RetrogeneDB ID: retro_btau_501

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:69574461..69576660(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000047008
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HSP90AA1
• Ensembl ID: ENSBTAG00000006270
• Aliases: HSP90AA1, HSPCA
• Description: Heat shock protein HSP 90-alpha [Source:UniProtKB/Swiss-Prot;Acc:Q76LV2]

Sequence

>retro_btau_501
ATGCCCGAGGAGACCCAGGCCCAGGACCAGCCGATGGAAGAGGAGGAGGTGGAGACTTTCACCTTCTAGGCGGAAATTGC
CCAGTTGATGTCACTGATCATCAACACTTTCTACTCGAATAAGGAGATTTTTTTGAGGGAGCTGATTTCAAACTCGTCTG
ACGCCCTGGACAAGATCAGGTATGAGAGCTTGACCAATCCCAGTAAGTTAGATTCTGGGAAAGAGCTGCACATTAATCTC
ATACCGAACAAGCAAGATTGAACCCTTACCATCGTGGACACCGGCATTGGGATGACCAAGGCCGATTTGATTAATAACCT
GGGCACCATCGCCAAGTCCGGGACCAAAGCGTTCATGGAGGCTTTGCAGGCTGGCGCTGATATCTCCACGATTGGCCAGT
TTGGTGTCGGGTTTTATTCAGCCTATTTGGTGGCTGAGAAAGTGACCGTCATCACCAAACATAACGATGATGAGCAGTAT
GCCTGGGAGTGTTCTGCAGGAGGGTCCTTCACAGTGAGGACTGACACAGGAGAACCAATGGGATGTGGAACAAAGGTTAT
TCTGCATCTGAAAGAAGACCAGACTGAGTACCTGGAGGAGCGGAGAATAAAGGAGATTGTGAAGAAGCATTCTCAGTTCA
TTGGTTATCCCATCACTCTTTTTGTGGAAAAGGAACGTGATAAAGAAGTTAGTGATGATGAAGCAGAAGAGAAGGAAGAC
AAAGAGGAAGAGAAGGAGAAAGAAGAAAAGGAGTCTGATGACAAGCCCGAGATAGAAGATGTTGGCTCAGATGAAGAGGA
GGAAGAGAAGAAGGACGGGGACAAGAAGAAGAAATAGAAGATCAAGGAGAAGTACATCGATCAAGAAGAGCTGAACAAGA
CAAAGCCTATCTGGACCAGAAACCCTGATGACATCACTAACGAGGAGTATGGAGAGTTCTACAAGAGCCTGACCAACGAT
TGGGAGGATCACTTGGCGGTCAAGCATTTTTCAGTTGAAGGACAGTTGGAATTCAGAGCCCTTCTTTTTGTCCCAAGACG
AGCTCCTTTTGACCTGTTCGAAAACAGAAAGAAGAAGAACAACATTAAGTTGTATGTTTGCAGAGTATTCATCATGGATA
ACTGTGAGGAGCTAATCCCTGAATACCTGAATTTCATTAGAGGTGTGGTGGATTCTGAGGATCTCCCTCTGAACATTTCC
CGTGAGATGTTGCAACAAAGCAAAATTTTGAAAGTTATCAGGAAGAATTTGGTCAAAAAGTGCTTGGAACTCTTCACTGA
ACTGGCAGAAAATAAGGAGAACTACAAGAAGTTTTATGAGCAGTTCTCTAAAAATATTAAGCTTGGAATACATGAAGATT
CTCAAAATCGGAAGAAGCTTTCAGAGCTGTTGAGGTACCATACTTCTGCTTCTGGTGATGAGATGGTTTCTCTCAAGGAC
TATTGCACAAGAATGAAGGAAAACCAGAAACACATCTATTACATCACAGGTGAGACCAAGGACCAGGTGGCCAACTCGGC
CTTCGTGGAGCGCCTCCGGAAGCATGGCTTGGAAGTGATCTACATGATCGAGCCCATTGATGAGTACTGTGTGCAGCACC
TGAAGGAGTTTGAGGGGAAGACCTTAGTGTCAGTCACCAAAGAGGGCCTGGAACTTCCAGAAGATGAGGAAGAGAAAAAG
AAACAAGAAGAGAAAAAGACAAAGTTTGAAAACCTCTGCAAAATCATGAAGGATATTTTGGAGAAGAAAGTTGAAAAGGT
GGTTGTGTCAAACCGGTTGGTGACATCCCCGTGCTGCATTGTCATGAGCACATACGGCTGGACAGCAAACATGGAACGGA
TCATGAAGGCTCAAGCCCTGAGAGACAACTCCAAGATGGGTTACATGGCTGCCAAGAAGCACCTGGAGATCAACCCTGAC
CATTCCATCATTGAGACCTTGAGGCAAAAGGCAGAGGCTGACAAGAATGACAAGTCTGTGAAGGATCTGGTCATCCTGCT
GTACGATACAGCTCTCCTGTCTTCTGGCTTCAGTCTGGAGGATCCCCAGACACATGCCAACACAATGTACAGGATGATCA
AACTTGGTCTCGGTATTGACGAGGATGACCCCACTGCTGATGACAGCAGCGCCGAGGTCACTGAGGAAATGCCACCCCTG
GAAGGAGACGACGACACGTCCCGCATGGAGGAAGTGGAC

Alignment

ORF - retro_btau_501 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPEETQAQDQPMEEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKL
          MPEETQAQDQPMEEEEVETF.F.AEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLT.PSKL
Retrocopy MPEETQAQDQPMEEEEVETFTF*AEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTNPSKL

Parental  DSGKELHINLIPNKQDRTLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYS
          DSGKELHINLIPNKQD.TLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADIS.IGQFGVGFYS
Retrocopy DSGKELHINLIPNKQD*TLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISTIGQFGVGFYS

Parental  AYLVAEKVTVITKHNDDEQYAWESSAGGSFTVRTDTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVKKH
          AYLVAEKVTVITKHNDDEQYAWE.SAGGSFTVRTDTGEPMG.GTKVILHLKEDQTEYLEERRIKEIVKKH
Retrocopy AYLVAEKVTVITKHNDDEQYAWECSAGGSFTVRTDTGEPMGCGTKVILHLKEDQTEYLEERRIKEIVKKH

Parental  SQFIGYPITLFVEKERDKEVSDDEAEEKEDKEEEKEKEEKESDDKPEIEDVGSDEEEEEKKDGDKKKKKK
          SQFIGYPITLFVEKERDKEVSDDE.................SDDKPEIEDVGSDE...............
Retrocopy SQFIGYPITLFVEKERDKEVSDDEXXXXXXXXXXXXXXXXXSDDKPEIEDVGSDEXXXXXXXXXXXXXXX

Parental  IKEKYIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFVPRRAPF
          ....YIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFVPRRAPF
Retrocopy XXXXYIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFVPRRAPF

Parental  DLFENRKKKNNIKLYVRRVFIMDNCEELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNLVKK
          DLFENRKKKNNIKLYV.RVFIMDNCEELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNLVKK
Retrocopy DLFENRKKKNNIKLYVCRVFIMDNCEELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNLVKK

Parental  CLELFTELAEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSASGDEMVSLKDYCTRMKENQK
          CLELFTELAE.KENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRY.TSASGDEMVSLKDYCTRMKENQK
Retrocopy CLELFTELAENKENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYHTSASGDEMVSLKDYCTRMKENQK

Parental  HIYYITGETKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQQLKEFEGKTLVSVTKEGLELPEDEEEKK
          HIYYITGETKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQ.LKEFEGKTLVSVTKEGLELPEDE....
Retrocopy HIYYITGETKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQHLKEFEGKTLVSVTKEGLELPEDEXXXX

Parental  KQEEKKTKFENLCKIMKDILEKKVEKVVVSNRLVTSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMA
          ...........LCKIMKDILEKKVEKVVVSNRLVTSPCCIV.STYGWTANMERIMKAQALRDNS.MGYMA
Retrocopy XXXXXXXXXXXLCKIMKDILEKKVEKVVVSNRLVTSPCCIVMSTYGWTANMERIMKAQALRDNSKMGYMA

Parental  AKKHLEINPDHSIIETLRQKAEADKNDKSVKDLVILLYETALLSSGFSLEDPQTHANRIYRMIKLGLGID
          AKKHLEINPDHSIIETLRQKAEADKNDKSVKDLVILLY.TALLSSGFSLEDPQTHAN..YRMIKLGLGID
Retrocopy AKKHLEINPDHSIIETLRQKAEADKNDKSVKDLVILLYDTALLSSGFSLEDPQTHANTMYRMIKLGLGID

Parental  EDDPTADDSSAAVTEEMPPLEGDDDTSRMEEVD
          EDDPTADDSSA.VTEEMPPLEGDDDTSRMEEVD
Retrocopy EDDPTADDSSAEVTEEMPPLEGDDDTSRMEEVD

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
ERP005899_liver	0.79 RPM	609.21 RPM
ERP005899_muscle	15.73 RPM	922.49 RPM
SRP017611_brain	8.68 RPM	1576.39 RPM
SRP017611_kidney	0.89 RPM	749.25 RPM
SRP017611_liver	2.72 RPM	368.10 RPM
SRP030211_testis	26.76 RPM	1568.13 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_501 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_501 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_501 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006270	1 retrocopy	retro_btau_501 ,
Callithrix jacchus	ENSCJAG00000033945	8 retrocopies	retro_cjac_1818, retro_cjac_2300, retro_cjac_2835, retro_cjac_3514, retro_cjac_3596, retro_cjac_3601, retro_cjac_3626, retro_cjac_502,
Cavia porcellus	ENSCPOG00000002015	1 retrocopy	retro_cpor_1372,
Homo sapiens	ENSG00000080824	2 retrocopies	retro_hsap_237, retro_hsap_859,
Monodelphis domestica	ENSMODG00000013302	3 retrocopies	retro_mdom_1653, retro_mdom_2010, retro_mdom_817,
Mus musculus	ENSMUSG00000021270	1 retrocopy	retro_mmus_2139,
Nomascus leucogenys	ENSNLEG00000015925	3 retrocopies	retro_nleu_714, retro_nleu_822, retro_nleu_854,
Pongo abelii	ENSPPYG00000006153	1 retrocopy	retro_pabe_1760,
Pan troglodytes	ENSPTRG00000006736	2 retrocopies	retro_ptro_207, retro_ptro_596,
Rattus norvegicus	ENSRNOG00000007219	1 retrocopy	retro_rnor_860,