RetrogeneDB ID: retro_btau_1456

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:59001804..59002228(+)
• Located in intron of: ENSBTAG00000013699

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLBP
• Ensembl ID: ENSBTAG00000001328
• Aliases: None
• Description: histone RNA hairpin-binding protein [Source:RefSeq peptide;Acc:NP_001039345]

Sequence

>retro_btau_1456
TCCAGATGTTCAGACTGGGCAAGTATAGTGGAAGAAGATGAAATGAGGTCTACAGTTAACAAAGAAATTTCAAGTTATAG
AAGGAAACACTTCATAAATGACTTTGGAAGGGAGAGAAAGTCATCATCAGGGAGTTTGGCTTCAAAGGAGCCTGTGTCTG
CGTTGTCAGCCAACTTGAAGACTGATGAACGTGTCCTGATGAGGAGCCAGATGCAGATCACTTACGGAAAGAACACCATC
GCCTGTGACCGCTATATTAAAGAAGTCCCTGGGCACCTTTGACAGCCTGGCATTCATCCTGAAACCCCCAGTGAATTCAA
AAGTATAGTCAATGATATTGGGACCAACAGACCAAAAGCTGGAAGGTGTTTCTGCAGCTTAGGGTCCCCCAGCTGAAGAA
GGATGTGATTTGCAAGACATGTAC

Alignment

ORF - retro_btau_1456 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.53 %
• Parental protein coverage: 51.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRCSDWASAVEEDEMRTSVNKEIARYKRKLLINDFGRERKSSSGSSDSKESVSALPADLETDESVLMRRQ
          SRCSDWAS.VEEDEMR..VNKEI..Y.RK..INDFGRERKSSSGS..SKE.VSAL.A.L.TDE.VLMR.Q
Retrocopy SRCSDWASIVEEDEMRSTVNKEISSYRRKHFINDFGRERKSSSGSLASKEPVSALSANLKTDERVLMRSQ

Parental  KQINYGKNTIAYDRYIKEVPRHLRQPGVHPKTPNKFK-KYSRRSWDQQIRLWKVALHFW-DPPAEEGCDL
          .QI.YGKNTIA.DRYIKEVP.HL.QPG.HP.TP..FK.KYS...WDQQ...WKV.L.....PPAEEGCDL
Retrocopy MQITYGKNTIACDRYIKEVPGHL*QPGIHPETPSEFK<KYSQ*YWDQQTKSWKVFLQLR<GPPAEEGCDL

Parental  QEIH
          Q...
Retrocopy QDMY

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	12.47 RPM
ERP005899_muscle	0.00 RPM	24.60 RPM
SRP017611_brain	0.05 RPM	23.89 RPM
SRP017611_kidney	0.00 RPM	15.00 RPM
SRP017611_liver	0.00 RPM	8.83 RPM
SRP030211_testis	0.09 RPM	58.78 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1456 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1456 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1456 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001328	1 retrocopy	retro_btau_1456 ,
Cavia porcellus	ENSCPOG00000000031	1 retrocopy	retro_cpor_364,
Mus musculus	ENSMUSG00000004642	1 retrocopy	retro_mmus_1169,
Otolemur garnettii	ENSOGAG00000009750	1 retrocopy	retro_ogar_1463,
Pteropus vampyrus	ENSPVAG00000002807	2 retrocopies	retro_pvam_490, retro_pvam_941,
Rattus norvegicus	ENSRNOG00000037162	2 retrocopies	retro_rnor_1864, retro_rnor_2016,
Tarsius syrichta	ENSTSYG00000000376	2 retrocopies	retro_tsyr_1595, retro_tsyr_482,
Tursiops truncatus	ENSTTRG00000010901	1 retrocopy	retro_ttru_10,