RetrogeneDB ID: retro_ecab_257

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 11:46958821..46959163(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOC
• Ensembl ID: ENSECAG00000010174
• Aliases: None
• Description: ras homolog family member C [Source:HGNC Symbol;Acc:669]

Sequence

>retro_ecab_257
TATTCAAGAACCAACACTCAAGAGAGTTACCAGCCAGGGTGTTTGAGAGCCACCTGGCAGACATGGAAGTGGACAGGAAG
CAGCTGGAACTGGCTCTGTGGGACATAGCTGGGCAGGAAGACTACGACCTCCTGAGGCCTCTCTCCTACCCACACTTCAG
CCTTATACCAATCTGCTTCTCTGTAGTTGCTGTAATAGTTTATAAAACATCGCAGTAAAAGGACCCCTGAGGTCCAACAT
GTCTACACTAATGTGCCCATCATCCTGGTGAACAAGAAGGACCTCCCCTACGATGAATGCAAAAGACAGTAAAACCTAAA
GAAGTCCCCAAAATGGCCTATA

Alignment

ORF - retro_ecab_257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.46 %
• Parental protein coverage: 59.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FSKDQFPEVYVP-TVFENYIADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSI-DSPDSL
          .S.....E.Y.P..VFE...AD.EVD.KQ.ELALWD.AGQEDYD.LRPLSYP....I..CFS......SL
Retrocopy YSRTNTQESYQP<RVFESHLADMEVDRKQLELALWDIAGQEDYDLLRPLSYPHFSLIPICFSV<SCCNSL

Parental  ENIP-EKWTPEVKHFCPNVPIILVGNKKDLRQDEHTRR-ELAKMKQEPV
          .NI...K.TPEV.H...NVPIILV.NKKDL..DE..R...L.K....P.
Retrocopy *NIA<SKRTPEVQHVYTNVPIILV-NKKDLPYDECKRQ*NLKKSPKWPI

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	96.93 RPM
SRP021940_cerebellum	0.00 RPM	25.14 RPM
SRP021940_embryo	0.00 RPM	118.48 RPM
SRP021940_placental_villous	0.00 RPM	197.30 RPM
SRP021940_synovial_membrane	0.00 RPM	168.39 RPM
SRP021940_testis	0.00 RPM	79.61 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_257 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_257 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_257 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014299	1 retrocopy	retro_btau_1171,
Canis familiaris	ENSCAFG00000013413	1 retrocopy	retro_cfam_1152,
Callithrix jacchus	ENSCJAG00000013657	2 retrocopies	retro_cjac_1657, retro_cjac_2027,
Equus caballus	ENSECAG00000010174	3 retrocopies	retro_ecab_112, retro_ecab_257 , retro_ecab_932,
Ficedula albicollis	ENSFALG00000000736	1 retrocopy	retro_falb_11,
Gorilla gorilla	ENSGGOG00000002741	2 retrocopies	retro_ggor_18, retro_ggor_732,
Macropus eugenii	ENSMEUG00000004807	1 retrocopy	retro_meug_37,
Monodelphis domestica	ENSMODG00000000981	1 retrocopy	retro_mdom_1245,
Otolemur garnettii	ENSOGAG00000027678	3 retrocopies	retro_ogar_2606, retro_ogar_3360, retro_ogar_58,
Sarcophilus harrisii	ENSSHAG00000001981	1 retrocopy	retro_shar_455,
Taeniopygia guttata	ENSTGUG00000017533	1 retrocopy	retro_tgut_11,
Tetraodon nigroviridis	ENSTNIG00000015041	1 retrocopy	retro_tnig_2,
Xenopus tropicalis	ENSXETG00000006898	1 retrocopy	retro_xtro_15,
Xiphophorus maculatus	ENSXMAG00000008103	1 retrocopy	retro_xmac_13,