RetrogeneDB ID: retro_btau_583

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:51667477..51669072(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000040380
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAF1
• Ensembl ID: ENSBTAG00000014482
• Aliases: None
• Description: FAS-associated factor 1 [Source:RefSeq peptide;Acc:NP_001039783]

Sequence

>retro_btau_583
ATGACGTCCAACATGGACCGGGAGATGATCCTGGCGGATTTTCAGGCATGTATTGGCATTGAAAACATTGATGAAGCTAT
TACACTGCTTGAACAAAATAATCGGGACTTAGTGGCAGCTATTAATGGTGTAATACCCCAGGAAAATGGCATTCTGCAAA
GTGACTATGGAGGTGAGACTATATCAGGACCTGCATTTGATCCAGCAAGTCACCCAGCTCCAGCTCCTGCTCCCTCTTCC
TCTTCAGCATTTCGACCTGTAATGCCATCTAGGCAAATTGTAGAAAGGCAACCGCGGATGCTGGACTTCAGGGTTGAGTA
CAGAGACAGAAATGTTGGTGTGGTACTGGAAGACAGCTGTACTGTTGGAGAAATTAAACAGATTTTAGAAAGTGAACTTC
AGATACCTATGTCTAAAATGCTTTTAAAAGGCTGAAGACTGGAGACGTGGAAGACAGTACCGTCTTAAAATCACTACACT
TGCCAAAAAACAACAGTCTTTATGTCCTTACCCCAGATTTGCCACCACCTTCATCATCTAGTCATGCTGGTGCCCTGCAG
GAGTCATTAAATCAAAACTTCATGCTGATCATCACCCACCGAGAAGTTCAGCGGGAGTACAACCTGAACTTCTCAGGAAG
CAGTACCATTCAAGAGGTAAAGAGAAATGTGTATGACCTCACGAGTATCCCTGTTCGCCATCAGTTATGGGAGGGCTGGC
CAACTTCTGCCACAGATGACTCCATGTGTCTTGCTGAATCAGGGCTCTCTTATCCCTGCCATCGACTTACAGTGGGAAGA
AGATCTTCACCTGCACAGACCCGGGAGCAATCTGAAGAGCAAAGCACCGATGTTCATATGGTTAGTGATAGTGATGGAGA
TGACTTTGAAGATGCTTCCGAATTTGGGGTGGATGATGGAGAAGTATTCGACATGGCATCATCTGCCCTGAGAAAATCTC
CAATGATGCCAGAAAACGCAGGAAATGAAGGAGATGCCTTATTACAATTTACAGCAGAGTTTTCTTCAAGATATGGTGAC
TGCCATCCTGTATTTTTTATTGGCTCATTAGAAGCAGCTTTTCAAGAGGCCTTCTATGTGAAAGCCCGAGATAGAAAGCT
TCTTGCTATCTACCTCCACCGTGATGAAAGTGTATTAACCAACATGTTCTGCTCACAAATGCTTTGTGCTGAATCTATTG
TCTCTTATCTGAGTCAAAATTTTATAACCTGGGCTTGGGATCTGACAAAGGATGCCAACAGAGCAAGATTTCTGACAATG
TGCAGTAGACACTTTGGCAGTGTTGTTGCCCAAACCATTCGGACTCAAAAAACAGATCAGTTTCCACTTTTTCTGATTAT
TATGGGAAAGCGATCATCTAATGAAGTGTTAAGTGTGATACAAGGTAACACAACAGTGGATGAGTTAATGATGAGACTCA
TGGCTGCAATGGAGATCTTCACAGCCCAACAACAGGAAGATATAAAGGATGAGGATGAACGAGAAGCCAGAGAAAATGTG
AAGAGAGAACAAGATGAGGCCTATCGCCTTTCACTTGAGGCTGACAGAGCAGAGGGAAGCTCATGAGAGAGAGAT

Alignment

ORF - retro_btau_583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.81 %
• Parental protein coverage: 81.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTSNMDREMILADFQACTGIENIDEAITLLEQNNWDLVAAINGVIPQENGILQSDYGGETISGPAFDPAS
          MTSNMDREMILADFQAC.GIENIDEAITLLEQNN.DLVAAINGVIPQENGILQSDYGGETISGPAFDPAS
Retrocopy MTSNMDREMILADFQACIGIENIDEAITLLEQNNRDLVAAINGVIPQENGILQSDYGGETISGPAFDPAS

Parental  HPAPAPAPSSSSAFRPVMPSRQIVERQPRMLDFRVEYRDRNVDVVLEDSCTVGEIKQILESELQIPMSKM
          HPAPAPAPSSSSAFRPVMPSRQIVERQPRMLDFRVEYRDRNV.VVLEDSCTVGEIKQILESELQIPMSKM
Retrocopy HPAPAPAPSSSSAFRPVMPSRQIVERQPRMLDFRVEYRDRNVGVVLEDSCTVGEIKQILESELQIPMSKM

Parental  LLKG-WKTGDVEDSTVLKSLHLPKNNSLYVLTPDLPPPSSSSHAGALQESLNQNFMLIITHREVQREYNL
          LLKG..KTGDVEDSTVLKSLHLPKNNSLYVLTPDLPPPSSSSHAGALQESLNQNFMLIITHREVQREYNL
Retrocopy LLKG<LKTGDVEDSTVLKSLHLPKNNSLYVLTPDLPPPSSSSHAGALQESLNQNFMLIITHREVQREYNL

Parental  NFSGSSTIQEVKRNVYDLTSIPVRHQLWEGWPTSATDDSMCLAESGLSYPCHRLTVGRRSSPAQTREQSE
          NFSGSSTIQEVKRNVYDLTSIPVRHQLWEGWPTSATDDSMCLAESGLSYPCHRLTVGRRSSPAQTREQSE
Retrocopy NFSGSSTIQEVKRNVYDLTSIPVRHQLWEGWPTSATDDSMCLAESGLSYPCHRLTVGRRSSPAQTREQSE

Parental  EQSTDVHMVSDSDGDDFEDASEFGVDDGEVFGMASSALRKSPMMPENAENEGDALLQFTAEFSSRYGDCH
          EQSTDVHMVSDSDGDDFEDASEFGVDDGEVF.MASSALRKSPMMPENA.NEGDALLQFTAEFSSRYGDCH
Retrocopy EQSTDVHMVSDSDGDDFEDASEFGVDDGEVFDMASSALRKSPMMPENAGNEGDALLQFTAEFSSRYGDCH

Parental  PVFFIGSLEAAFQEAFYVKARDRKLLAIYLHHDESVLTNVFCSQMLCAESIVSYLSQNFITWAWDLTKDA
          PVFFIGSLEAAFQEAFYVKARDRKLLAIYLH.DESVLTN.FCSQMLCAESIVSYLSQNFITWAWDLTKDA
Retrocopy PVFFIGSLEAAFQEAFYVKARDRKLLAIYLHRDESVLTNMFCSQMLCAESIVSYLSQNFITWAWDLTKDA

Parental  NRARFLTMCNRHFGSVVAQTIRTQKTDQFPLFLIIMGKRSSNEVLNVIQGNTTVDELMMRLMAAMEIFTA
          NRARFLTMC.RHFGSVVAQTIRTQKTDQFPLFLIIMGKRSSNEVL.VIQGNTTVDELMMRLMAAMEIFTA
Retrocopy NRARFLTMCSRHFGSVVAQTIRTQKTDQFPLFLIIMGKRSSNEVLSVIQGNTTVDELMMRLMAAMEIFTA

Parental  QQQEDIKDEDEREARENVKREQDEAYRLSLEADRAKREAHERE
          QQQEDIKDEDEREARENVKREQDEAYRLSLEADRA.....ER.
Retrocopy QQQEDIKDEDEREARENVKREQDEAYRLSLEADRAEGSS*ERD

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	2.45 RPM	21.92 RPM
ERP005899_muscle	0.11 RPM	42.65 RPM
SRP017611_brain	1.05 RPM	22.61 RPM
SRP017611_kidney	1.30 RPM	29.99 RPM
SRP017611_liver	1.36 RPM	19.25 RPM
SRP030211_testis	0.54 RPM	81.46 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_btau_583 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DY455462	51668111	51668330	97.3	213	6	207

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_583 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_583 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014482	1 retrocopy	retro_btau_583 ,
Canis familiaris	ENSCAFG00000003903	1 retrocopy	retro_cfam_1797,