RetrogeneDB ID: retro_btau_391

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:17295395..17297021(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAF6
• Ensembl ID: ENSBTAG00000036009
• Aliases: None
• Description: TNF receptor-associated factor 6 [Source:UniProtKB/Swiss-Prot;Acc:Q3ZCC3]

Sequence

>retro_btau_391
ATGAGTCTGCTACACTGTGAAAACAGCTGTGCATCCAGCCAGTCCGAGAGCGACTGTTGCGCCGCCATGGCTGCCAGCTC
CTGTGGGACTGCAGCAAAAGACGACAGTGTGAGTGGGACGGCCAGCACGGTGACTCTCTCCAGCTCTTTCATGGAGGAGA
TCCAGGGGTACGACGTGGAATTTGACCCACCCCTGGAAAGCAAATACGAGTGCCCCATTTGCTTGATGGCTTTGCGGGAA
GCGGTGCAGACACCTTGCGGCCACAGGTTCTGCAAAGCCTGCATCATCAAATCAATAAGGGATGCAGGTCACAAATGTCC
AGTTGACAATGAAATACTGCTGGAAAACCAACTATTTCCTGACAATTTTGCAAAATGAGAGATTCTTTCGCTGATGGTGA
AATGTCCAAATGAAGGTTGTTTGCACAAGATGGAACTGAGGCATCTTGAGGAGCATCAAGCACACTGTGAGTTTGCTCTT
ATGAGTTGTCCGCAATGCCAGCGTCCCTTCCAGAAATGCCATCTTAATATTCATATTCTCAAGGAGTGTCCAAGGAGACA
GGTTCCTTGTGAAAACTGTGCTGTATCAATGGCATTTGAAGATAAAGAGATTCATGAGCAGAACTGTCCTTTGGCAAATG
TCATCTGTGAATACTGCAATACCATGCTCATCAGAGAACAGATGCCCAATCACTATGATCTAGACTGCCCTACAGCCCCA
GTCCCATGCACGTTCAGTGCTTTTGGTTGCCATGAAAAGATGCAGAGGAATCACTTGGCACGCCACCTGCAAGAGAATAC
CCAGTCGCATATGAGAATGAAGGCCCAGGCTGTTCAGACTTTAAGCCTCGCGGTAGCTCCTGCGCCTCAGTGTACCATGC
CTCTGTATGACTCTGTGCCTCCCACCCGGCCTTCCTCTGGGCGTCACTCAGAAGTCCACAATTTCCAAGAAACCATTCAA
CAGTTAGAGGGTCGCCTTGTAAGACAAGACCATCAAATCCGGGAACTGACTGCAAAAATGGAAACCCAGAGCATGTATGT
AAATGAGCTCAAGCGAACTATTCGAACCCTTGAGGACAAAGTTGCTGAAACAGAAGCACAGCAGTGCAATGGGATTTACA
TCTGGAAGATTGGCAACTTTGGGATGCACTTGAAATCGCAAGAAGAGGAGAAGCCTGTTGTCATTCACAGCCCCGGGTTC
TACACAGGCAAACCCGGCTACAAACTGTGCATGCGGCTGCACCTGCAGCTGCCGAGCGTGCAGCGCTGCGCCAACTACAT
ATCGCTCTTTGTCCACACGATGCAAGGGGAGTACGACAGCCACCTGCCGTGGCCCTTCCAGGGGACAATACGCCTTACCA
TCCTTGACCAGTCTGAAGCAACTGTGAGGCAAAACCACGAAGAAATAATGGACGCCAAACCAGAGCTCCTGGCCTTTCAG
AGACCCACCATCCCCCGGAACCCCAAGGGTTTTGGCTACGTGACTTTAATGCATCTGGAAGCCCTCAGACAAAGAACCTT
CATCAAGGATGACACGTTATTAGTACGCTGTGAGGTCTCCACCGGCTTCGACATGGGCAGTCTTCGGAGGGAGGGTTTTC
AGCCACGGAGTACTGACTCAGGGATA

Alignment

ORF - retro_btau_391 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLLHCENSCGSSQSESDCCAAMAASSCGTAAKDDSVSGTASTVTLSSSFMEEIQGYDVEFDPPLESKYE
          MSLLHCENSC.SSQSESDCCAAMAASSCGTAAKDDSVSGTASTVTLSSSFMEEIQGYDVEFDPPLESKYE
Retrocopy MSLLHCENSCASSQSESDCCAAMAASSCGTAAKDDSVSGTASTVTLSSSFMEEIQGYDVEFDPPLESKYE

Parental  CPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKREILSLMVKCPNEGC
          CPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAK.EILSLMVKCPNEGC
Retrocopy CPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAK*EILSLMVKCPNEGC

Parental  LHKMELRHLEEHQAHCEFALMSCPQCQRPFQKCHLNIHILKECPRRQVPCENCAVSMAFEDKEIHEQNCP
          LHKMELRHLEEHQAHCEFALMSCPQCQRPFQKCHLNIHILKECPRRQVPCENCAVSMAFEDKEIHEQNCP
Retrocopy LHKMELRHLEEHQAHCEFALMSCPQCQRPFQKCHLNIHILKECPRRQVPCENCAVSMAFEDKEIHEQNCP

Parental  LANVICEYCNTMLIREQMPNHYDLDCPTAPVPCTFSAFGCHEKMQRNHLARHLQENTQSHMRMMAQAVQT
          LANVICEYCNTMLIREQMPNHYDLDCPTAPVPCTFSAFGCHEKMQRNHLARHLQENTQSHMRM.AQAVQT
Retrocopy LANVICEYCNTMLIREQMPNHYDLDCPTAPVPCTFSAFGCHEKMQRNHLARHLQENTQSHMRMKAQAVQT

Parental  LSLAVAPVPQCTMPLYDSVPPTRPSSGRHSEVHNFQETIQQLEGRLVRQDHQIRELTAKMETQSMYVNEL
          LSLAVAP.PQCTMPLYDSVPPTRPSSGRHSEVHNFQETIQQLEGRLVRQDHQIRELTAKMETQSMYVNEL
Retrocopy LSLAVAPAPQCTMPLYDSVPPTRPSSGRHSEVHNFQETIQQLEGRLVRQDHQIRELTAKMETQSMYVNEL

Parental  KRTIRTLEDKVAEIEAQQCNGIYIWKIGNFGMHLKSQEEEKPVVIHSPGFYTGKPGYKLCMRLHLQLPSA
          KRTIRTLEDKVAE.EAQQCNGIYIWKIGNFGMHLKSQEEEKPVVIHSPGFYTGKPGYKLCMRLHLQLPS.
Retrocopy KRTIRTLEDKVAETEAQQCNGIYIWKIGNFGMHLKSQEEEKPVVIHSPGFYTGKPGYKLCMRLHLQLPSV

Parental  QRCANYISLFVHTMQGEYDSHLPWPFQGTIRLTILDQSEAAVRQNHEEIMDAKPELLAFQRPTIPRNPKG
          QRCANYISLFVHTMQGEYDSHLPWPFQGTIRLTILDQSEA.VRQNHEEIMDAKPELLAFQRPTIPRNPKG
Retrocopy QRCANYISLFVHTMQGEYDSHLPWPFQGTIRLTILDQSEATVRQNHEEIMDAKPELLAFQRPTIPRNPKG

Parental  FGYVTFMHLEALRQRTFIKDDTLLVRCEVSTRFDMGSLRREGFQPRSTDSGI
          FGYVT.MHLEALRQRTFIKDDTLLVRCEVST.FDMGSLRREGFQPRSTDSGI
Retrocopy FGYVTLMHLEALRQRTFIKDDTLLVRCEVSTGFDMGSLRREGFQPRSTDSGI

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	0.00 RPM	11.10 RPM
ERP005899_muscle	0.05 RPM	15.31 RPM
SRP017611_brain	0.05 RPM	6.53 RPM
SRP017611_kidney	0.12 RPM	16.00 RPM
SRP017611_liver	0.00 RPM	12.23 RPM
SRP030211_testis	0.10 RPM	15.06 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_391 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_391 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_391 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000036009	1 retrocopy	retro_btau_391 ,
Homo sapiens	ENSG00000175104	1 retrocopy	retro_hsap_680,
Gorilla gorilla	ENSGGOG00000005854	1 retrocopy	retro_ggor_586,
Nomascus leucogenys	ENSNLEG00000017949	1 retrocopy	retro_nleu_782,
Pan troglodytes	ENSPTRG00000003510	1 retrocopy	retro_ptro_488,