RetrogeneDB ID: retro_nleu_2596

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397378.1:1229931..1231173(-)
• 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_2596
GGCAGCAGCTTCCAGGGTGGCCTGGGTGGAGGCTATGGTGGGGCCAGCAGTATGGGAGGCATCACAGCTGTCATGGTCAA
CCAGAGCCTGCTGAGCCCCCTTAAGCTGGAGGTGGACCCAACATCCAGGCCGTGCACACCCAGGAGAAGGAGCAGGTCAA
GAGCCTCAACAACAAGTTTGCCTCCTTCATCGACAAGGTACAGTTCCTGGAGCAGCAGAACAAGATGCTGGAGACCAAGT
GGAGCCTCCTGCAGCAGCAGAAGACGGCTCGAGCAACGTGGACCACCAGTTCGAGAGCTACATCCAACAACCTTTGGCAG
CAGCTGGAGACTCTGGGCCAGGACAAGCTGAGGCTGGAGGTGGGGCTTGGCAACATGCAGGGGCTGGTGGAGGACTTCAA
GAACAAGTACGAGGATGAGATCAATGAGCGTGCAGAGATGGAGAATGAATTTGTCCTCCTCAAGAAGGATGTGGATGAAG
CTTACATAAACAAAGTAGAGCTGGAGTCTGGCCTGGAAGCGCTGACTGATGAGATCAACTTCCTCAGGCAGCTGTATGAA
GAGGAGATCCGGGAGCTGGAGTCCCAGATTTCCCACACGCCTGTGGTGCTGTCCATGGACAATAGCCGCTCCCTGGACAC
GGACAGCATCATCGCTGAGGTCAGGGTGCAGTATGAGGAGATCGCCAACCGCAGCCGGGCTGAGGCTGAGAGCATGCACC
AGATCAAGCATGAGGAGCTGCAGACGCTGGCTGGGAAGCACGGAGATGACCTGCAGCGCACAAAGACTGAGATCTCGGAG
ATGAACTGGAACATCAGCCAGCTCCAGGCTGAGATTGAGGGCCTCAAAGGCCAGAGGGCTTCCCTGGAGGCCGCCATCGC
AGATGCCGAGCAGTGAGGGAAGCTGGCCGTTAAGGACGCCAATGCCAAGTTGTCCGAGCTGGAGGCTGCCCTGCGGCAGG
CCAAGCAGGTCATGGTGTGGCAGCTGCCTGAGTACCAGGAGCTGATGAACGTCAAGCTGGTCCTGGACATGGAGATCCCA
CCTACAGGAAGCTGCTGGAGGGCGAGGAGAGCCGACTGGCGTCTGGGATGCAGAACATGAGTATCCACACGAAGACTACC
AGTGGCTATGCCGATGTGCTGAGCTCGGGCTACGGGGGTGTCACAAGCCCCAGCCTCAGCTTACGGCCTGGGCTCGAGCT
TTGGCTCTGGCTGGGTGCTCCAGCTCTTTCAGCTGCACCAGC

Alignment

ORF - retro_nleu_2596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.64 %
• Parental protein coverage: 71.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  GAGFGGGFGGPGFPVCPPGGIQEVTVNQSLLTPLNLQIDPS-IQRVRTEEREQIKTLNNKFASFIDKVRF
          G..F.GG.GG........GGI..V.VNQSLL.PL.L..DP..IQ.V.T.E.EQ.K.LNNKFASFIDKV.F
Retrocopy GSSFQGGLGGGYGGASSMGGITAVMVNQSLLSPLKLEVDPT<IQAVHTQEKEQVKSLNNKFASFIDKVQF

Parental  LEQQNKVLDTKWTLLQEQGTKTVR-QNLEPLFEQYI-NNLRRQLDSIVGERGRLDSELRNMQDLVEDFKN
          LEQQNK.L.TKW.LLQ.Q..KT.R..N....FE.YI.NNL..QL........RL...L.NMQ.LVEDFKN
Retrocopy LEQQNKMLETKWSLLQQQ--KTAR<SNVDHQFESYI>NNLWQQLETLGQDKLRLEVGLGNMQGLVEDFKN

Parental  KYEDEINKRTTAENEFVMLKKDVDAAYMNKVELEAKVDALMDEINFMKMFFDAELSQMQTHVSDTSVVLS
          KYEDEIN.R...ENEFV.LKKDVD.AY.NKVELE....AL.DEINF.......E........S.T.VVLS
Retrocopy KYEDEINERAEMENEFVLLKKDVDEAYINKVELESGLEALTDEINFLRQLYEEEIRELESQISHTPVVLS

Parental  MDNNRNLDLDSIIAEVKAQYEEIANRSRTEAESWYQTKYEELQQTAGRHGDDLRNTKHEISEMNRMIQRL
          MDN.R.LD.DSIIAEV..QYEEIANRSR.EAES..Q.K.EELQ..AG.HGDDL..TK.EISEMN..I..L
Retrocopy MDNSRSLDTDSIIAEVRVQYEEIANRSRAEAESMHQIKHEELQTLAGKHGDDLQRTKTEISEMNWNISQL

Parental  RAEIDNVKKQCANLQNAIADAEQRGELALKDARNKLAELEEALQKAKQDMARLLREYQELMNTKLALDVE
          .AEI...K.Q.A.L..AIADAEQ.G.LA.KDA..KL.ELE.AL..AKQ.M...L.EYQELMN.KL.LD.E
Retrocopy QAEIEGLKGQRASLEAAIADAEQ*GKLAVKDANAKLSELEAALRQAKQVMVWQLPEYQELMNVKLVLDME

Parental  I-ATYRKLLEGEECRLSGEGVGPVNISVVTSSVSSGYGGGSGYSSGLGGGLGGGL-GGGLGGGLGGG-GS
          I..TYRKLLEGEE.RL.....G..N.S..T...S...G.....SSG.GG.....L...GLG...G.G.G.
Retrocopy I<PTYRKLLEGEESRLAS---GMQNMSIHTKTTS---GYADVLSSGYGGVTSPSL>AYGLGSSFGSG>GC

Parental  GSYYSSSS
          .S..S..S
Retrocopy SSSFSCTS

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_2596 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,