RetrogeneDB ID: retro_btau_531

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 13:51003523..51003857(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000007199
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HBEGF
• Ensembl ID: ENSBTAG00000021766
• Aliases: HBEGF, DTR, HB-EGF
• Description: proheparin-binding EGF-like growth factor precursor [Source:RefSeq peptide;Acc:NP_001137562]

Sequence

>retro_btau_531
CAAGGAGGAGGGAAGAAGAGAAACCCATGTCTTCGGAGATACAAGGACTTCTGCATCCACGGAGAATGCAAATACGTGAA
GGAGCTCCGGGTTCCAACCTGCATCTGCTACCCAGGTTATTATGGAGAGAGGTGCCATGGGCTGAGCCTCCCAGTGAAAA
ATCGCTTATATACATACGTGCGATCACACAACCATCCTGGTTGTGGTGGCTGTGGTGCTGTCATCCGTCTGTCTGCTGGT
CATCATGCGGCTTCTCATGTTTTGGTACTACAGGAGAGGAGGTTATGACGTGGAAAATGAAGAGAAAGTGAAGTTGGGTG
TGACTACGTCCCAC

Alignment

ORF - retro_btau_531 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.61 %
• Parental protein coverage: 52.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KGLGKKRNPCLRRYKDFCIHGECKYVKELRVPTCICHPGYHGERCHGLSLPVKNRLYTYDHT-TILVV-V
          .G.GKKRNPCLRRYKDFCIHGECKYVKELRVPTCIC.PGY.GERCHGLSLPVKNRLYTY....T...V.V
Retrocopy QGGGKKRNPCLRRYKDFCIHGECKYVKELRVPTCICYPGYYGERCHGLSLPVKNRLYTYVRS>TTILVVV

Parental  AVVLSSVCLLVIMGLLMFWYHRRGGYDVENEEKVKLGMTTSH
          AVVLSSVCLLVIM.LLMFWY.RRGGYDVENEEKVKLG.TTSH
Retrocopy AVVLSSVCLLVIMRLLMFWYYRRGGYDVENEEKVKLGVTTSH

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	0.65 RPM
ERP005899_muscle	0.00 RPM	1.32 RPM
SRP017611_brain	0.00 RPM	4.57 RPM
SRP017611_kidney	0.00 RPM	3.85 RPM
SRP017611_liver	0.00 RPM	1.28 RPM
SRP030211_testis	0.01 RPM	0.79 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_531 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_531 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_531 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021766	1 retrocopy	retro_btau_531 ,