RetrogeneDB ID: retro_btau_165

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:50343554..50344106(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000001350
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PERP
• Ensembl ID: ENSBTAG00000020097
• Aliases: None
• Description: p53 apoptosis effector related to PMP-22 [Source:RefSeq peptide;Acc:NP_001029522]

Sequence

>retro_btau_165
ATGCTGCGCTGCGGCCTGGCCTGCGAGCGCTGCAGGTGGATCCTGCCGCTGCTACTGCTTAGCGCCATCGTCTTTGACAT
CATCGCGCTGGCCGGCCGCGGCTGGCTGCAGTCGAGCGATGACAGCCAGACGTCCTCGCTGTGGTGGCATTGTTTACTAG
AAGTCTGCGACAGCCTCATGACATATGCTTGGGGAAGGGCAGCCGCCGCTATGCTGCTCTGCGGTTTCATCATCCTGGTG
ATCTGCTTCATCCTCTCCTTCTTTGCCCTCTGTGGACCCCAAATGCTTGCCTTCCTGAGAGTAATCAGAGGCCTTCTGGC
CCTGGCTGCTGTGTTCCAGATCATCTCCCTGGTAATTTACCCTGTGAAGTACACTCAGACCTTTAACCTTCACCTCAACC
CTGCTGTCACTTACATCTATAACTGGGCCTATGGCTTCGGGTGGGCAGCCACTATTATCCTGATTGGCTGTGCCTTCTTC
TGTTGCCTTCCCAACTATGAAGATGACCTGCTGGGCAATGCCAAGCCCAGGTACTTCTACACATCTGCCTAA

Alignment

ORF - retro_btau_165 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRCGLACERCRWILPLLLLSAIVFDIIALAGRGWLQSSDDSQTSSLWWHCLLEVCDSLMTYAWGRAAAA
          MLRCGLACERCRWILPLLLLSAIVFDIIALAGRGWLQSSDDSQTSSLWWHCLLEVCDSLMTYAWGRAAAA
Retrocopy MLRCGLACERCRWILPLLLLSAIVFDIIALAGRGWLQSSDDSQTSSLWWHCLLEVCDSLMTYAWGRAAAA

Parental  MLLCGFIILVICFILSFFALCGPQMLVFLRVIGGLLALAAVFQIISLVIYPVKYTQTFNLHLNPAVTYIY
          MLLCGFIILVICFILSFFALCGPQML.FLRVI.GLLALAAVFQIISLVIYPVKYTQTFNLHLNPAVTYIY
Retrocopy MLLCGFIILVICFILSFFALCGPQMLAFLRVIRGLLALAAVFQIISLVIYPVKYTQTFNLHLNPAVTYIY

Parental  NWAYGFGWAATIILIGCAFFFCCLPNYEDDLLGNAKPRYFYTSA
          NWAYGFGWAATIILIGCA.FFCCLPNYEDDLLGNAKPRYFYTSA
Retrocopy NWAYGFGWAATIILIGCA-FFCCLPNYEDDLLGNAKPRYFYTSA

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	114.34 RPM
ERP005899_muscle	0.05 RPM	102.99 RPM
SRP017611_brain	0.05 RPM	5.89 RPM
SRP017611_kidney	0.12 RPM	12.98 RPM
SRP017611_liver	0.08 RPM	67.13 RPM
SRP030211_testis	0.03 RPM	1.01 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_165 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_165 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_165 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020097	1 retrocopy	retro_btau_165 ,
Callithrix jacchus	ENSCJAG00000019024	1 retrocopy	retro_cjac_3992,
Homo sapiens	ENSG00000112378	2 retrocopies	retro_hsap_1523, retro_hsap_2901,
Gorilla gorilla	ENSGGOG00000028340	1 retrocopy	retro_ggor_1165,
Macropus eugenii	ENSMEUG00000004872	1 retrocopy	retro_meug_845,
Microcebus murinus	ENSMICG00000013979	1 retrocopy	retro_mmur_353,
Myotis lucifugus	ENSMLUG00000001473	1 retrocopy	retro_mluc_2287,
Macaca mulatta	ENSMMUG00000000997	1 retrocopy	retro_mmul_2156,
Nomascus leucogenys	ENSNLEG00000014930	2 retrocopies	retro_nleu_1934, retro_nleu_631,
Oryctolagus cuniculus	ENSOCUG00000004238	1 retrocopy	retro_ocun_170,
Otolemur garnettii	ENSOGAG00000011669	1 retrocopy	retro_ogar_631,
Pongo abelii	ENSPPYG00000017043	3 retrocopies	retro_pabe_1267, retro_pabe_2400, retro_pabe_2416,