RetrogeneDB ID: retro_btau_972

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 22:25460546..25461071(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000006727
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PABPN1L
• Ensembl ID: ENSBTAG00000023752
• Aliases: None
• Description: None

Sequence

>retro_btau_972
AGCCAGGGGCCGGAGCCGCCCAGGGTGCAGAACCTGGATGAAGGAGAGGAAGCCACCGGGGCCCTGCTGGCCAGGCAGCT
ACTGAGTCCCGAGACAGACAGCCCCCTGGAGAAAGCAGAGGCTGACCACAGATCCATCTACGTGGGCAATGTGGACTATG
GGGGCACGGCCCAGGAGCTGGAGGCCTATTTCAACCACTGTGGGGAGATCCACCAGGTCACCATCCTGTGTGACAAGTTC
TCTGGACACCCCAAGGGCTATGCCTACATAGAGTTTGCCACGGAGAGCTCGGCCCAGGCCGCCGTGGAGCTGGACAAGAG
CATCTTTCGAGGCCGGGTCATCAAGGTGCTGCCCAAAAGGACCAATTTACCAGGGATCAGTTCCACGGACCGCGGGGGCC
TTCGGGGACACCCAGGCGCCAGAGTGGGATCCTTCCCCTACGGCGGCCTTCAAGGCGGGGCCCGTTTCAGGCCACGAGGG
CGGAGCCGGGGACGCGGAAGATTCTCACCGTGGTTTTCTCCATAT

Alignment

ORF - retro_btau_972 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.29 %
• Parental protein coverage: 60.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AQGPEPPRVQNLDEGEEAAGALLARQLLSPETDSPLEKAEADHRSIYVGNVDYGGTAQELEAYFNHCGEI
          .QGPEPPRVQNLDEGEEA.GALLARQLLSPETDSPLEKAEADHRSIYVGNVDYGGTAQELEAYFNHCGEI
Retrocopy SQGPEPPRVQNLDEGEEATGALLARQLLSPETDSPLEKAEADHRSIYVGNVDYGGTAQELEAYFNHCGEI

Parental  HRVTILCDKFSGHPKGYAYIEFATESSAQAAVELDKSIFRGRVIKVLPKRTNLPGISSTDRGGLRGHPGA
          H.VTILCDKFSGHPKGYAYIEFATESSAQAAVELDKSIFRGRVIKVLPKRTNLPGISSTDRGGLRGHPGA
Retrocopy HQVTILCDKFSGHPKGYAYIEFATESSAQAAVELDKSIFRGRVIKVLPKRTNLPGISSTDRGGLRGHPGA

Parental  RVGSFPYGGLQGGARFRPRGRSRGRGRFSPWFSPY
          RVGSFPYGGLQGGARFRPRGRSRGRGRFSPWFSPY
Retrocopy RVGSFPYGGLQGGARFRPRGRSRGRGRFSPWFSPY

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	0.00 RPM
ERP005899_muscle	0.00 RPM	0.00 RPM
SRP017611_brain	0.00 RPM	0.05 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP030211_testis	0.07 RPM	0.17 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_972 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_972 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_972 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006884	1 retrocopy	retro_btau_693,
Bos taurus	ENSBTAG00000023752	1 retrocopy	retro_btau_972 ,
Erinaceus europaeus	ENSEEUG00000004747	1 retrocopy	retro_eeur_633,
Ochotona princeps	ENSOPRG00000005597	2 retrocopies	retro_opri_1001, retro_opri_174,
Tursiops truncatus	ENSTTRG00000004691	3 retrocopies	retro_ttru_1488, retro_ttru_243, retro_ttru_822,