RetrogeneDB ID: retro_btau_1655

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:67661774..67662152(-)
• Located in intron of: None

Retrocopy information

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

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_1655
TCGTTCTTCAAATTACCTGGTGGTGAGCTTAATCCAGGAGAAGATGAAGTTGAAGGACTAAAACACTTAATGACAGAGAT
ATTGGGTCGTCAAGATGGAGTCCTGCAAGACTGGGTCATCGATGACTGCACTGGAAACTGGTGGAGACCAAATTTTGAGC
CTCCTCACTATCCATATATTCCTGCACATATTACAAAACCTAAGGAACATAGGAAGTTGTTTCTGGTTCAGCTTCAAGAG
AAAGCCTTGTTTGCAGTCCCTAAAAATTACAAGCTGGCAGCTGCACCGCTATTTGAACTGTATGACAATGCACCTGGATA
TGGACCCATCATTTCTAGTCTTCCCCAGCTTTTGAGCAGGTTCAATTTTATATACAAC

Alignment

ORF - retro_btau_1655 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.24 %
• Parental protein coverage: 55.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEH
          .FFKLPGGELNPGEDEVEGLK.LMTEILGRQDGVLQDWVIDDC.GNWWRPNFEPP.YPYIPAHITKPKEH
Retrocopy SFFKLPGGELNPGEDEVEGLKHLMTEILGRQDGVLQDWVIDDCTGNWWRPNFEPPHYPYIPAHITKPKEH

Parental  KKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN
          .KLFLVQLQEKALFAVPKNYKL.AAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN
Retrocopy RKLFLVQLQEKALFAVPKNYKLAAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN

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	0.05 RPM	18.69 RPM
SRP017611_brain	0.05 RPM	14.30 RPM
SRP017611_kidney	0.00 RPM	21.46 RPM
SRP017611_liver	0.00 RPM	6.87 RPM
SRP030211_testis	0.03 RPM	27.03 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1655 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1655 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1655 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,