RetrogeneDB ID: retro_btau_1510

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:109162853..109163614(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: BLMH
• Ensembl ID: ENSBTAG00000021370
• Aliases: None
• Description: None

Sequence

>retro_btau_1510
TTCTTAAATGCTTTTGTGGACACAGCTCAGAAAAAGGAGCCTGAGGATGGTAGGCTGGTGCAGTATTTGCTTATGAATCC
TACCAATGATGGAGGACAATGGGATATGCTTGTCATATTGTTGAAAAATATGGTGTTATCCCTAAGAAGTGCTTCCCTGA
AACTTACACCACAGAGGCAACCAGAAGGATGAATGATATTCTGGATCACAAGATGAGAGAATTCTGCATATGACTACGGA
ATCTGGTACACACTGGTGCAACCAAAGAAGAAATCTCAGCCACACAGGACTCCATGATGGAGGAGATATTCAGAGTTGTA
TGCATCTGTTTGGGTAATCCACCAGAGACATTCATCTGGAAGTATGGAGACAAAGATAAAAACTATCAAAAGACTGGCCC
TATAACATCCTTGAAGTTTTACAGGGAACATGTCAAGCTGCTGTTCAATATGGAAGATAAGATTCGTTTAGTGAATGACC
CTCGGCCTCAGCACAAGTACAACAAACTTTACCCAGTGGACTATTTAAGCAATATGGTCAGAGGGAGAAAACCTCTATAA
CAACCAGCCCGTTGAGTTTTGAAAAAGATGGTTGCTGCCTCCATCAGAGATGGAGAGGCTGTATGGTTTGGCTGTGATGT
TGGGAAACACTTCAGTGGCAAACTGGGCCTCAGTGACGTGAACATCTGTGACCATGGGTTGGTGTTTGGCGTCTCCATTG
AGAACGTGAGTAAAGCTGAGAGGCTGACTTTCGGCGAGTCA

Alignment

ORF - retro_btau_1510 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.82 %
• Parental protein coverage: 55.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FLNAFVDTAQKKEPEDGRLVQYLLMNPANDGGQWDMLV-NIVEKYGVIPKKCFPETYTTEATRRMNDILN
          FLNAFVDTAQKKEPEDGRLVQYLLMNP.NDGGQWDMLV..IVEKYGVIPKKCFPETYTTEATRRMNDIL.
Retrocopy FLNAFVDTAQKKEPEDGRLVQYLLMNPTNDGGQWDMLV<HIVEKYGVIPKKCFPETYTTEATRRMNDILD

Parental  HKMREFCIRLRNLVHSGATKEEISATQDSMMEEIFRVVCICLGNPPETFTWEYRDKDKNYQKIGPITPLK
          HKMREFCI.LRNLVH.GATKEEISATQDSMMEEIFRVVCICLGNPPETF.W.Y.DKDKNYQK.GPIT.LK
Retrocopy HKMREFCI*LRNLVHTGATKEEISATQDSMMEEIFRVVCICLGNPPETFIWKYGDKDKNYQKTGPITSLK

Parental  FYRQHVKPLFNMEDKICLVNDPRPQHKYNKLYTVDYLSNMVGGRKTLYNNQPVDFLKKMVAA-SIKDGEA
          FYR.HVK.LFNMEDKI.LVNDPRPQHKYNKLY.VDYLSNMV.GRK.L...QP.....K...A.SI.DGEA
Retrocopy FYREHVKLLFNMEDKIRLVNDPRPQHKYNKLYPVDYLSNMVRGRKPL--*QPAR*VLKKMVAASIRDGEA

Parental  VWFGCDVGKHFNGKLGLSDMNVYDHELVFGVSMKNMNKAERLTFGES
          VWFGCDVGKHF.GKLGLSD.N..DH.LVFGVS..N..KAERLTFGES
Retrocopy VWFGCDVGKHFSGKLGLSDVNICDHGLVFGVSIENVSKAERLTFGES

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	12.40 RPM
ERP005899_muscle	0.00 RPM	35.32 RPM
SRP017611_brain	0.09 RPM	12.61 RPM
SRP017611_kidney	0.12 RPM	28.39 RPM
SRP017611_liver	0.00 RPM	22.95 RPM
SRP030211_testis	2.41 RPM	35.18 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1510 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1510 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1510 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021370	1 retrocopy	retro_btau_1510 ,
Callithrix jacchus	ENSCJAG00000013781	1 retrocopy	retro_cjac_2998,
Cavia porcellus	ENSCPOG00000005048	1 retrocopy	retro_cpor_896,
Macropus eugenii	ENSMEUG00000008938	1 retrocopy	retro_meug_2120,
Rattus norvegicus	ENSRNOG00000003563	1 retrocopy	retro_rnor_566,
Tursiops truncatus	ENSTTRG00000016341	1 retrocopy	retro_ttru_1915,
Vicugna pacos	ENSVPAG00000003571	1 retrocopy	retro_vpac_74,