RetrogeneDB ID: retro_pabe_1103

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:38560487..38561672(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRT5
• Ensembl ID: ENSPPYG00000004548
• Aliases: None
• Description: keratin 5 [Source:HGNC Symbol;Acc:6442]

Sequence

>retro_pabe_1103
GGAAGCATCACCGCTGTCACAGTCAACCAGAGCCTGCTGAGCCCCCTTAACCTGGAAGTGGACCCCAACATCCAGGCCAT
CTGCACCCAGGAGAAGGAGCGGAACAAGATCCTCAACAACAAGTTTGCCTCCTTCATTGACAAGGTATGGTTCCTGGAAC
AGCAGGACAAGATGCTGGAGACCAACTGGAGCCTCCTGCATCAGCAGAAGACAGCTTGGAGCAACATGGACAACACGTTC
CAGAGCTACATCAAAAACCTTAGGCGGCAGCTGGAGACTCTGGGCCAGGAGCAGCTGAAGCTGGAGGCGGAGCTTGGCAA
TACACAGGGGCTGGTGGAGGACTTCAAGAACAAGTACGAGGATGAGATCAATAAGCGTACAGAGATGGAGGATGAATTTG
TCCTCATCAAGAAGGATGTGGATGAAGCTTACCTGAACAAGTTAAAGCTGGAGTCTCGCCTGGAAGGTCTGACTGACCAG
ATCAACTTCCTCAGGCAGCTGTGTGAAGAAGAGATCTGGGAGCTGCAGTCCCAGGTCTGGGACACGTCTGTGGTGCTGTC
CATGGACAACAGCCGTTCCCTGGACATGGACAGCATCATCGCTGAGGTCAAGGCTTAGTAGGAGGAGATAGCCAAGCGCA
GCAGGGCTGAGGCTGAGTGCATGTACCAGATCAAGTATGAGAAGCTGCAGACGCTGGCTAGGAAGCACGGGGATGAACTG
CAGCGCACAAAGGCAGATCTCCGAGATGAACCGGAACATCAGCCGGCTCTAGGCTGAGATTGAGGGCCTCAAAGGCCAGA
GGGCTTCCCTGGAGACCACCATCACAGTTGCCGAGCAGCTGGGGAGCTGGCCATTAAAGATGCCAACACCAAGCTGTCCG
AGCTGGAGGGTACCCTGCAGCAAGCCAAGCAGGACTTGGAGCTTCAGCTGCGCGAGTACCAGGAGCTGATGAACATCAAG
CTGGCCCTGGACATCGAGATTGCCACCTACAGAAACCTGCTGGAGGGCGAGGAGAACCGGTTGGAGTCTGGGATGCAGAA
CATGAGTATCCATATGAAGACCACCAGCGGCTATGCAGGTGGGCTGAGTTCGGCCTGTGGGGACCTCACAACTCCTGGCC
TCAGCTATGGCCTGGGATCCAGCTTTGGCTCTGTCGCGGGCTCTAGCTCCTTCAGCCATACCAGC

Alignment

ORF - retro_pabe_1103 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.18 %
• Parental protein coverage: 67.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGIQEVTVNQSLLTPLNLQIDPSIQRVRTEEREQIKTLNNKFASFIDKVRFLEQQNKVLDTKWTLLQEQG
          G.I..VTVNQSLL.PLNL..DP.IQ...T.E.E..K.LNNKFASFIDKV.FLEQQ.K.L.T.W.LL..Q.
Retrocopy GSITAVTVNQSLLSPLNLEVDPNIQAICTQEKERNKILNNKFASFIDKVWFLEQQDKMLETNWSLLHQQ-

Parental  TKTVRQNLEPLFEQYINNLRRQLDSIVGERGRLDSELRNMQDLVEDFKNKYEDEINKRTTAENEFVMLKK
          .KT...N....F..YI.NLRRQL.....E...L..EL.N.Q.LVEDFKNKYEDEINKRT..E.EFV..KK
Retrocopy -KTAWSNMDNTFQSYIKNLRRQLETLGQEQLKLEAELGNTQGLVEDFKNKYEDEINKRTEMEDEFVLIKK

Parental  DVDAAYMNKVELEAKVDALMDEINFMKMFFDAELSQMQTHVSDTSVVLSMDNNRNLDLDSIIAEVKAQYE
          DVD.AY.NK..LE.....L.D.INF.......E....Q..V.DTSVVLSMDN.R.LD.DSIIAEVKA..E
Retrocopy DVDEAYLNKLKLESRLEGLTDQINFLRQLCEEEIWELQSQVWDTSVVLSMDNSRSLDMDSIIAEVKA**E

Parental  EIANRSRTEAESWYQTKYEELQQTAGRHGDDLR-NTKHEISEMNRMIQRLRAEIDNVKKQCANLQNAIAD
          EIA.RSR.EAE..YQ.KYE.L.QT..R...D........ISEMNR.I.RL.AEI...K.Q.A.L...I..
Retrocopy EIAKRSRAEAECMYQIKYEKL-QTLARKHGDEL>SAQRQISEMNRNISRL*AEIEGLKGQRASLETTITV

Parental  AEQ-RGELALKDARNKLAELEEALQKAKQDMARLLREYQELMNTKLALDVEIATYRKLLEGEECRLSGEG
          AEQ..GELA.KDA..KL.ELE..LQ.AKQD....LREYQELMN.KLALD.EIATYR.LLEGEE.RL....
Retrocopy AEQ<AGELAIKDANTKLSELEGTLQQAKQDLELQLREYQELMNIKLALDIEIATYRNLLEGEENRLES--

Parental  VGPVNISVVTSSVSSGYGGG--SGYGGGLGGGLGGGLGGGLGGGGSGSYYSSSS
          .G..N.S.......SGY.GG..S..G.....GL..GLG...G.....S..S..S
Retrocopy -GMQNMS-IHMKTTSGYAGGLSSACGDLTTPGLSYGLGSSFGSVAGSSSFSHTS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	2.88 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.06 RPM
SRP007412_kidney	0.00 RPM	0.10 RPM
SRP007412_liver	0.00 RPM	0.06 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1103 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1103 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1103 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 46 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	ENSNLEG00000017746	5 retrocopies	retro_nleu_2270, retro_nleu_2596, retro_nleu_354, retro_nleu_457, retro_nleu_852,
Pongo abelii	ENSPPYG00000004548	1 retrocopy	retro_pabe_1103 ,
Pongo abelii	ENSPPYG00000004562	31 retrocopies	retro_pabe_1102, retro_pabe_1261, retro_pabe_1289, retro_pabe_1460, retro_pabe_1743, retro_pabe_2063, retro_pabe_2077, retro_pabe_2129, retro_pabe_2142, retro_pabe_2214, retro_pabe_2270, retro_pabe_2352, retro_pabe_2544, retro_pabe_2741, retro_pabe_2763, retro_pabe_2787, retro_pabe_2842, retro_pabe_2926, retro_pabe_2943, retro_pabe_3138, retro_pabe_332, retro_pabe_3439, retro_pabe_3644, retro_pabe_3716, retro_pabe_417, retro_pabe_460, retro_pabe_569, retro_pabe_605, retro_pabe_701, retro_pabe_803, retro_pabe_851,
Vicugna pacos	ENSVPAG00000011707	3 retrocopies	retro_vpac_334, retro_vpac_551, retro_vpac_555,