RetrogeneDB ID: retro_nleu_1530

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397298.1:4133678..4134455(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC137
• Ensembl ID: ENSNLEG00000013830
• Aliases: None
• Description: None

Sequence

>retro_nleu_1530
ATCGCGCAAGCTGGACGTGGAGCAGCGGTGCCCAGGGCGCCGGCGGGTCCTGGGAGTCCCCGGCGAGCGTAGCAGCGGCA
GCAAGTGCAGCCCTGGGGAAGCAGCGCCCAGCCCCGTGGTCCAGGCTTCACGCAAACAGGAGAAAGTGAATTGCAAACTC
AAAACCCAGGATGAGCAGGAGATCCCTTTCCGGCTCCGGGAGATTATGAGGAGCGGCTGGGAGATGAAAAATCTGACCGG
TAACAAGAAGAGGAAGAAAGCAGCCCAGGTGGCCTTCAGAAAGACATTGGAAAAGGAAGCAAAGGGAGTGGAGCCCGACA
TTGCCCTCCCCAAGTTCAAGCAGAGGAAGGGGGAGTCTGCCTAGGCCTATATCGAGCGCATGCAGCAAGAGACCCAGCAC
GTGCTATTCCTCAGAAAGAACCAGGCCACCCGGCAGCCAGAGATCCAGGCAGCTCCCAAGGAGAAGTCTGAGCTGAAAAA
AGCAAACAAAGCATTCCAGAAGTGACGACTAGATAAAGTCTGGCAGAAAAAGGAGGAAAAGATGGCAGACAGGCTGGAGC
AGGAGTTGCTCCGAGACACGGTGAAGTTTAGTGAGGTTGTCCTGCAGCGCCCAGAGCTGACTACCAGGCCCTGAAGGAGC
GTAAGAAGGATCAGCCTGGCAGGAGATTGCAGATGCTGAGGATGCTTCTGAGCCCCCGCGGTGTATTCCAGCCTCTGACT
GCCTCCCTGGCCTACCAGAGGACTGCTGGGGAGGAGAGAGAGTGGGCCATGCAGGCC

Alignment

ORF - retro_nleu_1530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.97 %
• Parental protein coverage: 90.31 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MARAGQGAAVPRVQAGPGSPRRARRRQQVQPL-GKQRPAPWPGLR-SKEKKKVNCKPKNQDEQEIPFRLR
          .A.AG.GAAVPR....P..P...RR..Q.Q........AP.P....S....KVNCK.K.QDEQEIPFRLR
Retrocopy IAQAGRGAAVPRA---PAGPGSPRRA*QRQQV>SPGEAAPSPVVQASRKQEKVNCKLKTQDEQEIPFRLR

Parental  EIMRSRQEMKNPISNKKRKKAAQVTFRKTLEKEAKGAEPDIAIPKFKQRKGESDGAYIQRMQQEAQHVLF
          EIMRS..EMKN...NKKRKKAAQV.FRKTLEKEAKG.EPDIA.PKFKQRKGES..AYI.RMQQE.QHVLF
Retrocopy EIMRSGWEMKNLTGNKKRKKAAQVAFRKTLEKEAKGVEPDIALPKFKQRKGESA*AYIERMQQETQHVLF

Parental  LSKNQAIRQPEMQAAPKEKSEQKKAKKAFQKRRLDKVRRKKEEKAADRLEQELLQDMVKFGEVVLQPPEL
          L.KNQA.RQPE.QAAPKEKSE.KKA.KAFQK.RLDKV..KKEEK.ADRLEQELL.D.VKF.EVVLQ.PEL
Retrocopy LRKNQATRQPEIQAAPKEKSELKKANKAFQK*RLDKVWQKKEEKMADRLEQELLRDTVKFSEVVLQRPEL

Parental  TARPRRSV-SKDQPGRRSQMPRMLLNPGCVSQPLTASLARQRIVGEERERAVQA
          T.RP.RSV..KDQPGRR.QM.RMLL.P..V.QPLTASLA.QR..GEERE.A.QA
Retrocopy TTRP*RSV<KKDQPGRRLQMLRMLLSPRGVFQPLTASLAYQRTAGEEREWAMQA

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_1530 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000014878	1 retrocopy	retro_eeur_523,
Homo sapiens	ENSG00000185298	1 retrocopy	retro_hsap_2661,
Gorilla gorilla	ENSGGOG00000009333	1 retrocopy	retro_ggor_1857,
Macaca mulatta	ENSMMUG00000008831	1 retrocopy	retro_mmul_1511,
Monodelphis domestica	ENSMODG00000002713	1 retrocopy	retro_mdom_1355,
Mus musculus	ENSMUSG00000049957	1 retrocopy	retro_mmus_641,
Nomascus leucogenys	ENSNLEG00000013830	3 retrocopies	retro_nleu_1264, retro_nleu_1530 , retro_nleu_586,
Pongo abelii	ENSPPYG00000008741	1 retrocopy	retro_pabe_2312,
Pan troglodytes	ENSPTRG00000009767	1 retrocopy	retro_ptro_1793,
Rattus norvegicus	ENSRNOG00000048712	1 retrocopy	retro_rnor_472,