RetrogeneDB ID: retro_btau_1782

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:128408666..128409038(+)
• Located in intron of: ENSBTAG00000000419

Retrocopy information

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

Parental gene information

• Parental gene symbol: HINT1
• Ensembl ID: ENSBTAG00000010959
• Aliases: None
• Description: Histidine triad nucleotide-binding protein 1 [Source:UniProtKB/Swiss-Prot;Acc:P62958]

Sequence

>retro_btau_1782
GATGAGATCACCAAGGCTCAGGTCGCCCGGCCTGGCGGCGACACGATCTTCGGGAAGATCATTCGCAGGGAAATCCCAGC
CAAAATCATTTATGAGGATGACCAGTGTCTTGCTTTCCATGACATTTCCCCTCAAGCACCAACACATTTTCTGGTGATAC
CCAAGAAATATATATCTCAGATTTCTGCAGCAGAAGATGATGATGAAAGTCTTCTTGGGCATTTGATGATTGTTGGCAAG
AAATGTGCTGCTGATCTGGGCCTGAAGAAGGGCTATCGAATGGTGGTGAATGAAGGTTCAGATGGGGGCCAGTCTGTCTA
TCATGTTCATCTCCATGTTCTTGGAGGTCGGCAGATGAACTGGCCTCCTGGT

Alignment

ORF - retro_btau_1782 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.39 %
• Parental protein coverage: 98.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DEIAKAQVARPGGDTIFGKIIRKEIPAKIIYEDDQCLAFHDISPQAPTHFLVIPKKYISQISAAEDDDES
          DEI.KAQVARPGGDTIFGKIIR.EIPAKIIYEDDQCLAFHDISPQAPTHFLVIPKKYISQISAAEDDDES
Retrocopy DEITKAQVARPGGDTIFGKIIRREIPAKIIYEDDQCLAFHDISPQAPTHFLVIPKKYISQISAAEDDDES

Parental  LLGHLMIVGKKCAADLGLKKGYRMVVNEGSDGGQSVYHVHLHVLGGRQMNWPPG
          LLGHLMIVGKKCAADLGLKKGYRMVVNEGSDGGQSVYHVHLHVLGGRQMNWPPG
Retrocopy LLGHLMIVGKKCAADLGLKKGYRMVVNEGSDGGQSVYHVHLHVLGGRQMNWPPG

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	1.37 RPM	34.97 RPM
ERP005899_muscle	0.32 RPM	79.71 RPM
SRP017611_brain	0.32 RPM	21.47 RPM
SRP017611_kidney	2.73 RPM	71.66 RPM
SRP017611_liver	0.23 RPM	22.43 RPM
SRP030211_testis	0.28 RPM	39.46 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1782 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1782 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1782 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017774	4 retrocopies	retro_amel_1426, retro_amel_1657, retro_amel_460, retro_amel_511,
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,
Canis familiaris	ENSCAFG00000032152	1 retrocopy	retro_cfam_473,
Callithrix jacchus	ENSCJAG00000014398	3 retrocopies	retro_cjac_134, retro_cjac_142, retro_cjac_87,
Echinops telfairi	ENSETEG00000010127	1 retrocopy	retro_etel_1,
Gorilla gorilla	ENSGGOG00000011967	1 retrocopy	retro_ggor_89,
Macropus eugenii	ENSMEUG00000005368	2 retrocopies	retro_meug_1001, retro_meug_848,
Myotis lucifugus	ENSMLUG00000001091	2 retrocopies	retro_mluc_1388, retro_mluc_2100,
Monodelphis domestica	ENSMODG00000028727	3 retrocopies	retro_mdom_102, retro_mdom_1741, retro_mdom_286,
Mustela putorius furo	ENSMPUG00000011639	4 retrocopies	retro_mputfur_1337, retro_mputfur_1376, retro_mputfur_45, retro_mputfur_93,
Oryctolagus cuniculus	ENSOCUG00000006607	5 retrocopies	retro_ocun_1374, retro_ocun_214, retro_ocun_643, retro_ocun_821, retro_ocun_968,
Rattus norvegicus	ENSRNOG00000000622	1 retrocopy	retro_rnor_98,
Sarcophilus harrisii	ENSSHAG00000005834	2 retrocopies	retro_shar_113, retro_shar_301,
Sus scrofa	ENSSSCG00000014264	2 retrocopies	retro_sscr_371, retro_sscr_894,
Ictidomys tridecemlineatus	ENSSTOG00000027920	4 retrocopies	retro_itri_1129, retro_itri_114, retro_itri_177, retro_itri_260,
Tursiops truncatus	ENSTTRG00000008653	4 retrocopies	retro_ttru_1364, retro_ttru_1660, retro_ttru_217, retro_ttru_349,