RetrogeneDB ID: retro_btau_438

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:46404613..46404925(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000047637
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ERH
• Ensembl ID: ENSBTAG00000017798
• Aliases: None
• Description: Enhancer of rudimentary homolog [Source:UniProtKB/Swiss-Prot;Acc:Q3SZC0]

Sequence

>retro_btau_438
ATGTCTCACACCATCTTGCTGGTACAGCCTACCAAGAGGCCAGAAGGCAGAACTTACGCTGACTATGAATCTGTGAATGA
GTGTATGGAAGGTGTTTGTAAAATGTATGAAGAATATCTGAAGAGAATGAATCCCAACAGCCCCTCTATCACATATGATA
TCAGTCAGTTGTTTGATTTTATTGATGACCTGGCAGACCTCAGCTGCCTTGTTTACCGAGCTGATACCCAGACATACCAG
CCTTATAACAAAGATTGGATTAAAGAGAAGATCTACGTGCTCCTTCGTGGACAGGCCCAACAGGCTGGGAAA

Alignment

ORF - retro_btau_438 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.08 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSHTILLVQPTKRPEGRTYADYESVNECMEGVCKMYEEHLKRMNPNSPSITYDISQLFDFIDDLADLSCL
          MSHTILLVQPTKRPEGRTYADYESVNECMEGVCKMYEE.LKRMNPNSPSITYDISQLFDFIDDLADLSCL
Retrocopy MSHTILLVQPTKRPEGRTYADYESVNECMEGVCKMYEEYLKRMNPNSPSITYDISQLFDFIDDLADLSCL

Parental  VYRADTQTYQPYNKDWIKEKIYVLLRRQAQQAGK
          VYRADTQTYQPYNKDWIKEKIYVLLR.QAQQAGK
Retrocopy VYRADTQTYQPYNKDWIKEKIYVLLRGQAQQAGK

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	28.19 RPM
ERP005899_muscle	0.16 RPM	51.15 RPM
SRP017611_brain	0.05 RPM	15.94 RPM
SRP017611_kidney	0.06 RPM	24.48 RPM
SRP017611_liver	0.00 RPM	15.55 RPM
SRP030211_testis	0.58 RPM	75.58 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_438 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_438 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_438 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017798	4 retrocopies	retro_btau_1260, retro_btau_438 , retro_btau_651, retro_btau_795,
Callithrix jacchus	ENSCJAG00000014940	2 retrocopies	retro_cjac_209, retro_cjac_846,
Equus caballus	ENSECAG00000019178	1 retrocopy	retro_ecab_45,
Erinaceus europaeus	ENSEEUG00000007758	6 retrocopies	retro_eeur_105, retro_eeur_108, retro_eeur_115, retro_eeur_116, retro_eeur_185, retro_eeur_546,
Echinops telfairi	ENSETEG00000016172	5 retrocopies	retro_etel_1122, retro_etel_1451, retro_etel_715, retro_etel_716, retro_etel_975,
Homo sapiens	ENSG00000100632	2 retrocopies	retro_hsap_3594, retro_hsap_3799,
Myotis lucifugus	ENSMLUG00000011879	1 retrocopy	retro_mluc_142,
Oryctolagus cuniculus	ENSOCUG00000004636	1 retrocopy	retro_ocun_42,
Ochotona princeps	ENSOPRG00000000086	2 retrocopies	retro_opri_1140, retro_opri_519,
Pongo abelii	ENSPPYG00000005939	2 retrocopies	retro_pabe_2954, retro_pabe_3104,
Sus scrofa	ENSSSCG00000002307	1 retrocopy	retro_sscr_748,
Tursiops truncatus	ENSTTRG00000013963	2 retrocopies	retro_ttru_1671, retro_ttru_614,
Vicugna pacos	ENSVPAG00000006444	1 retrocopy	retro_vpac_423,