RetrogeneDB ID: retro_btau_1162

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 28:29374231..29375055(-)
• Located in intron of: ENSBTAG00000000315

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRMT11
• Ensembl ID: ENSBTAG00000001957
• Aliases: None
• Description: tRNA (guanine(10)-N2)-methyltransferase homolog [Source:UniProtKB/Swiss-Prot;Acc:Q05B63]

Sequence

>retro_btau_1162
GAGAGCTTATTGAGTCATACAGTGTCAAAAAGAGACACTATTTGAAATACAAGCATGGATGCTGGTTTATCATTCATCAT
GGCCAACCATGGAAAAGTGAAAAAAAAGGATACTGTATTTGATCCATCTGTTGGACCAGGTGGCCTTTTGATCGCTTCTG
CTCATTTTGGTGCGTACGTATATGGGACAGGCGTAGACTGCAATACTGTTCATGGCTTGGGAAAGGCTAGTAGGAAAAAC
CGGAAATGGAGAGGACCGGATGAAAACATCTTCATCAGTTTGGTTTAGGGCAAATCTTCATCAGTATGGTTTAGAGAAGT
ATTACCTTGATGTCCTGGTTTCTAAACCTTCCTGGAAGAAGGGTACTTATTTTGATGCAATCATGACTGATCCTCCATAT
GGTATTAGAGAATCTACAAGAACAGGTTCACAGAAGGAAGTACCAAAGGGAATAGGAAATGTCCAGAAAGCCACGTTCCT
GTTTCTTTGAGTTATCTGTGTGATATGTTTTTTGACCTGTTAAAGTTCTCAGCAGAGACCCTCGTATTAGGTGGAAGACT
CGTCTATTGGTTACCAGTATACACTGAGCAGATGGTACCCTGGCACCTCTGCTTGAAACTCATCAGCAACTGCAAGCAGA
AGCTTTCCAGTCACACATCAAGGTGCTTGATAACATGGAAAAGGTGAAGGAATTTGAGAACTGGGACCAGTATTCACATT
TGCTGAGTGATCATTTTCTGCTATACCAAGGTCATAATTCCTTCCATGAGAAATATTTCAGCGGGGTAACAAAAAGAATT
ACCAAGGAAGAAAAATCTAGCAGG

Alignment

ORF - retro_btau_1162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.87 %
• Parental protein coverage: 60.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ELIESYSVKKRHFIGNTSMDAGLSFIMANHGKVKKNDIVFDPFVGTGGLLIASAHFGAYVYGTDIDYNTV
          E...S..V.KR..I.NTSMDAGLSFIMANHGKV...D.VFDP.VG.GGLLIASAHFGAYVYGT..D.NTV
Retrocopy ESLLSHTVSKRDTI*NTSMDAGLSFIMANHGKVXXXDTVFDPSVGPGGLLIASAHFGAYVYGTGVDCNTV

Parental  HGLGKASRKNQKWRGPDENIRANL-RQYGLEKYYLDVLVSD--ASKPSWRKGTYFDAIITDPPYGIREST
          HGLGKASRKN.KWRGPDENI...L.....L..Y.L.....D...SKPSW.KGTYFDAI.TDPPYGIREST
Retrocopy HGLGKASRKNRKWRGPDENIFISL>FRANLHQYGLEKYYLDVLVSKPSWKKGTYFDAIMTDPPYGIREST

Parental  RRTGSQKEIPKGI-EKCPESHVPVSLSYHLSDMFFDLLNFSAETLVLGGRLVYWLPVYTPEYTEEMVPWH
          .RTGSQKE.PKGI..KCPESHVPVSLSY.L.DMFFDLL.FSAETLVLGGRLVYWLPVYT....E.MVPWH
Retrocopy -RTGSQKEVPKGI<RKCPESHVPVSLSY-LCDMFFDLLKFSAETLVLGGRLVYWLPVYT----EQMVPWH

Parental  PCLKLISNCEQKLSSHTSRRLIT-MEKVKEFENRDQYSHLLSDHFLLYQGHNSFREKYFSGVTKRIAKEE
          .CLKLISNC.QKLSSHTSR.LIT.MEKVKEFEN.DQYSHLLSDHFLLYQGHNSF.EKYFSGVTKRI.KEE
Retrocopy LCLKLISNCKQKLSSHTSRCLIT<MEKVKEFENWDQYSHLLSDHFLLYQGHNSFHEKYFSGVTKRITKEE

Parental  KSSQ
          KSS.
Retrocopy KSSR

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	1.66 RPM	6.49 RPM
ERP005899_muscle	0.58 RPM	3.70 RPM
SRP017611_brain	1.10 RPM	6.26 RPM
SRP017611_kidney	0.83 RPM	8.36 RPM
SRP017611_liver	0.45 RPM	3.32 RPM
SRP030211_testis	0.48 RPM	6.09 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1162 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1162 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1162 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001957	1 retrocopy	retro_btau_1162 ,