RetrogeneDB ID: retro_nleu_1680

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397303.1:19493873..19495398(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA7
• Ensembl ID: ENSNLEG00000010827
• Aliases: None
• Description: Importin subunit alpha [Source:UniProtKB/TrEMBL;Acc:G1RIW6]

Sequence

>retro_nleu_1680
GACGCTCCAGAAAACAGGCTAAGAAAATTTAATTACCGAGGCAAAGATGCATCTCTGAGGCAACAGCAGAGGATAGCGGT
CAGCCTGGAGCTCCGAAAAGCCAAGAAAGATGAACAGATCTTAAAGAGAAGGAATATCACCAGCTTCTGCCCTGACACAG
CTTCCGAAAAACCAGCCAAAGGGGTGGCAGTCAGCCTCACTCTGGGTGAAATAATCAAAGGTGTGAATAGCTCAGATTCA
TTCCTATGTTTCCAGGCCACCCAGACAGCCAGGAAAATTCTATCCCAGGAAAAGAACCCCCTTCTGAAACTGATCATTGA
AGCGGGCCTCATTCCCAGGATGGTGGAGTTCCTGAAGTCATCACTTTACCCCTGCTTGCAGTTTGAGGCCGCCTGGGCCC
TGATCAACATTGCTTCAGGGAATTCCAAGCAGATTTGAGCCGTCATAGAAGGGGGACCCATCCAGCCCTTGATCAAGCTC
CTGTCTTCCCACAACGTGGCTGTGTGTGAACAGGCAATGTGGGCTCTTGGTAATATACCCGGTGACGGCCTGGAGTTCAG
AGATAATGTCATCTCAAGCAATGCCATCCCACATCTGCTGACCTTGATTTCACCCACCCTACTAATCACATTTCTGTGGA
ACATCACGTGGACCTTGTCGAACCTATGCCTAAAAAAGACCCCGTACCCTTGCGAAACTGCAGTGAAGCAGATGCTGCCG
GCCCTGTCACTCCTGCAGCACCACGACAGCGAGGTTCTCTCAGAAGCCTGCTGGTCACTGTCCTACCTCACAGACGGCTG
CAAAGAGCACATCGGCCAAGTGGTTGACACAGGGGTCCTGCCCAGGCTGGTAGCGCTCATGACCAGCTCAGAACTCAATG
TCTGGACCCCTTCTCTCTGTACCGTGGGGAACATTATCACAGGCACAGATGAGCAGAAGCAGATGGCCATTGACGTGGGC
ATGCTGAACGTGCTGCCCCAGCTCCTGCAGCACAACAAGCCCTCCATCCAGAAGGAGGCGGCCTGGGCCCTGAGCAACGT
GGTGGCAGGGCCTTCTTACCACACCCAGCAGCTGCTTGCCTACAACGTCTTGCCTCCCTTGGTGGCTCTGCTAAAAAAAT
GGAGAATTTGAAGTCCAGAAAGAGGCTGTCTGGACGGTGGCTAACTTTGCAATGTGGGTCACCGTGGATCAGTTGATCTT
CCATTCTGGGGTCCTGGAGCCACTGGCAAATCTGCTCATTGCCCCAGATGTTAAAATTGTTCTCATCATCCTCGATGTAA
TCTCTTGCATCCTCCAGGCAGCAGAGAAACGGTCTGAGAAGGAAATCCTATGTTTTCTGATAGAAGAACTCGGTGGGATC
GATAGAATTGAGGCTTTACAACTGCATGAGAACTGTCAGATTGGCCAGTCTGCTTTGAGCATCATTGAGAAGCATTTTGG
TGAGGAAGAAGATGAGAGCCTAACTTTACTGAGCCAAGTCCTAGACCAAGATTGTGAATTTACAGATTGTGAATGCTTAG
CAAAA

Alignment

ORF - retro_nleu_1680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.35 %
• Parental protein coverage: 99.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DALEERRRKFKYRGKDASLRRQQRMAVSLELRKAKKDEQTLKRRNITSFCPDTPSEKPAKGVAVSLTLGE
          DA.E.R.RKF.YRGKDASLR.QQR.AVSLELRKAKKDEQ.LKRRNITSFCPDT.SEKPAKGVAVSLTLGE
Retrocopy DAPENRLRKFNYRGKDASLRQQQRIAVSLELRKAKKDEQILKRRNITSFCPDTASEKPAKGVAVSLTLGE

Parental  IIKGVNSSDPVLCFQATQTARKMLSQEKNPPLKLVIEAGLIPRMVEFLKSSLYPCLQFEAAWALTNIASG
          IIKGVNSSD..LCFQATQTARK.LSQEKNP.LKL.IEAGLIPRMVEFLKSSLYPCLQFEAAWAL.NIASG
Retrocopy IIKGVNSSDSFLCFQATQTARKILSQEKNPLLKLIIEAGLIPRMVEFLKSSLYPCLQFEAAWALINIASG

Parental  TSEQTRAVVEGGAIQPLIELLSSSNVAVCEQAVWALGNIAGDGPEFRDNVISSNAIPHLLALISPTLPIT
          .S.Q..AV.EGG.IQPLI.LLSS.NVAVCEQA.WALGNI.GDG.EFRDNVISSNAIPHLL.LISPTL.IT
Retrocopy NSKQI*AVIEGGPIQPLIKLLSSHNVAVCEQAMWALGNIPGDGLEFRDNVISSNAIPHLLTLISPTLLIT

Parental  FLRNITWTLSNLCRNKNPYPCDTAVKQILPALLHLLQHQDSEVLSDACWALSYLTDGSNKRIGQVVDTGV
          FL.NITWTLSNLC..K.PYPC.TAVKQ.LPA.L.LLQH.DSEVLS.ACW.LSYLTDG....IGQVVDTGV
Retrocopy FLWNITWTLSNLCLKKTPYPCETAVKQMLPA-LSLLQHHDSEVLSEACWSLSYLTDGCKEHIGQVVDTGV

Parental  LPRLVVLMTSSELSVLTPSLRTVGNIVTGTDEQTQMAIDAGMLNVLPQLLQHNKPSIQKEAAWALSNVAA
          LPRLV.LMTSSEL.V.TPSL.TVGNI.TGTDEQ.QMAID.GMLNVLPQLLQHNKPSIQKEAAWALSNV.A
Retrocopy LPRLVALMTSSELNVWTPSLCTVGNIITGTDEQKQMAIDVGMLNVLPQLLQHNKPSIQKEAAWALSNVVA

Parental  GPCHHIQQLLAYDVLPPLVALL-KNGEFKVQKEAVWTVANFATGATMDQLIQLVHSGVLEPLVNLLTAPD
          GP..H.QQLLAY.VLPPLVALL.KNGEF.VQKEAVWTVANFA...T.DQLI...HSGVLEPL.NLL.APD
Retrocopy GPSYHTQQLLAYNVLPPLVALL>KNGEFEVQKEAVWTVANFAMWVTVDQLI--FHSGVLEPLANLLIAPD

Parental  VKIVLIILDVISCILQAAEKRSEKENLCLLIEELGGIDRIEALQLHENRQIGRSALNIIEKHFGEEEDES
          VKIVLIILDVISCILQAAEKRSEKE.LC.LIEELGGIDRIEALQLHEN.QIG.SAL.IIEKHFGEEEDES
Retrocopy VKIVLIILDVISCILQAAEKRSEKEILCFLIEELGGIDRIEALQLHENCQIGQSALSIIEKHFGEEEDES

Parental  LTLLSQVIEQDYEFIDYECLAK
          LTLLSQV..QD.EF.D.ECLAK
Retrocopy LTLLSQVLDQDCEFTDCECLAK

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_1680 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.

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015125	2 retrocopies	retro_cfam_459, retro_cfam_861,
Choloepus hoffmanni	ENSCHOG00000004243	1 retrocopy	retro_chof_805,
Callithrix jacchus	ENSCJAG00000015943	1 retrocopy	retro_cjac_2964,
Equus caballus	ENSECAG00000000554	1 retrocopy	retro_ecab_981,
Echinops telfairi	ENSETEG00000000096	1 retrocopy	retro_etel_1548,
Homo sapiens	ENSG00000185467	1 retrocopy	retro_hsap_3337,
Mus musculus	ENSMUSG00000038770	2 retrocopies	retro_mmus_2844, retro_mmus_3301,
Nomascus leucogenys	ENSNLEG00000001749	3 retrocopies	retro_nleu_1052, retro_nleu_1634, retro_nleu_208,
Nomascus leucogenys	ENSNLEG00000010827	1 retrocopy	retro_nleu_1680 ,
Otolemur garnettii	ENSOGAG00000031106	3 retrocopies	retro_ogar_1289, retro_ogar_3237, retro_ogar_353,
Ochotona princeps	ENSOPRG00000015434	2 retrocopies	retro_opri_1101, retro_opri_118,
Pongo abelii	ENSPPYG00000017369	1 retrocopy	retro_pabe_2750,
Pan troglodytes	ENSPTRG00000019446	2 retrocopies	retro_ptro_102, retro_ptro_2142,
Tupaia belangeri	ENSTBEG00000009007	3 retrocopies	retro_tbel_1475, retro_tbel_3862, retro_tbel_3962,
Tursiops truncatus	ENSTTRG00000002998	2 retrocopies	retro_ttru_1426, retro_ttru_430,