RetrogeneDB ID: retro_btau_1341

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:33378580..33379599(-)
• Located in intron of: ENSBTAG00000020878

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF4
• Ensembl ID: ENSBTAG00000004571
• Aliases: None
• Description: U4/U6 small nuclear ribonucleoprotein Prp4 [Source:UniProtKB/Swiss-Prot;Acc:Q3MHE2]

Sequence

>retro_btau_1341
GTGAAGAAACCACACATCTATTATGGAAGTTTGGAAGAGAAGGAGAGGGAGCATCTGGCCAAAGGAGAATCTGGGCTTTT
GGGAAAAGAAGGACTCAAAGCAGGAAACATTAACATAACCTCTGGAGAAGTGTTTGAAATTGAAGAGCACATCAGTGAGA
GACAGGCTGAAGTGTTAGCAGAGTTTGAGAGAAGGAAGCGATCCCGGCAAATCAACATTTCCACAGATGACTCAGAGGTC
AAGGCTTGCCTTAGAGCTTTGGGGGAACCCATCACACTTTTTGGAGAAGGTCCTGCTGAACGAAGAGAAAGGTTAAGACG
TATCCTCTCAGTGGTCGGTACCAATGCCTTAAAAAAGACCAAAAAAGATTATGAAAAATCAAAGAAGTTCAAAGAAGAGT
ATCAGCAGACCTGGTACCATGAAGGACCAAACAGCCTGAAGGTTGCTAGACTGCAGATTGCTAATTATTCACTGCCCAGG
GCAATGAAATACTTAGAAGAGGCCCATCTTCATAAAGAGGTTCCTGAGACAACTAGAACCTCCCAGATGCAAGAGCTGCA
CAAATCTCTCTGATCTTTGAATAATTTCTGTGGTCAGATTGGGGATGATTGGCCTATCTCCTACTGTCACTTTAGTCCCA
ATTCCAAAATGCTGGCCACAGCTTGTTTGAGTGGGCTTTGCAAGCTCTGGTCTGTTCCTGATTGCAACCTCCTTCACACT
CTTCGAGGCCATAACACAAACGTGGGAGCGATCATATTCCATCCCAAATCCACGGTCTCCTTGGACCAAAAAGATGTCAA
TCTGGCCTCTTGTGCTGCTGACAGTTCTGTGAAGCTGTGGAGCCTTGACAGTGATGAAAGGTGGCAGATATTGAAGGCCA
CACAATGCATGTGGCTCATGTAATGTGGCATCCATCAGGACGTTTCTTAGGTACCACCTGCTATGACCGATCATGGCACT
TATGGGATTTGGAAGCTCAAGAGGAAATCCTGCATTAGGAGGGCCACAGCATGGGTGTC

Alignment

ORF - retro_btau_1341 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.96 %
• Parental protein coverage: 66.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKKPHIYYGSLEEKERERLAKGESGLLGKEGLKAGIEAGNINITSGEVFEIEEHISERQAEVLAEFERRK
          VKKPHIYYGSLEEKERE.LAKGESGLLGKEGLK....AGNINITSGEVFEIEEHISERQAEVLAEFERRK
Retrocopy VKKPHIYYGSLEEKEREHLAKGESGLLGKEGLK----AGNINITSGEVFEIEEHISERQAEVLAEFERRK

Parental  RARQINVSTDDSEVKACLRALGEPITLFGEGPAERRERLRNILSVVGTDALKKTKKDDEKSKKSKEEYQQ
          R.RQIN.STDDSEVKACLRALGEPITLFGEGPAERRERLR.ILSVVGT.A.................YQQ
Retrocopy RSRQINISTDDSEVKACLRALGEPITLFGEGPAERRERLRRILSVVGTNAXXXXXXXXXXXXXXXXXYQQ

Parental  TWYHEGPHSLKVARLWIANYSLPRAMKRLEEARLHKEIPETTRTSQMQELHKSLRSLNNFCSQIGDDRPI
          TWYHEGP.SLKVARL.IANYSLPRAMK.LEEA.LHKE.PETTRTSQMQELHKSL.SLNNFC.QIGDD.PI
Retrocopy TWYHEGPNSLKVARLQIANYSLPRAMKYLEEAHLHKEVPETTRTSQMQELHKSL*SLNNFCGQIGDDWPI

Parental  SYCHFSPNSKMLATACWSGLCKLWSVPDCNLLHTLRGHNTNVGAIVFHPKSTVSLDQKDVNLASCAADGS
          SYCHFSPNSKMLATAC.SGLCKLWSVPDCNLLHTLRGHNTNVGAI.FHPKSTVSLDQKDVNLASCAAD.S
Retrocopy SYCHFSPNSKMLATACLSGLCKLWSVPDCNLLHTLRGHNTNVGAIIFHPKSTVSLDQKDVNLASCAADSS

Parental  VKLWSLDSDE-PVADIEGHTVRVARVTWHPSGRFLGTTCYDRSWRLWDLEAQEEILHQEGHSMGV
          VKLWSLDSDE..VADIEGHT..VA.V.WHPSGRFLGTTCYDRSW.LWDLEAQEEILH.EGHSMGV
Retrocopy VKLWSLDSDE<KVADIEGHTMHVAHVMWHPSGRFLGTTCYDRSWHLWDLEAQEEILH*EGHSMGV

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	0.94 RPM	22.78 RPM
ERP005899_muscle	0.90 RPM	22.91 RPM
SRP017611_brain	1.64 RPM	21.79 RPM
SRP017611_kidney	1.54 RPM	37.76 RPM
SRP017611_liver	0.45 RPM	16.08 RPM
SRP030211_testis	0.34 RPM	37.78 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1341 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1341 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1341 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004571	1 retrocopy	retro_btau_1341 ,
Bos taurus	ENSBTAG00000047031	1 retrocopy	retro_btau_299,
Cavia porcellus	ENSCPOG00000010747	2 retrocopies	retro_cpor_1531, retro_cpor_548,
Myotis lucifugus	ENSMLUG00000015309	1 retrocopy	retro_mluc_77,
Otolemur garnettii	ENSOGAG00000007802	1 retrocopy	retro_ogar_2854,