RetrogeneDB ID: retro_btau_488

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:19563298..19563529(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRIP1
• Ensembl ID: ENSBTAG00000047229
• Aliases: None
• Description: Cysteine-rich protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q56K04]

Sequence

>retro_btau_488
ATGCCCATGTGCCCCAAGTGTGACATGGAGGTATACTTTGGTGAGTGGGTGACCTCCCTGGGGAAGGACTGGCATCAGCC
TTGCCTGAAGTGTGAGAATGTGGAAAGACACTGACCTTGGGGGAGTCATGCAGAACATGAAGGCAAGCCCTTTGGCAACC
ACCCCTGCTACACAACCATGTTTGGACCCAAAGGCTTTAGGCACAGTGGAGCTAAGAGCCACTCTTTCAAG

Alignment

ORF - retro_btau_488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKCPKCSKEVYFAERVTSLGKDWHRPCLKCE-KCGKTLTS-GGHAEHEGKPYCNHPCYAAMFGPKGFGR
          MP.CPKC..EVYF.E.VTSLGKDWH.PCLKCE..CGKTLT..G.HAEHEGKP..NHPCY..MFGPKGF..
Retrocopy MPMCPKCDMEVYFGEWVTSLGKDWHQPCLKCE<ECGKTLTL>GSHAEHEGKPFGNHPCYTTMFGPKGFRH

Parental  GGAESHTFK
          .GA.SH.FK
Retrocopy SGAKSHSFK

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	6.92 RPM
ERP005899_muscle	0.11 RPM	210.31 RPM
SRP017611_brain	0.05 RPM	4.80 RPM
SRP017611_kidney	0.12 RPM	12.15 RPM
SRP017611_liver	0.23 RPM	13.14 RPM
SRP030211_testis	0.10 RPM	14.90 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_488 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_488 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_488 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047229	1 retrocopy	retro_btau_488 ,
Callithrix jacchus	ENSCJAG00000019788	1 retrocopy	retro_cjac_163,
Dipodomys ordii	ENSDORG00000001365	1 retrocopy	retro_dord_70,
Homo sapiens	ENSG00000213145	1 retrocopy	retro_hsap_2550,
Gorilla gorilla	ENSGGOG00000027381	1 retrocopy	retro_ggor_3,
Macropus eugenii	ENSMEUG00000001631	1 retrocopy	retro_meug_93,
Macaca mulatta	ENSMMUG00000007158	2 retrocopies	retro_mmul_1479, retro_mmul_553,
Pongo abelii	ENSPPYG00000006209	1 retrocopy	retro_pabe_114,
Pan troglodytes	ENSPTRG00000033768	1 retrocopy	retro_ptro_43,
Pteropus vampyrus	ENSPVAG00000014240	1 retrocopy	retro_pvam_1304,
Rattus norvegicus	ENSRNOG00000027990	2 retrocopies	retro_rnor_2590, retro_rnor_2599,
Sarcophilus harrisii	ENSSHAG00000000807	1 retrocopy	retro_shar_341,
Tursiops truncatus	ENSTTRG00000004063	1 retrocopy	retro_ttru_1367,