RetrogeneDB ID: retro_ecab_356

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 16:12288741..12289088(+)
• Located in intron of: None

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_356
AGGCTCAGGCCACCCAACCAGATAACAACACGATCTTCAGGAAGAATACCTGCAAGGAAATCTCGGCCAAAAGTCATTTT
TGAGGATGACTGACATCTTGCTTTCCATGATATTTTCCTTCAAGCACCAACACATTTTGTGGTGACATCTAAGAAACAGG
TTTCTCGGATTTCTGTAGCAGAGGTGATGATAAAAGTCTTCTTGGACATTTAATGATTGTTGGTAGGAAATGTGCTGCTG
CTCTGGGCCTGAAGAAGGGTTGTGGAATGGCGGTGAAGGAAGGTTCCAGTAAGGGACAGGCTGGCTGTCACTTTCATCCC
CGTGTTCCTAGAAGTCAGCAGATGAAT

Alignment

ORF - retro_ecab_356 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.1 %
• Parental protein coverage: 93.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLRPLGLVGTRSSGRSFAKESQPKIIFEDDQCLAFHDISPQAPTHFLVIPKKHISQISVAE-DDDESLLG
          RLRP.....TRSSGR..A..S.PK.IFEDD..LAFHDI..QAPTHF.V..KK..S.ISVAE..DD.SLLG
Retrocopy RLRPPNQITTRSSGRIPARKSRPKVIFEDD*HLAFHDIFLQAPTHFVVTSKKQVSRISVAE<GDDKSLLG

Parental  HLMIVGKKCAADLGLKKGYRMVVNEGSDGGQSVYHVHLHVLGGRQMN
          HLMIVG.KCAA.LGLKKG..M.V.EGS..GQ...H.H..V....QMN
Retrocopy HLMIVGRKCAAALGLKKGCGMAVKEGSSKGQAGCHFHPRVPRSQQMN

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	0.00 RPM	32.70 RPM
SRP021940_cerebellum	0.00 RPM	77.48 RPM
SRP021940_embryo	0.00 RPM	43.24 RPM
SRP021940_placental_villous	0.00 RPM	44.50 RPM
SRP021940_synovial_membrane	0.00 RPM	36.04 RPM
SRP021940_testis	0.00 RPM	47.25 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_356 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_356 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_356 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_371

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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,