RetrogeneDB ID: retro_btau_1139

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 28:7151581..7152075(+)
• Located in intron of: ENSBTAG00000020361

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJB13
• Ensembl ID: ENSBTAG00000003682
• Aliases: None
• Description: dnaJ homolog subfamily B member 13 [Source:RefSeq peptide;Acc:NP_001029708]

Sequence

>retro_btau_1139
CTATTCTTTGACTGAACTCAGAAAATTAAGAGCTCCCAAAGAGTGCTGAACGAGGATGGGTACTCCTCTACCATCAGGGA
CGAGATCCTCACGGATGACGTAAAGCCTGGTTGAAGGCAGGGCACGTGTATCACCTTCGAGAAGGAAGAGGACCAGAATC
CCAACATCATCTCAGCTGACATCATCTTATCATAAAGGAGAAACTGCACCCTTGCTTCCACAGGGAGAACGACAACCTCT
TCTTTGTGATCTCCATCTCCTTGAGTAAGGCTCTGACCCACTACTCCATGGAGGTGAAGACCCTAGATGACTGTCTGCTC
AACATCCCTGCCAGTAACATTGTCCACCCCAAGGACTACAAGAAGGTGCCAGGTAAGGGGATGTTGCCAGAGAACCCCAT
GAAGAAGGGGGATGTCTTCATTTTCTGCACCAGCCAGTTCCCTACCTGTCTCACACCCCAGCAGAAAGAGATGCTATGCC
AGTCATTGCTGACC

Alignment

ORF - retro_btau_1139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.46 %
• Parental protein coverage: 52.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFFGCTKKIKISRRVLNDDGYSSTIKDKILTIDVKPGWRQGTRITFEKEGDQGPNIIPADIIF-IVKEKL
          LFF..T.KIK.S.RVLN.DGYSSTI.D.ILT.DVKPG.RQGT.ITFEKE.DQ.PNII.ADII..I.KEKL
Retrocopy LFFD*TQKIKSSQRVLNEDGYSSTIRDEILTDDVKPG*RQGTCITFEKEEDQNPNIISADIIL<IIKEKL

Parental  HPRFRRENDNLFFVNSIPLGKALTCCTVEVKTLDDRLLNIPINDIVHPKYFKKVPGEGMPLPEDPTKKGD
          HP.F.RENDNLFFV.SI.L.KALT....EVKTLDD.LLNIP...IVHPK..KKVPG.GM.LPE.P.KKGD
Retrocopy HPCFHRENDNLFFVISISLSKALTHYSMEVKTLDDCLLNIPASNIVHPKDYKKVPGKGM-LPENPMKKGD

Parental  LFIYFDIQFPTRLTPQKKQMLRQALLT
          .FI....QFPT.LTPQ.K.ML.Q.LLT
Retrocopy VFIFCTSQFPTCLTPQQKEMLCQSLLT

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	0.07 RPM
ERP005899_muscle	0.00 RPM	0.16 RPM
SRP017611_brain	0.00 RPM	1.74 RPM
SRP017611_kidney	0.00 RPM	0.41 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP030211_testis	0.02 RPM	78.13 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1139 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1139 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1139 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006460	2 retrocopies	retro_acar_166, retro_acar_178,
Bos taurus	ENSBTAG00000000771	3 retrocopies	retro_btau_163, retro_btau_222, retro_btau_248,
Bos taurus	ENSBTAG00000003682	1 retrocopy	retro_btau_1139 ,