RetrogeneDB ID: retro_ecab_264

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 11:24920309..24920680(-)
• Located in intron of: ENSECAG00000022092

Retrocopy information

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

Parental gene information

• Parental gene symbol: HINT1
• Ensembl ID: ENSECAG00000023180
• Aliases: None
• Description: histidine triad nucleotide binding protein 1 [Source:HGNC Symbol;Acc:4912]

Sequence

>retro_ecab_264
ATGAGATCACTGAGGCTCAGGCCGCTTGGCCTGGTGGGGACACGATCTTCCGGAAGATCATTCACAAGGAAATCCCAGCC
AAAATCATTTTTGAGGATGACCAGTGCCTTGCTTTCCGTGACATTTCCCCTCAAGTGCCAACACATTTTCTGGTGATACC
CAAAAAACATATATCCCAGATTTCTGTAGCAGAAGATGATGATGAAAGTCTTCTTGGACATTTAATGATTGTTGGCAAGA
AATGTGCTGCTGATCTGGGCCTGAAGAACGGTTACCGAATGGTGGTGAATGAAGGTTCAGATGGGGGCCAGTCTGTCTAT
CATGTTCATCTCCATGTGCTTGGAGGTTGGCAGATGAATTGGCCTCCTGGT

Alignment

ORF - retro_ecab_264 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.8 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRSPRLRPLGLVGTRSSGRSFAKESQPK-IIFEDDQCLAFHDISPQAPTHFLVIPKKHISQISVAEDDDE
          MRS.RLRPLGLVGTRSSGRSF...SQPK.IIFEDDQCLAF.DISPQ.PTHFLVIPKKHISQISVAEDDDE
Retrocopy MRSLRLRPLGLVGTRSSGRSFTRKSQPK<IIFEDDQCLAFRDISPQVPTHFLVIPKKHISQISVAEDDDE

Parental  SLLGHLMIVGKKCAADLGLKKGYRMVVNEGSDGGQSVYHVHLHVLGGRQMNWPPG
          SLLGHLMIVGKKCAADLGLK.GYRMVVNEGSDGGQSVYHVHLHVLGG.QMNWPPG
Retrocopy SLLGHLMIVGKKCAADLGLKNGYRMVVNEGSDGGQSVYHVHLHVLGGWQMNWPPG

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
SRP021940_articular_cartilage	2.42 RPM	32.70 RPM
SRP021940_cerebellum	4.41 RPM	77.48 RPM
SRP021940_embryo	3.17 RPM	43.24 RPM
SRP021940_placental_villous	4.81 RPM	44.50 RPM
SRP021940_synovial_membrane	2.31 RPM	36.04 RPM
SRP021940_testis	4.03 RPM	47.25 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_264 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_264 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_264 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032152	1 retrocopy	retro_cfam_473,
Callithrix jacchus	ENSCJAG00000014398	3 retrocopies	retro_cjac_134, retro_cjac_142, retro_cjac_87,
Equus caballus	ENSECAG00000023180	3 retrocopies	retro_ecab_264 , retro_ecab_356, retro_ecab_550,
Erinaceus europaeus	ENSEEUG00000008175	1 retrocopy	retro_eeur_582,
Echinops telfairi	ENSETEG00000010127	1 retrocopy	retro_etel_1,
Homo sapiens	ENSG00000169567	1 retrocopy	retro_hsap_3913,
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,
Macaca mulatta	ENSMMUG00000009985	2 retrocopies	retro_mmul_1896, retro_mmul_759,
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,
Mus musculus	ENSMUSG00000020267	1 retrocopy	retro_mmus_718,
Nomascus leucogenys	ENSNLEG00000012431	1 retrocopy	retro_nleu_2155,
Oryctolagus cuniculus	ENSOCUG00000006607	5 retrocopies	retro_ocun_1374, retro_ocun_214, retro_ocun_643, retro_ocun_821, retro_ocun_968,
Otolemur garnettii	ENSOGAG00000008850	2 retrocopies	retro_ogar_1028, retro_ogar_1599,
Procavia capensis	ENSPCAG00000004737	1 retrocopy	retro_pcap_407,
Pongo abelii	ENSPPYG00000015747	2 retrocopies	retro_pabe_3189, retro_pabe_909,
Pan troglodytes	ENSPTRG00000017206	1 retrocopy	retro_ptro_2661,
Rattus norvegicus	ENSRNOG00000000622	1 retrocopy	retro_rnor_98,
Sarcophilus harrisii	ENSSHAG00000005834	2 retrocopies	retro_shar_113, retro_shar_301,
Ictidomys tridecemlineatus	ENSSTOG00000027920	4 retrocopies	retro_itri_1129, retro_itri_114, retro_itri_177, retro_itri_260,