RetrogeneDB ID: retro_btau_1368

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:13756350..13756907(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000014765
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.62775
• Ensembl ID: ENSBTAG00000004106
• Aliases: None
• Description: PRKR-interacting protein 1 [Source:RefSeq peptide;Acc:NP_001073109]

Sequence

>retro_btau_1368
ATGGGGAGCTCGGCGGCCTCTTCTGTGAGGCCGCCGAGGCCCAAGAAGGAGCCGCAGGGCTCATCATCCCCAAGAATGCC
GCGGAGGAGCAGAAGCTCAAGTTGGAACGGCTCATGAAGAACCCGGATAAAGCAGTTCAAATTCCAGAAAAAATGAGTGA
ATGGGCACCTCGACCTCCCCCAGAATTTGTCCGAGATGTAATGGGTTCAAGCGCTGGGGCCGGCAGCGGAGAATTCCACG
TGTACAGGCATCTGCACCGGAGAGAGTACCAGCGCCAGGACTACATGGATGCCATGGCTGAGAAGCAAAAATTGGATGCA
GAGTTTCAGAAGAGGCTGGAAAGGAATAAAATTGCTGCAGAGGAGCAGACTGCAAAGCGTCGGAAAAAGCGCCAGAAGTT
GAAAGAGAAGAAATTACTGGCAAAGAAGATGAAACTTGAACAGAAGAAGCAAAGTGAAGCATCCAGTGAGACCCAGGAGC
AGCCATCCAGTGGCTCCGAGGAGGCATCTGGGACGGAGGACGAGGAGGAGGATGCACCCAGCTTCGTCACGGGGCGA

Alignment

ORF - retro_btau_1368 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASSAASSVRPPRPKKEPQA-LIIPKNAAEEQKLKLERLMKNPDKAVPIPEKMSEWAPRPPPEFVRDVMG
          M.SSAASSVRPPRPKKEPQ..LIIPKNAAEEQKLKLERLMKNPDKAV.IPEKMSEWAPRPPPEFVRDVMG
Retrocopy MGSSAASSVRPPRPKKEPQG<LIIPKNAAEEQKLKLERLMKNPDKAVQIPEKMSEWAPRPPPEFVRDVMG

Parental  SSAGAGSGEFHVYRHLRRREYQRQDYMDAMAEKQKLDAEFQKRLERNKIAAEEQTAKRRKKRQKLKEKKL
          SSAGAGSGEFHVYRHL.RREYQRQDYMDAMAEKQKLDAEFQKRLERNKIAAEEQTAKRRKKRQKLKEKKL
Retrocopy SSAGAGSGEFHVYRHLHRREYQRQDYMDAMAEKQKLDAEFQKRLERNKIAAEEQTAKRRKKRQKLKEKKL

Parental  LAKKMKLEQKKQSEASSETQEQPSSGSEEASGTEDEEEDAPSFVTGR
          LAKKMKLEQKKQSEASSETQEQPSSGSEEASGTEDEEEDAPSFVTGR
Retrocopy LAKKMKLEQKKQSEASSETQEQPSSGSEEASGTEDEEEDAPSFVTGR

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	0.07 RPM	1.08 RPM
ERP005899_muscle	0.00 RPM	4.80 RPM
SRP017611_brain	0.14 RPM	3.38 RPM
SRP017611_kidney	0.18 RPM	4.50 RPM
SRP017611_liver	0.23 RPM	2.27 RPM
SRP030211_testis	0.18 RPM	24.16 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1368 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1368 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1368 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004106	1 retrocopy	retro_btau_1368 ,
Mus musculus	ENSMUSG00000039737	1 retrocopy	retro_mmus_2388,