RetrogeneDB ID: retro_btau_1129

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 27:9792194..9792524(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HINT2
• Ensembl ID: ENSBTAG00000011444
• Aliases: None
• Description: Histidine triad nucleotide-binding protein 2, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q8SQ21]

Sequence

>retro_btau_1129
GCTGGCTGGATGGTGCTGCCCTCTGGGCCCTGCATGGCCACACTGGGCGGTGGCAGTGTTGGGACCAGGGGTGGGGAGGG
GGCGCAGGTCAGAGGAGCTGCAGGTGTGACTCACCGCAGTCAAGTGGCTGAGGGCCAGCACACAGGCCCTGGGGCAGCAG
CCCTAACCGTCTTCTCCTGGATCTTGGATCGAAGCCTCCCATCTGGCATTTTATATGAGGACCAGATGTTTCTCACGTTC
TGTGATGTGGCCCCTTAGGCTCCTGTGCTCTTTCTGGTAATTCCTAAGAAGTCCATTTCTCAGGTTAACCAGGTTGAAGA
CAACCAACAG

Alignment

ORF - retro_btau_1129 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.45 %
• Parental protein coverage: 65.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAVVLAAGLCVARR---AVAVAGPRGVQVRGAAGVTDGDEVAKAQQAAPGGAAPTIFSRILDRSLPADI
          A...VL..G.C.A......V...G..G.QVRGAAGVT....VA..Q...PG.AA.T.FS.ILDRSLP..I
Retrocopy AGWMVLPSGPCMATLGGGSVGTRGGEGAQVRGAAGVTHRSQVAEGQHTGPGAAALTVFSWILDRSLPSGI

Parental  LYEDQQCLAFRDVAPQAPVHFLVIPKKPIPRISQAEEEDQ
          LYEDQ..L.F.DVAP.APV.FLVIPKK.I....Q.E...Q
Retrocopy LYEDQMFLTFCDVAP*APVLFLVIPKKSISQVNQVEDNQQ

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	27.11 RPM
ERP005899_muscle	0.00 RPM	51.84 RPM
SRP017611_brain	0.00 RPM	11.28 RPM
SRP017611_kidney	0.00 RPM	48.01 RPM
SRP017611_liver	0.00 RPM	33.53 RPM
SRP030211_testis	0.00 RPM	37.36 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1129 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1129 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1129 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010959	5 retrocopies	retro_btau_1036, retro_btau_1149, retro_btau_1782, retro_btau_926, retro_btau_978,
Bos taurus	ENSBTAG00000011444	1 retrocopy	retro_btau_1129 ,
Callithrix jacchus	ENSCJAG00000010068	1 retrocopy	retro_cjac_1343,
Cavia porcellus	ENSCPOG00000000419	1 retrocopy	retro_cpor_181,
Dasypus novemcinctus	ENSDNOG00000009083	2 retrocopies	retro_dnov_201, retro_dnov_854,
Echinops telfairi	ENSETEG00000017929	1 retrocopy	retro_etel_486,
Homo sapiens	ENSG00000137133	1 retrocopy	retro_hsap_2603,
Gorilla gorilla	ENSGGOG00000011265	1 retrocopy	retro_ggor_1823,
Loxodonta africana	ENSLAFG00000015022	1 retrocopy	retro_lafr_737,
Macaca mulatta	ENSMMUG00000016337	1 retrocopy	retro_mmul_1509,
Nomascus leucogenys	ENSNLEG00000026914	1 retrocopy	retro_nleu_1534,
Oryctolagus cuniculus	ENSOCUG00000027206	1 retrocopy	retro_ocun_66,
Otolemur garnettii	ENSOGAG00000011830	1 retrocopy	retro_ogar_765,
Pongo abelii	ENSPPYG00000019082	1 retrocopy	retro_pabe_2310,
Pan troglodytes	ENSPTRG00000020923	1 retrocopy	retro_ptro_1754,
Pteropus vampyrus	ENSPVAG00000003028	1 retrocopy	retro_pvam_842,
Tupaia belangeri	ENSTBEG00000013020	1 retrocopy	retro_tbel_4676,
Tarsius syrichta	ENSTSYG00000002700	7 retrocopies	retro_tsyr_1210, retro_tsyr_1356, retro_tsyr_1483, retro_tsyr_1485, retro_tsyr_311, retro_tsyr_468, retro_tsyr_48,
Tursiops truncatus	ENSTTRG00000011932	1 retrocopy	retro_ttru_1302,