RetrogeneDB ID: retro_btau_1740

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:42441679..42442015(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.20582
• Ensembl ID: ENSBTAG00000018527
• Aliases: None
• Description: hepatoma-derived growth factor-related protein 3 [Source:RefSeq peptide;Acc:NP_001178297]

Sequence

>retro_btau_1740
ATGAAGGGCTACCTGCACTAACCCACCGGGATTGATGAACTCCCAGAGGGAGCTGTGAAGCCTCCAGGCAGTAAGTACCC
TATCTTCTTTTTGGCACCTACAAAACTGCTTTTCTAGGTCCCAAACAGCTCTTCCCTTACAAGGAATACAAAGAAGTTTG
GAAAATCAAACAAATGTAAAGAATTTAATGAAGGATTGTGGGAAATAGAAAATAACCCAGGAGTAAAGTTTACTGGATAT
CAGGCAATTCAGCCACAGAGCTCTTCAGAAACTGAGGGAGAAGGTGGGAATACCACTGACACAAGCAGTGAGGAAGAAGG
TGACAGAGTAGAGGAA

Alignment

ORF - retro_btau_1740 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.45 %
• Parental protein coverage: 61.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKGYPHWPARIDELPEGAVKPPANKYPIFFFGTHETAFLGPKDLFPYKEYKDKFGKSNKRKGFNEGLWEI
          MKGY.H.P..IDELPEGAVKPP..KYPIFF.......F..P.........K.KFGKSNK.K.FNEGLWEI
Retrocopy MKGYLH*PTGIDELPEGAVKPPGSKYPIFFLAPTKLLF*VPNSSSLTRNTK-KFGKSNKCKEFNEGLWEI

Parental  ENNPGVKFTGYQAIQQQSSSETEGEGGNTADASSEEEGDRVEE
          ENNPGVKFTGYQAIQ.QSSSETEGEGGNT.D.SSEEEGDRVEE
Retrocopy ENNPGVKFTGYQAIQPQSSSETEGEGGNTTDTSSEEEGDRVEE

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	2.16 RPM
ERP005899_muscle	0.00 RPM	4.43 RPM
SRP017611_brain	0.00 RPM	28.92 RPM
SRP017611_kidney	0.00 RPM	17.78 RPM
SRP017611_liver	0.00 RPM	0.76 RPM
SRP030211_testis	0.02 RPM	51.22 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1740 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1740 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1740 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018527	1 retrocopy	retro_btau_1740 ,
Bos taurus	ENSBTAG00000039793	1 retrocopy	retro_btau_216,
Callithrix jacchus	ENSCJAG00000015775	1 retrocopy	retro_cjac_4165,
Dasypus novemcinctus	ENSDNOG00000003696	2 retrocopies	retro_dnov_619, retro_dnov_819,
Echinops telfairi	ENSETEG00000010466	1 retrocopy	retro_etel_1234,
Loxodonta africana	ENSLAFG00000002512	1 retrocopy	retro_lafr_676,
Ictidomys tridecemlineatus	ENSSTOG00000028389	2 retrocopies	retro_itri_292, retro_itri_864,
Tursiops truncatus	ENSTTRG00000004950	1 retrocopy	retro_ttru_1471,
Vicugna pacos	ENSVPAG00000004599	1 retrocopy	retro_vpac_380,