RetrogeneDB ID: retro_btau_298

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:66864775..66865437(-)
• Located in intron of: ENSBTAG00000013069

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIR
• Ensembl ID: ENSBTAG00000009477
• Aliases: None
• Description: pirin [Source:RefSeq peptide;Acc:NP_001095828]

Sequence

>retro_btau_298
CCAGGCGGATTTCTTGATCACCCGCACTGAGGTTTTGAAACAATATCTTACCTCCTGAAAGGAGGGTGTAGCATAGCCCA
GGAAGACTGCCATGGACATGTTGGTCAGTTGAACTCAGGAGGCCTGTACTGGATGATCTCAGGCTGGGGCATTGTGTATG
AGGAGACGCCTTGCTCAGAGGAGCCAGTCCATGACCATCCACTCTGGGTTAATTTGAGGACCTCACAGAAGATATTGGAG
CCTTGCTACCAGGAACTGAAAAGCAGTGAAATCCCTAAACCCAGTAAGGATAATGTGACCATTGCTGTCATTTCTGGAGA
AGCCCTGGGAGTCAAGTCAAAGATTTACATCTACACACCAACCTTATATTTGGACTTCAAATTGGACAAAGGAGCAAAGC
ATTCCCAGCCTATTCCTAAAGGATGGACAAGCTCCCTTTGTACCATATCTGGAAATGTGTATACTGTACGGATAATATGC
AACAAAAAACAGAACCTCATCACACAGCTGTGTTACGGGAAGGTGACAGTGTCCAGGTGGAGAATAAAGATCCTGAGAGA
AGCCACTGCATCCTAATTCTTGAGGAGCCATTAAGAGAACCAGCTGTTCAGCATGGAAAAGTATACTTACCCTTAGAGAA
TCCAAAATGTGATGCTTTCTTG

Alignment

ORF - retro_btau_298 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.37 %
• Parental protein coverage: 76.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PGGFPDHPHRGFETVSYLLEGG-SMAHEDFCGHAGQLNPGDLQWMTAGQGIMHAEMPCSEEPVHGLQLWV
          PGGF.DHPH.GFET.SYLL.GG.S.A.ED..GH.GQLN.G.L.WM..G.GI...E.PCSEEPVH...LWV
Retrocopy PGGFLDHPH*GFETISYLLKGGCSIAQEDCHGHVGQLNSGGLYWMISGWGIVYEETPCSEEPVHDHPLWV

Parental  NLRSSQKMVKPRYQELKSDEIPKPSQDGVTVAVISGEALGIKSKIYTYTPTLYLDFKLDQGAKHVQSIPK
          NLR.SQK...P.YQELKS.EIPKPS.D.VT.AVISGEALG.KSKIY.YTPTLYLDFKLD.GAKH.Q.IPK
Retrocopy NLRTSQKILEPCYQELKSSEIPKPSKDNVTIAVISGEALGVKSKIYIYTPTLYLDFKLDKGAKHSQPIPK

Parental  GWTSFIYTISGNVY-IGPDDAQQKIEPHHTAVLGEGDSVHVENKDPERSHFVLIAGEPLKEPVVQHGPFV
          GWTS...TISGNVY....D..QQK.EPHHTAVL.EGDSV.VENKDPERSH..LI..EPL.EP.VQHG...
Retrocopy GWTSSLCTISGNVY<YCTDNMQQKTEPHHTAVLREGDSVQVENKDPERSHCILILEEPLREPAVQHGKVY

Parental  MNTDEEISQAIL
          .........A.L
Retrocopy LPLENPKCDAFL

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	10.81 RPM
ERP005899_muscle	0.21 RPM	18.27 RPM
SRP017611_brain	0.37 RPM	7.72 RPM
SRP017611_kidney	0.36 RPM	7.17 RPM
SRP017611_liver	0.15 RPM	8.08 RPM
SRP030211_testis	0.16 RPM	2.19 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_298 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_298 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_298 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009477	1 retrocopy	retro_btau_298 ,
Felis catus	ENSFCAG00000010486	1 retrocopy	retro_fcat_779,
Otolemur garnettii	ENSOGAG00000003304	2 retrocopies	retro_ogar_1073, retro_ogar_1118,
Tupaia belangeri	ENSTBEG00000008256	1 retrocopy	retro_tbel_1669,
Tursiops truncatus	ENSTTRG00000006770	1 retrocopy	retro_ttru_448,