RetrogeneDB ID: retro_btau_1648

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:38683735..38684116(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000011161
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.91103
• Ensembl ID: ENSBTAG00000004820
• Aliases: POLR2F, RPB6
• Description: DNA-directed RNA polymerases I, II, and III subunit RPABC2 [Source:RefSeq peptide;Acc:NP_001032552]

Sequence

>retro_btau_1648
ATGTCAGACAACGAGGACAATTTTGATGGAGACGACTTTGATGACGTGGAGGAGGATGAAGGGCTCGATGACTTGGAGAA
TGCCGAGGAGGAGGGCCAGGAGAACGTTGAGATTCTCCCTTCTGGAGAGCGACCGCAGGCCAACCAGAAACGAATCACCA
CACCATATATGACCAAGTATGAGCAAGCCCGTGTGCTGGGCACCCGAGCCCTTCAGATTGCGATGTGCGCCCCTGTGATG
GTGGAGCTGGAGGGGGAGACAGATCCCTTACTGATCGCCATGAAGGAGCTCAAGGCCCGGAAGATCCCCATCATCATTCG
CCGCTACCTACCCGACGGGAGCTACGAAGACTGGGGCGTCGACGAGCTCATCATCACCAAC

Alignment

ORF - retro_btau_1648 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.43 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKYERARVLGTRA
          MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKYE.ARVLGTRA
Retrocopy MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKYEQARVLGTRA

Parental  LQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD
          LQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIIT.
Retrocopy LQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITN

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	4.11 RPM
ERP005899_muscle	0.21 RPM	18.32 RPM
SRP017611_brain	0.00 RPM	8.45 RPM
SRP017611_kidney	0.06 RPM	15.59 RPM
SRP017611_liver	0.00 RPM	6.57 RPM
SRP030211_testis	0.45 RPM	28.97 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1648 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1648 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010331	1 retrocopy	retro_amel_716,
Bos taurus	ENSBTAG00000004820	1 retrocopy	retro_btau_1648 ,
Canis familiaris	ENSCAFG00000001437	1 retrocopy	retro_cfam_596,
Myotis lucifugus	ENSMLUG00000014315	1 retrocopy	retro_mluc_199,
Monodelphis domestica	ENSMODG00000019063	2 retrocopies	retro_mdom_1276, retro_mdom_2015,
Mustela putorius furo	ENSMPUG00000012997	1 retrocopy	retro_mputfur_1158,
Otolemur garnettii	ENSOGAG00000025463	1 retrocopy	retro_ogar_1639,