RetrogeneDB ID: retro_btau_1352

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:72527227..72527652(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRNP27
• Ensembl ID: ENSBTAG00000037746
• Aliases: SNRNP27, RY1
• Description: small nuclear ribonucleoprotein 27kDa (U4/U6.U5) [Source:RefSeq peptide;Acc:NP_001091631]

Sequence

>retro_btau_1352
AGGCGGTCCGGGTCCACATCTGGGAAAGATGAACCCAGGCGCCTAGAAAGGTCCCAGTCTGGGGAGTGAGATAGAAGCAG
CCGCTCTCCTTCCCGCACAGAAGGCGGTCCAGGTCCAGGTCCCCAAGAAGACATAGATCCACATCTCCTGCCCCTTCTCG
ACTGAAAGAAAGAAGAGATGAGAAGAAGAAAGAAACAAAAGAAACAAAGAGCAAAGAACATCAGATAACTGAGGAAGACT
TAGAAGGCAACATAGAGGAAGAAATAGAAATGAAGTTAATGGGATTTGCCTCCTTTGACTCCACAAAAGGGAAAAAGGTG
GATGGCTCTGTAAATGCCTATTCCATAAATGTGTCGCAGAAGAGAAAGTATAGGCAGTACATGAATTGAAAAGGTGGATT
CAACAGACCTTTGGGTTTCATTGCA

Alignment

ORF - retro_btau_1352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.03 %
• Parental protein coverage: 91.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RRSRSTSRERERRRRERSRSRERDRRRSRSRS-PHRRRSRS--PRRHRSTSPSPSRLKERRDEEKKETKE
          RRS.STS...E.RR.ERS.S.E.DR..SRS.S.PHRRRSRS..PRRHRSTSP.PSR..............
Retrocopy RRSGSTSGKDEPRRLERSQSGE*DRS-SRSPS<PHRRRSRSRSPRRHRSTSPAPSRXXXXXXXXXXXXXX

Parental  TKSKERQITEEDLEGKTEEEIEMMKLMGFASFDSTKGKKVDGSVNAYAINVSQKRKYRQYMNRKGGFNRP
          ......QITEEDLEG..EEEIE.MKLMGFASFDSTKGKKVDGSVNAY.INVSQKRKYRQYMN.KGGFNRP
Retrocopy XXXXXXQITEEDLEGNIEEEIE-MKLMGFASFDSTKGKKVDGSVNAYSINVSQKRKYRQYMN*KGGFNRP

Parental  LDFIA
          L.FIA
Retrocopy LGFIA

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	18.02 RPM
ERP005899_muscle	0.00 RPM	6.86 RPM
SRP017611_brain	0.00 RPM	4.61 RPM
SRP017611_kidney	0.12 RPM	10.19 RPM
SRP017611_liver	0.00 RPM	5.06 RPM
SRP030211_testis	0.05 RPM	10.73 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1352 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1352 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1352 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000037746	4 retrocopies	retro_btau_1352 , retro_btau_375, retro_btau_514, retro_btau_515,
Choloepus hoffmanni	ENSCHOG00000003042	1 retrocopy	retro_chof_2589,
Echinops telfairi	ENSETEG00000017344	1 retrocopy	retro_etel_655,
Homo sapiens	ENSG00000124380	1 retrocopy	retro_hsap_3387,
Mus musculus	ENSMUSG00000001158	2 retrocopies	retro_mmus_1977, retro_mmus_2105,
Oryctolagus cuniculus	ENSOCUG00000022967	1 retrocopy	retro_ocun_1281,
Pongo abelii	ENSPPYG00000012332	2 retrocopies	retro_pabe_1990, retro_pabe_2782,
Pan troglodytes	ENSPTRG00000012022	1 retrocopy	retro_ptro_2300,
Sus scrofa	ENSSSCG00000025674	1 retrocopy	retro_sscr_285,