RetrogeneDB ID: retro_nleu_852

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397275.1:7870287..7871517(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRT5
• Ensembl ID: ENSNLEG00000017746
• Aliases: None
• Description: None

Sequence

>retro_nleu_852
GGCAGCAGCAGCTTTCCGGGTGGCCTGGGCGGTGGCTATGGTGGGGCCAGCGGCATGGGAGGCATCACCGCAGTCATGGT
CAACCAGAGCCTGCTGAGCTCCCTTGTCCTGGAGGTGCACCCCAACATCCAGGCCGTGCGCACCCAGGAGAAGGAGCAGA
TCAAGACCCTCAACAACAAGTTTGCCTCCTTCATAGACAAGGTGCGGTTCCTGGAGCAGCAGAACAAGATGCTGGAGACC
AAGTGGAGCCTCCTGCAGCAGCAGAAGACAGCTCGGAGCAACATGGACAACAAGCTCCAGAGCTACATCAACAACCTTAG
GCGGCAGCTGGAGACTCTGGGCCAGGAGAAGCTGAAGCTGGAGGCGGAGCTTGGCAACATGCAGGGGCTGGTGGAGGACT
TCAAGAACAAGTATGAGGATGAGATCAATAAGCGTACAGAGATGGAGAATGAATTTGTCCTCACCAAGAAGGATGTGGAT
GAAGCTTACATGAACGAGCTGGAGTCTCGCCTGGAAGGGCTAACTGAAGAGATCAACTTCCTCAGGCAGCTGTATGCAGA
GGAGATCCGGGAGCTGCAGTCCCAGATCTCGGACAGATCTGTGGTGCTGTCCATGGACAACAGCCGCTCCCAGGACAGGG
ACAGCATCATCGCTGAGGTCAAGGCACAGTACGAAGAGATCGCCAACCGCAGCCAGGCTGAGCTGAGAGCATGTACCAGA
TCAGACGAGAGCTGCAGAGCCTGCTGGGAGCACGGGGATGACCTGTGTCGCACAAAGACTGAGATCTCCGAGATAACCGG
AACATCAGCCGGCTCAGGCTGAGATTGAGGGCCCCAAAGGCCAGAGGGCTTCCCTGGAGGCCGCCATCGCAGATGCGGAG
CAGCGCAGAGAGCTGGTATTAAGTATGCCAACGCCAAGTTGTCCGAGCTGGAGGCTGCCCTGCAGCGGGCCAAGCAGGAC
GTGTTGCGGCAGCTGCGTGAGTACCAGGAGCTGATGAACGTCAAGCTGGCCCTGGACATCGAGATCGCCACCTACAGGAA
GCTGCTGGAGGGCAAGGAGAGCCGACTGGAGTCTGGGATGCAGAACATGAGTATTCACACGAAGACCACCAGCGGCTATG
CAGGTGGTTTGAGCTCGGCCTATGCGGGCCTCACAAGCCCCGGCCTCAGCTGTGGCCTGGGATCCAGCTTTGGCTCTGGT
GCGGGCTCTAGCTCCTTCAGCCGCACCAGC

Alignment

ORF - retro_nleu_852 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.37 %
• Parental protein coverage: 71.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  GGAGFGGGFGGPGFPVCPPGGIQEVTVNQSLLTPLNLQIDPSIQRVRTEEREQIKTLNNKFASFIDKVRF
          G...F.GG.GG........GGI..V.VNQSLL..L.L...P.IQ.VRT.E.EQIKTLNNKFASFIDKVRF
Retrocopy GSSSFPGGLGGGYGGASGMGGITAVMVNQSLLSSLVLEVHPNIQAVRTQEKEQIKTLNNKFASFIDKVRF

Parental  LEQQNKVLDTKWTLLQEQGTKTVRQNLEPLFEQYINNLRRQLDSIVGERGRLDSELRNMQDLVEDFKNKY
          LEQQNK.L.TKW.LLQ.Q..KT.R.N.......YINNLRRQL.....E...L..EL.NMQ.LVEDFKNKY
Retrocopy LEQQNKMLETKWSLLQQQ--KTARSNMDNKLQSYINNLRRQLETLGQEKLKLEAELGNMQGLVEDFKNKY

Parental  EDEINKRTTAENEFVMLKKDVDAAYMNKVELEAKVDALMDEINFMKMFFDAELSQMQTHVSDTSVVLSMD
          EDEINKRT..ENEFV..KKDVD.AYMN..ELE.....L..EINF.......E....Q...SD.SVVLSMD
Retrocopy EDEINKRTEMENEFVLTKKDVDEAYMN--ELESRLEGLTEEINFLRQLYAEEIRELQSQISDRSVVLSMD

Parental  NNRNLDLDSIIAEVKAQYEEIANRSRTE-AESWYQTKYEELQ-QTAGRHG-DDLRNTKHEISEM-NRMIQ
          N.R..D.DSIIAEVKAQYEEIANRS..E.AES.YQ....ELQ...AG..G.DDL..TK.EISE..NR.I.
Retrocopy NSRSQDRDSIIAEVKAQYEEIANRSQAE<AESMYQIR-RELQ<EPAGSTG<DDLCRTKTEISEI<NRNIS

Parental  RLR-AEIDNVKKQCANLQNAIADAEQRGELAL-KDARNKLAELEEALQKAKQDMARLLREYQELMNTKLA
          RLR.AEI...K.Q.A.L..AIADAEQR.EL.L.K.A..KL.ELE.ALQ.AKQD..R.LREYQELMN.KLA
Retrocopy RLR<AEIEGPKGQRASLEAAIADAEQRRELVL<KYANAKLSELEAALQRAKQDVLRQLREYQELMNVKLA

Parental  LDVEIATYRKLLEGEECRLSGEGVGPVNISVVTSSVSSGYGGGSGYSSGLGGGLGGGLGGGLGGGLGGGG
          LD.EIATYRKLLEG.E.RL.....G..N.S..T....SGY.G..G.SS...G....GL..GLG...G.G.
Retrocopy LDIEIATYRKLLEGKESRLES---GMQNMSIHTKT-TSGYAG--GLSSAYAGLTSPGLSCGLGSSFGSGA

Parental  SGSYYSSSS
          ..S..S..S
Retrocopy GSSSFSRTS

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_852 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 12 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011913	4 retrocopies	retro_chof_1848, retro_chof_2381, retro_chof_2385, retro_chof_778,
Erinaceus europaeus	ENSEEUG00000009412	1 retrocopy	retro_eeur_521,
Echinops telfairi	ENSETEG00000007907	1 retrocopy	retro_etel_1586,
Nomascus leucogenys	ENSNLEG00000017733	8 retrocopies	retro_nleu_1913, retro_nleu_225, retro_nleu_2285, retro_nleu_2421, retro_nleu_2485, retro_nleu_2727, retro_nleu_2787, retro_nleu_672,
Nomascus leucogenys	ENSNLEG00000017740	1 retrocopy	retro_nleu_1808,
Nomascus leucogenys	ENSNLEG00000017746	5 retrocopies	retro_nleu_2270, retro_nleu_2596, retro_nleu_354, retro_nleu_457, retro_nleu_852 ,
Nomascus leucogenys	ENSNLEG00000017748	2 retrocopies	retro_nleu_2823, retro_nleu_3100,
Nomascus leucogenys	ENSNLEG00000017753	1 retrocopy	retro_nleu_1726,
Nomascus leucogenys	ENSNLEG00000017758	2 retrocopies	retro_nleu_593, retro_nleu_726,
Nomascus leucogenys	ENSNLEG00000026579	1 retrocopy	retro_nleu_311,
Pongo abelii	ENSPPYG00000004548	1 retrocopy	retro_pabe_1103,
Vicugna pacos	ENSVPAG00000011707	3 retrocopies	retro_vpac_334, retro_vpac_551, retro_vpac_555,