIMENPFVQSMLSNPDLMRQLIM
          S..SNPFGLG.LGGLAGLSSLGL..TNFSELQSQMQ.QL...PEMM.QIMENPFVQSMLSNPDLMRQLIM
Retrocopy STNSNPFGLGSLGGLAGLSSLGLSSTNFSELQSQMQQQLMASPEMMIQIMENPFVQSMLSNPDLMRQLIM

Parental  ANPQMQQLIQRNPEISHMLNNPDIMRQTLELARNPAMMQEMMRNQDRALSNLESIPGGYNALRRMYTDIQ
          ANPQMQQLIQRNPEISH.LNNPDIMRQTLE.ARNPAMMQEMMRNQD.ALSNLESIPGGYNALRRMYTDIQ
Retrocopy ANPQMQQLIQRNPEISHLLNNPDIMRQTLEIARNPAMMQEMMRNQDLALSNLESIPGGYNALRRMYTDIQ

Parental  EPMLSAAQEQFGGNPFASLVSNTSSGEGSQPSRTENRDPLPNPWAPQTSQSSSASSGTASTVGGTTGSTA
          EPML.AAQEQFGGNPFAS..S..SSGEG.QPSRTENRDPLPNPWAP.....SSA...T....G...G...
Retrocopy EPMLNAAQEQFGGNPFASVGSSSSSGEGTQPSRTENRDPLPNPWAPPPATQSSATTSTTTSTGSGSGNSS

Parental  SGTSGQSTTAPNLVPGVGASMFNTPGMQSLLQQITENPQLMQNMLSAPYMRSMMQSLSQNPDLAAQMMLN
          S...G....A.N.V....AS.F.TPGMQSLLQQITENPQL.QNMLSAPYMRSMMQSLSQNPDLAAQMMLN
Retrocopy SNATGNTVAAANYV----ASIFSTPGMQSLLQQITENPQLIQNMLSAPYMRSMMQSLSQNPDLAAQMMLN

Parental  NPLFAGNPQLQEQMRQQLPTFLQQMQNPDTLSAMSNPRAMQALLQIQQGLQTLATEAPGLIPGFTPGLGA
          .PLF..NPQLQEQMR.QLP.FLQQMQNPDTLSAMSNPRAMQAL.QIQQGLQTLATEAPGLIP.FTPG.G.
Retrocopy SPLFTANPQLQEQMRPQLPAFLQQMQNPDTLSAMSNPRAMQALMQIQQGLQTLATEAPGLIPSFTPGVG-

Parental  LGSTGGSSGTNG
          .G..G...G..G
Retrocopy VGVLGTAIGPVG

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_31 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 20 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014827	2 retrocopies	retro_btau_1087, retro_btau_188,
Canis familiaris	ENSCAFG00000001435	1 retrocopy	retro_cfam_236,
Callithrix jacchus	ENSCJAG00000003609	2 retrocopies	retro_cjac_3977, retro_cjac_4067,
Cavia porcellus	ENSCPOG00000004849	1 retrocopy	retro_cpor_113,
Dasypus novemcinctus	ENSDNOG00000012687	1 retrocopy	retro_dnov_14,
Dipodomys ordii	ENSDORG00000015266	1 retrocopy	retro_dord_680,
Equus caballus	ENSECAG00000019110	1 retrocopy	retro_ecab_1063,
Echinops telfairi	ENSETEG00000002822	1 retrocopy	retro_etel_39,
Felis catus	ENSFCAG00000015049	1 retrocopy	retro_fcat_83,
Homo sapiens	ENSG00000135018	1 retrocopy	retro_hsap_58,
Myotis lucifugus	ENSMLUG00000002036	2 retrocopies	retro_mluc_1774, retro_mluc_33,
Mustela putorius furo	ENSMPUG00000002028	1 retrocopy	retro_mputfur_55,
Mus musculus	ENSMUSG00000005312	1 retrocopy	retro_mmus_83,
Nomascus leucogenys	ENSNLEG00000003306	1 retrocopy	retro_nleu_31 ,
Otolemur garnettii	ENSOGAG00000012947	1 retrocopy	retro_ogar_276,
Pongo abelii	ENSPPYG00000019323	1 retrocopy	retro_pabe_87,
Pan troglodytes	ENSPTRG00000021055	1 retrocopy	retro_ptro_93,
Rattus norvegicus	ENSRNOG00000019282	1 retrocopy	retro_rnor_339,
Ictidomys tridecemlineatus	ENSSTOG00000013462	1 retrocopy	retro_itri_157,
Tursiops truncatus	ENSTTRG00000004696	1 retrocopy	retro_ttru_1475,