RetrogeneDB ID: retro_btau_1785

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:133023521..133024105(+)
• Located in intron of: ENSBTAG00000039195

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHP
• Ensembl ID: ENSBTAG00000027173
• Aliases: CHP1, CHP
• Description: Calcium-binding protein p22 [Source:UniProtKB/Swiss-Prot;Acc:Q3SYS6]

Sequence

>retro_btau_1785
ATGGGGTCTCAGGCTTCCATGTCACTGTGGAGGGAAGAGCTTGAGGAGGATCAAGACAGAGACCTGCTTCTCCCACAATC
AAATCATCTACCTCTACAGCCAGTTCACCAGCCTGGACAAAAGTGAGAATGGGACCCTCAGCTGGGAAGATTTCCAGTGG
ATTCCAGGACTTGTCATCAAGCCACTTGGGGACTGGCTCATCAGCGGCTTCTTTCCAGACGGAAAAGATCAGGCAGGCTT
CCATGGCTTCATAAAATCTTTGGCTCACTTCTGACCCACTGAAGATAGTGCAAAGTGCAAAGATAAGAATGGACCAGAAC
CACTTAACAGTCGAAGCAACAAACTGTACTTTGCTTTTCGACTATATGATTTGGATAAAAATGACAAAATCTTCCACAAT
GAGCTATTCCAGGTTCTTTGCATGATGGCTGGAGTGAATGTCTCGGATGAGCAGCTGGGTGGCATCACAGACAGGACCAT
TCAGGAGGCTGATCTAGAGAGGGATGGTGCCATATCTTTTGAAGAATTTGTTGAGGCTTTGGAGAAGGTGAACTGGCAAG
CAGAAAGTGAGCATCCAATTTCTT

Alignment

ORF - retro_btau_1785 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.39 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGSRASTLLRDEELEE-IKKETGFSHSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINA
          MGS.AS..L..EELEE.IK.ET.FSH.QI..LYS.FTSLDK.ENGTLS.EDFQ.IP.L.I.PLGD..I..
Retrocopy MGSQASMSLWREELEE>IKTETCFSHNQIIYLYSQFTSLDKSENGTLSWEDFQWIPGLVIKPLGDWLISG

Parental  FFPEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAFRLYDLDKDDKISRDELLQVL
          FFP.G.DQ..F.GF...LAHF.P.ED..K.KD.NGPEPLNSRSNKL.FAFRLYDLDK.DKI...EL.QVL
Retrocopy FFPDGKDQAGFHGFIKSLAHF*PTEDSAKCKDKNGPEPLNSRSNKLYFAFRLYDLDKNDKIFHNELFQVL

Parental  RMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVE-QKMSIRFL
          .MM.GVN.SDEQLG.I.DRTIQEAD...D.AISF.EFV..LEKV....QK.SI.FL
Retrocopy CMMAGVNVSDEQLGGITDRTIQEADLERDGAISFEEFVEALEKVNWQ>QKVSIQFL

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	22.06 RPM
ERP005899_muscle	0.00 RPM	131.02 RPM
SRP017611_brain	0.00 RPM	101.77 RPM
SRP017611_kidney	0.06 RPM	148.53 RPM
SRP017611_liver	0.00 RPM	30.35 RPM
SRP030211_testis	0.04 RPM	201.76 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1785 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1785 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1785 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Oryctolagus cuniculus	retro_ocun_68
Canis familiaris	retro_cfam_2136
Equus caballus	retro_ecab_1099

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010619	1 retrocopy	retro_btau_1660,
Bos taurus	ENSBTAG00000027173	1 retrocopy	retro_btau_1785 ,
Callithrix jacchus	ENSCJAG00000020761	1 retrocopy	retro_cjac_2396,
Equus caballus	ENSECAG00000019751	1 retrocopy	retro_ecab_1099,
Felis catus	ENSFCAG00000006346	1 retrocopy	retro_fcat_1964,
Gorilla gorilla	ENSGGOG00000007312	2 retrocopies	retro_ggor_1293, retro_ggor_2392,
Loxodonta africana	ENSLAFG00000014743	3 retrocopies	retro_lafr_221, retro_lafr_795, retro_lafr_838,
Oryctolagus cuniculus	ENSOCUG00000013832	1 retrocopy	retro_ocun_68,
Otolemur garnettii	ENSOGAG00000013099	2 retrocopies	retro_ogar_2442, retro_ogar_628,
Procavia capensis	ENSPCAG00000005419	1 retrocopy	retro_pcap_240,
Pongo abelii	ENSPPYG00000006370	2 retrocopies	retro_pabe_2749, retro_pabe_2925,
Pteropus vampyrus	ENSPVAG00000003150	1 retrocopy	retro_pvam_1207,