RetrogeneDB ID: retro_nleu_354

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397263.1:27083148..27084371(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000006419
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_nleu_354
TTCCGGGGTAGCCTGGGAGGAGGCTATGGTGGGGCCAGTGGCATGGGAGGCATCACCACTGTCACTGTCAACCAGAGCCT
GCTGAGCCCCCTTAACCTGGAGGTGGACCCCAACATCCAGGCAGTGCACACTCAGAAGAAGGAGCAGATCAAGACCCTCA
ACAACAAGTTTGCCTCCTTCATATACAAGGTACAGTTCCTGGAGCAGCAAAGCAAGATGCTGGAGACCAAGTGGAGCCTC
CTGCAGCAGCAGAAGATGGCTCGGAGCAACATGGACAACATGTTCCAGAGCTACATCAACAACCTTAGGCGGCAGCTGGA
GACTCTGGGCCAGGAAAAGCTGAAGCTAGAGGCGGAGCTTGGCAACATGCAGGGGCTGGTGGAGGACTTCAAGAACAAGT
ATGAGGATGAGATCAATAAGCGTACAGAGATGGAGAATGAATTTGTCCTCATCAAGAAGGATGTGGATGAAGCTTGCATG
AACAAGGTAGAGCTGGAGTCTCGCCTGGAAGGGCTGACAGACGAAATCAACTTCCTCAGGCAGCTGTATGGAGAGGATAG
CCCGGAGCTGCAGTCCCGGGCTATGTCTGTGGTGCTGTCCATGGACAACAACCACTCCCTGGACGTGGACAGCATCATCA
ATGAGGTCAAGCGCAGTACGAGGTCACCAGCCACAGCCGGGTTGAGGCCGAGAGCATGTATCAGATCAAGTATGAGTAGC
TGCAGACGCTGGCTGGGAAGCACGGGGATGACCTGCAGCATACAAAGACTGAGATCTCCGCGATGAACCGGAACATCAGC
CGGCTCCAGGCTGAGATTGAGGGTCTCAAAGGCCAGAGGGCTTCCCTGGAGGCCGCCATCGCAGATGCGGAGCAGCGCAG
GGAGTTGGCTGTTAAGGATGCCAGCGCCAAGCTGTCTGAGCTGGAGGCCGCCCTGCAGCAAGCCAAGCAGGACATGGTGC
GGCAGCTGCATTAGTACCAGGAGCTGATGAACGTCAAGCTGGCCCTGGACATCGAGATCGCCACCTACAGGAAGCTGCTG
GAGGGCGAGGAGAGCTGGCTGGAGTCTGGGATGCAGAGCATGAGTATCCATAGGAAGACCGCCAGCAGCTATGCAGGTGG
TCTGAGCTCGGCCTATGGGGGCCTCACAAGTCCCGGCCTCAGCTATGGACTGGGCTCCAGCTTTGGCTCTGGCGCGGGCT
CCAGTTCCTTCAGCTGCACCAGC

Alignment

ORF - retro_nleu_354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 70.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FGGGFGGPGFPVCPPGGIQEVTVNQSLLTPLNLQIDPSIQRVRTEEREQIKTLNNKFASFIDKVRFLEQQ
          F.G..GG........GGI..VTVNQSLL.PLNL..DP.IQ.V.T...EQIKTLNNKFASFI.KV.FLEQQ
Retrocopy FRGSLGGGYGGASGMGGITTVTVNQSLLSPLNLEVDPNIQAVHTQKKEQIKTLNNKFASFIYKVQFLEQQ

Parental  NKVLDTKWTLLQEQGTKTVRQNLEPLFEQYINNLRRQLDSIVGERGRLDSELRNMQDLVEDFKNKYEDEI
          .K.L.TKW.LLQ.Q..K..R.N....F..YINNLRRQL.....E...L..EL.NMQ.LVEDFKNKYEDEI
Retrocopy SKMLETKWSLLQQQ--KMARSNMDNMFQSYINNLRRQLETLGQEKLKLEAELGNMQGLVEDFKNKYEDEI

Parental  NKRTTAENEFVMLKKDVDAAYMNKVELEAKVDALMDEINFMKMFFDAELSQMQTHVSDTSVVLSMDNNRN
          NKRT..ENEFV..KKDVD.A.MNKVELE.....L.DEINF............Q......SVVLSMDNN..
Retrocopy NKRTEMENEFVLIKKDVDEACMNKVELESRLEGLTDEINFLRQLYGEDSPELQSRAM--SVVLSMDNNHS

Parental  LDLDSIIAEVK-AQYEEIANRSRTEAESWYQTKYEELQQTAGRHGDDLRNTKHEISEMNRMIQRLRAEID
          LD.DSII.EVK.AQYE.....SR.EAES.YQ.KYE.LQ..AG.HGDDL..TK.EIS.MNR.I.RL.AEI.
Retrocopy LDVDSIINEVK<AQYE-VTSHSRVEAESMYQIKYE*LQTLAGKHGDDLQHTKTEISAMNRNISRLQAEIE

Parental  NVKKQCANLQNAIADAEQRGELALKDARNKLAELEEALQKAKQDMARLLREYQELMNTKLALDVEIATYR
          ..K.Q.A.L..AIADAEQR.ELA.KDA..KL.ELE.ALQ.AKQDM.R.L..YQELMN.KLALD.EIATYR
Retrocopy GLKGQRASLEAAIADAEQRRELAVKDASAKLSELEAALQQAKQDMVRQLH*YQELMNVKLALDIEIATYR

Parental  KLLEGEECRLSGEGVGPVNISVVTSSVSSGYGGGSGYSSGLGGGLGGGLGGGLGGGLGGGGSGSYYSSSS
          KLLEGEE..L.....G....S......SS.Y.GG...SS..GG....GL..GLG...G.G...S..S..S
Retrocopy KLLEGEESWLES---GMQSMSIHRKTASS-YAGG--LSSAYGGLTSPGLSYGLGSSFGSGAGSSSFSCTS

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_354 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,