RetrogeneDB ID: retro_nleu_2073

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397326.1:9267326..9268268(+)
• Located in intron of: ENSNLEG00000006548

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSMCE4A
• Ensembl ID: ENSNLEG00000016919
• Aliases: None
• Description: None

Sequence

>retro_nleu_2073
TCTGGGGAGGCCGACATAGACCCAAAGCTCCTGGAGCTCACCGCTGACGAGGAGAAGTGCCGCAGCATCCGCAGGCGATA
CCGGCAGCTCATGTACTGCGTGCGGCAGAACCGGGAGGACATCGTGAACTCGGCGAACAACTCCTTAACCGAGGCTCTGG
AGGAAGCCAACGTCGTGTTTGATGGCGTGAGCCGAACCAGAGAAGCAGCCCTCGACGCCCAGTTTCTTGTTATGGCTTCT
GATTTGGGTAAAGAAAAGGCAAAGCAGTTAAACTCAGATATGAACTTCTTTAATCAGTTAGCATTTTGTGACTTTCTGTT
TCTGTTCGTGGGTCTGAATTGGATGGAAGGCGATCCTGACAAGTTGAGTGATTGTGATGATAGCATAGCTCTTTCCTTCT
GGAAGGCAATAGAAAAGGAAGCAACATCCTGGATGGTAAAAGCTGAGACATTCCATTTTGTTTTTTGTTCATTCAAGCTA
GAACCTTCTGCACCAAAGCCCCGACTTGAACACCGGAGAAAAGTTCGCAAGATAGAAGAAAATGGGAACATGCCTACAAA
GTTGCGGCAGTTGGACCTGAGTAGTTATCCAGAAGCGACAGAAAAAAACGTAGAAAGGATTTTGGGATTGTTGCAAACCT
ACTTTCGAAAGTATCCTGATACTCCTGTGTCCTATTTTGAGTTTGTGATTGATCCAAACTCTTTTTCTCGTACTGTGGAG
AATATATTTTATGTTTCTTTTATTGTAAGAGATGGTTTTGCAAGAATAAGGCTTGATGAAGACAGGCTGCCAATATTAGA
GCCGATGAATGTTAACCAAATCGATGAGGGAAATGATTCCAGTTGCCATGGCAGGAAACAGGGAGTTATATCTTTGACTT
TACAGGAGTGGAAAAACATTGTGGCAGCTTTTGAAATTTCTGAGGCTGTGATTACATACTCC

Alignment

ORF - retro_nleu_2073 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.89 %
• Parental protein coverage: 81.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGDEMMDPASLEAEADQGLCRQIRHQYRALINSVQQNREDILN-AGDKLTEVLEEANTLFNEVSRAREAV
          SG....DP..LE..AD...CR.IR..YR.L...V.QNREDI.N.A...LTE.LEEAN..F..VSR.REA.
Retrocopy SGEADIDPKLLELTADEEKCRSIRRRYRQLMYCVRQNREDIVNSANNSLTEALEEANVVFDGVSRTREAA

Parental  LDAHFLVLASDLGKEKAKQLRSDLSSFDMLRYVETLLTHMGVNPLEAEELIRDEDSPDFEFIVYDSWKIP
          LDA.FLV.ASDLGKEKAKQL.SD...F..L.....L....G.N..E......D..S.....I....WK..
Retrocopy LDAQFLVMASDLGKEKAKQLNSDMNFFNQLAFCDFLFLFVGLNWMEGDP---DKLSDCDDSIALSFWKAI

Parental  GKTAENTFNKTHTFHFLLGSIYGECPVAKQDPVSKKKKSLGVQERGK-GVWLRRME-ESHQEATEKEVER
          .K.A.....K..TFHF...S...E.P.A.........K.....E.G.....LR.....S..EATEK.VER
Retrocopy EKEATSWMVKAETFHFVFCSFKLE-PSAPKPRLEHRRKVRKIEENGNMPTKLRQLDLSSYPEATEKNVER

Parental  ILGLLQTYFREDPDTPMSFFDFVVDPHSFPRTVENIFHVSFIIRDGFARIRLDQDRLPIIEPVSTNEENE
          ILGLLQTYFR..PDTP.S.F.FV.DP.SF.RTVENIF.VSFI.RDGFARIRLD.DRLPI.EP...N...E
Retrocopy ILGLLQTYFRKYPDTPVSYFEFVIDPNSFSRTVENIFYVSFIVRDGFARIRLDEDRLPILEPMNVNQIDE

Parental  GFEHNTQVRNQGIIALSYRDWEEIVKTFEISEPVITPS
          G.......R.QG.I.L....W..IV..FEISE.VIT.S
Retrocopy GNDSSCHGRKQGVISLTLQEWKNIVAAFEISEAVITYS

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_2073 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 19 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010897	1 retrocopy	retro_amel_419,
Bos taurus	ENSBTAG00000019166	1 retrocopy	retro_btau_1387,
Canis familiaris	ENSCAFG00000012419	2 retrocopies	retro_cfam_1427, retro_cfam_379,
Choloepus hoffmanni	ENSCHOG00000003695	1 retrocopy	retro_chof_577,
Dipodomys ordii	ENSDORG00000003880	1 retrocopy	retro_dord_677,
Equus caballus	ENSECAG00000016651	2 retrocopies	retro_ecab_109, retro_ecab_465,
Erinaceus europaeus	ENSEEUG00000014906	1 retrocopy	retro_eeur_124,
Felis catus	ENSFCAG00000003647	1 retrocopy	retro_fcat_994,
Homo sapiens	ENSG00000107672	1 retrocopy	retro_hsap_43,
Loxodonta africana	ENSLAFG00000004214	1 retrocopy	retro_lafr_1051,
Macaca mulatta	ENSMMUG00000012044	1 retrocopy	retro_mmul_716,
Mustela putorius furo	ENSMPUG00000002960	1 retrocopy	retro_mputfur_396,
Nomascus leucogenys	ENSNLEG00000016919	1 retrocopy	retro_nleu_2073 ,
Otolemur garnettii	ENSOGAG00000010026	1 retrocopy	retro_ogar_280,
Pongo abelii	ENSPPYG00000002712	1 retrocopy	retro_pabe_878,
Pteropus vampyrus	ENSPVAG00000017186	2 retrocopies	retro_pvam_1163, retro_pvam_795,
Rattus norvegicus	ENSRNOG00000020452	1 retrocopy	retro_rnor_2515,
Ictidomys tridecemlineatus	ENSSTOG00000011112	1 retrocopy	retro_itri_36,
Vicugna pacos	ENSVPAG00000006534	1 retrocopy	retro_vpac_260,