RetrogeneDB ID: retro_btau_937

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 21:45486925..45487604(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000015143
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUDT21
• Ensembl ID: ENSBTAG00000010207
• Aliases: None
• Description: Cleavage and polyadenylation specificity factor subunit 5 [Source:UniProtKB/Swiss-Prot;Acc:Q3ZCA2]

Sequence

>retro_btau_937
ATGGCCGTGGTGCCGCCCAATCGATCGCAGAATGGCTGGCCCCGGGAGTCACCCAGTTCGGCAACAAGTACATCCAGCAG
ACCAAGCCCCTCACCCTAGAGCGCACCATCTACCTGTACCCTCTTACCAATTCCCTTTTTGGTACAAAAGAGCCCCTCTG
TGAGGACAGCTCTGTTGCAGCCAGATTTCAGCGCATGAGGAAGGAATTTGATAAAATTGGCGTGAGGAGGGCTGTAGAAA
CGGTTTTCATTGTTCATGAGCACGGGCTACCCCATGTGTTACTACTACAGCTGGGAACAACTTCTTCAAATTACCTGGTG
GTGAGCTTATTAACCCAGGAGAAGATGAAGTTGAAGGACTAAAACGCTTAATAACAGAGATATCGGGTGGTCAAGATGCA
GTCCTGCAAGACTGGGTCTTTGATGACTGCATTGGCAACTGGTGTAGACCAAATTTTGAACCTCCTCAGTATCCATATAT
TCCTGCACATAATACAAAACCTAAGGAACATAAGAAATTGTTTTTGGTTCAGCTTCAAGAGAAAGCCTTGTTTGCAGTCC
CTAAAAATTACAAGCTGGTAGCTGCACCACTGTTTGAACTGTGTAACAATGCACCTGGATATGGACCCATTATTTCTAGT
CTCCCCCAGCTTTTGAGCAGGGTCAATTTTATATACAAC

Alignment

ORF - retro_btau_937 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSVVPPNRSQTGWPR-GVTQFGNKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMRE
          M.VVPPNRSQ.GWPR.GVTQFGNKYIQQTKPLTLERTI.LYPLTN..FGTKEPL.E.DSSVAARFQRMR.
Retrocopy MAVVPPNRSQNGWPR<GVTQFGNKYIQQTKPLTLERTIYLYPLTNSLFGTKEPLCE-DSSVAARFQRMRK

Parental  EFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTT-FFKLPGGEL-NPGEDEVEGLKRLMTEILGRQDGVLQ
          EFDKIG.RR.VE.V.IVHEH.LPHVLLLQLGTT.FFKLPGGEL.NPGEDEVEGLKRL.TEI.G.QD.VLQ
Retrocopy EFDKIGVRRAVETVFIVHEHGLPHVLLLQLGTT<FFKLPGGELINPGEDEVEGLKRLITEISGGQDAVLQ

Parental  DWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPG
          DWV.DDCIGNW.RPNFEPPQYPYIPAH.TKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFEL..NAPG
Retrocopy DWVFDDCIGNWCRPNFEPPQYPYIPAHNTKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELCNNAPG

Parental  YGPIISSLPQLLSRFNFIYN
          YGPIISSLPQLLSR.NFIYN
Retrocopy YGPIISSLPQLLSRVNFIYN

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	6.49 RPM
ERP005899_muscle	0.00 RPM	18.69 RPM
SRP017611_brain	0.00 RPM	14.30 RPM
SRP017611_kidney	0.00 RPM	21.46 RPM
SRP017611_liver	0.00 RPM	6.87 RPM
SRP030211_testis	0.09 RPM	27.03 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_937 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_937 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_937 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010207	2 retrocopies	retro_btau_1655, retro_btau_937 ,
Callithrix jacchus	ENSCJAG00000012724	3 retrocopies	retro_cjac_1121, retro_cjac_2211, retro_cjac_4100,
Loxodonta africana	ENSLAFG00000028465	1 retrocopy	retro_lafr_610,
Mustela putorius furo	ENSMPUG00000003451	1 retrocopy	retro_mputfur_158,
Nomascus leucogenys	ENSNLEG00000001963	2 retrocopies	retro_nleu_1477, retro_nleu_2493,
Oryctolagus cuniculus	ENSOCUG00000017224	2 retrocopies	retro_ocun_154, retro_ocun_87,
Sorex araneus	ENSSARG00000006493	2 retrocopies	retro_sara_161, retro_sara_580,
Sus scrofa	ENSSSCG00000029848	2 retrocopies	retro_sscr_117, retro_sscr_185,