RetrogeneDB ID: retro_ecab_266

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 11:42589674..42590085(-)
• Located in intron of: ENSECAG00000020083

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000016948
• Aliases: None
• Description: None

Sequence

>retro_ecab_266
ATGGCCGGTACAAAGCAGACTGGCCACAAATCAACGGGTAGTAAAGCACCAAGGAAGCAACTGGCTACAAAAGCCGCTTG
CAAGAGTGTGCCCCCTACTGGCAGGGTGAAGAAACCTCATTGTTACAAGCCTGGTACTGAGGTGCTCTGTGAAATTAGAC
GTTATCTGAAGTCCCCTGAACTTCTGATTGACAAACTTCCTTTCCAGCATCTGGTGCGAGAAATTGCTCAGGACTTCAAA
ACAGATCTATGCTTCCAAAGCGCAGCTATTGGTGCTTTGCAGGAAGCAAGTGAGGCCTATCTGGTATGCCTTTTTGAAGA
CACCAACCTGTGTGCTATCCATGCCAAATGTGTAATGATGATGCCAAAAGACATCCAGCTAGCAGCACGCCACATACATG
GAGAATGTGCT

Alignment

ORF - retro_ecab_266 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.02 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
          MA.TKQT..KSTG.KAPRKQLATKAA.KS.P.TG.VKKPH.Y.PGT..L.EIRRY.KS.ELLI.KLPFQ.
Retrocopy MAGTKQTGHKSTGSKAPRKQLATKAACKSVPPTGRVKKPHCYKPGTEVLCEIRRYLKSPELLIDKLPFQH

Parental  LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQL-ARRIRGERA
          LVREIAQDFKTDL.FQSAAIGALQEASEAYLV.LFEDTNLCAIHAK.V..MPKDIQL.AR.I.GE.A
Retrocopy LVREIAQDFKTDLCFQSAAIGALQEASEAYLVCLFEDTNLCAIHAKCVMMMPKDIQLAARHIHGECA

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	0.24 RPM	240.02 RPM
SRP021940_cerebellum	1.56 RPM	209.75 RPM
SRP021940_embryo	1.05 RPM	374.54 RPM
SRP021940_placental_villous	1.64 RPM	293.96 RPM
SRP021940_synovial_membrane	1.24 RPM	210.91 RPM
SRP021940_testis	0.51 RPM	786.89 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_266 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_266 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_266 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012702	10 retrocopies	retro_cjac_145, retro_cjac_198, retro_cjac_201, retro_cjac_224, retro_cjac_235, retro_cjac_238, retro_cjac_307, retro_cjac_334, retro_cjac_366, retro_cjac_68,
Dasypus novemcinctus	ENSDNOG00000024843	2 retrocopies	retro_dnov_1624, retro_dnov_775,
Equus caballus	ENSECAG00000006904	1 retrocopy	retro_ecab_916,
Equus caballus	ENSECAG00000016948	1 retrocopy	retro_ecab_266 ,
Homo sapiens	ENSG00000132475	11 retrocopies	retro_hsap_1212, retro_hsap_1552, retro_hsap_2180, retro_hsap_24, retro_hsap_2971, retro_hsap_3231, retro_hsap_3294, retro_hsap_3299, retro_hsap_389, retro_hsap_4236, retro_hsap_911,
Latimeria chalumnae	ENSLACG00000004118	1 retrocopy	retro_lcha_104,
Loxodonta africana	ENSLAFG00000008083	3 retrocopies	retro_lafr_837, retro_lafr_959, retro_lafr_99,
Microcebus murinus	ENSMICG00000002139	2 retrocopies	retro_mmur_36, retro_mmur_371,
Mustela putorius furo	ENSMPUG00000004555	4 retrocopies	retro_mputfur_389, retro_mputfur_82, retro_mputfur_99, retro_mputfur_990,
Oreochromis niloticus	ENSONIG00000019975	5 retrocopies	retro_onil_41, retro_onil_46, retro_onil_56, retro_onil_60, retro_onil_63,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Pan troglodytes	ENSPTRG00000009655	12 retrocopies	retro_ptro_1742, retro_ptro_1915, retro_ptro_2009, retro_ptro_2227, retro_ptro_2231, retro_ptro_2234, retro_ptro_2238, retro_ptro_2640, retro_ptro_2879, retro_ptro_631, retro_ptro_695, retro_ptro_830,
Tupaia belangeri	ENSTBEG00000016171	7 retrocopies	retro_tbel_3459, retro_tbel_3605, retro_tbel_3824, retro_tbel_3856, retro_tbel_4243, retro_tbel_4350, retro_tbel_674,