RetrogeneDB ID: retro_btau_312

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:128005243..128005412(-)
• Located in intron of: ENSBTAG00000006222

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM32A
• Ensembl ID: ENSBTAG00000046846
• Aliases: None
• Description: Protein FAM32A [Source:UniProtKB/Swiss-Prot;Acc:A6QR31]

Sequence

>retro_btau_312
GACAAGGGTACTTCCACACAGTTGGCCTTCGAGGAGATGCAATAGAAATGGCAAGTGGGGAGGATCCTGAAGAAAGCTTC
CCAAACTCACAAGCTGAAAGCAGAGGGCTCAAGAGGCACCTGGACACACTCACTAGCACCGTGACACGCCCCGAGTGCCC
TGGGGGAAG

Alignment

ORF - retro_btau_312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.32 %
• Parental protein coverage: 50.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DKRTPAQAAFEKMQEKRQMERILKKASKTHKQRVE-DFNRHLDTLTE-HYDIPKVSWTK
          DK.T..Q.AFE.MQ.K.Q..RILKKAS.THK...E....RHLDTLT..H.D.P.V.W.K
Retrocopy DKGTSTQLAFEEMQ*KWQVGRILKKASQTHKLKAE<GLKRHLDTLTS<HRDTPRVPWGK

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	19.97 RPM
ERP005899_muscle	0.00 RPM	51.10 RPM
SRP017611_brain	0.00 RPM	52.12 RPM
SRP017611_kidney	0.00 RPM	57.08 RPM
SRP017611_liver	0.00 RPM	38.74 RPM
SRP030211_testis	0.05 RPM	59.56 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_312 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_312 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_312 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046846	1 retrocopy	retro_btau_312 ,
Callithrix jacchus	ENSCJAG00000014097	4 retrocopies	retro_cjac_15, retro_cjac_2459, retro_cjac_288, retro_cjac_979,
Homo sapiens	ENSG00000105058	4 retrocopies	retro_hsap_1116, retro_hsap_1950, retro_hsap_2541, retro_hsap_693,
Gorilla gorilla	ENSGGOG00000022418	4 retrocopies	retro_ggor_1420, retro_ggor_1587, retro_ggor_592, retro_ggor_872,
Loxodonta africana	ENSLAFG00000009394	1 retrocopy	retro_lafr_654,
Microcebus murinus	ENSMICG00000013721	3 retrocopies	retro_mmur_1449, retro_mmur_252, retro_mmur_500,
Myotis lucifugus	ENSMLUG00000000585	2 retrocopies	retro_mluc_2147, retro_mluc_59,
Monodelphis domestica	ENSMODG00000014904	1 retrocopy	retro_mdom_1401,
Mustela putorius furo	ENSMPUG00000016048	1 retrocopy	retro_mputfur_1493,
Mus musculus	ENSMUSG00000003039	2 retrocopies	retro_mmus_1612, retro_mmus_3017,
Nomascus leucogenys	ENSNLEG00000005441	3 retrocopies	retro_nleu_192, retro_nleu_2227, retro_nleu_2790,
Oryctolagus cuniculus	ENSOCUG00000002238	1 retrocopy	retro_ocun_1275,
Otolemur garnettii	ENSOGAG00000027763	2 retrocopies	retro_ogar_3348, retro_ogar_949,
Pan troglodytes	ENSPTRG00000010641	4 retrocopies	retro_ptro_1304, retro_ptro_1480, retro_ptro_497, retro_ptro_684,
Rattus norvegicus	ENSRNOG00000039528	1 retrocopy	retro_rnor_105,
Sus scrofa	ENSSSCG00000013855	2 retrocopies	retro_sscr_292, retro_sscr_870,
Tarsius syrichta	ENSTSYG00000009106	1 retrocopy	retro_tsyr_418,