RetrogeneDB ID: retro_ecab_112

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 15:74750987..74751578(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000002668
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

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_112
ATGGCGGCCATCCGCAAGAAGCTGGTGGTGGTGGGCGACGGCGCGTGCGGCAAGACGTGCCTGCTGATCGTGTTCAGTAA
GGACGAGTTCCCCGAGGTGTACGTGCCTACCGTCTTTGAGAACTATGTGGCCGACATCGAGGTGGACGGCAAGCAAGTGG
AGCTGGCGCTGTGGGATACGGCGGGCCAGGAGGACTACGACCGCCTGCGGCCGCTCTCCTACCCGGACACCGACGTGATC
CTCATGTGCTTCTCGGTGGACAGCCCGGATTCGCTGGAGAACATCCCCGAGAAGTGGGTGCCCGAGGTGAAGCACTTCTG
CCCTAACGTGCCCATCATCCTGGTGGCCAACAAGAAAGACCTGCGCAGCGACGAGCACGTCCGCACAGAGCTCGCCCGCA
TGAAGCAGGAACCCGTGCGCACAGATGACGGCCGCGCCATGGCCGTGCGCATCCAAGCCTACGACTACCTCGAGTGCTCG
GCTAAGACCAAGGAGGGCGTGCGCGAGGTCTTCGAGACGGCCACGCGCGCCGCGCTGCAGAAGCGCTACGGCTCCCAGAA
CGGCTGCATCAACTGCTGCAAGGTGCTATGA

Alignment

ORF - retro_ecab_112 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.79 %
• Parental protein coverage: 98.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYIADIEVDGKQVELALWDTAGQEDYDRLR
          MAAIRKKLV.VGDGACGKTCLLIVFSKD.FPEVYVPTVFENY.ADIEVDGKQVELALWDTAGQEDYDRLR
Retrocopy MAAIRKKLVVVGDGACGKTCLLIVFSKDEFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLR

Parental  PLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRQDEHTRRELAKMKQEPVR
          PLSYPDTDVILMCFS.DSPDSLENIPEKW.PEVKHFCPNVPIILV.NKKDLR.DEH.R.ELA.MKQEPVR
Retrocopy PLSYPDTDVILMCFSVDSPDSLENIPEKWVPEVKHFCPNVPIILVANKKDLRSDEHVRTELARMKQEPVR

Parental  SEEGRDMANRISAFGYLECSAKTKEGVREVFEMATRAGLQVRKNKRRRGC
          ...GR.MA.RI.A..YLECSAKTKEGVREVFE.ATRA.LQ.R......GC
Retrocopy TDDGRAMAVRIQAYDYLECSAKTKEGVREVFETATRAALQKRYGS-QNGC

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	21.72 RPM	96.93 RPM
SRP021940_cerebellum	118.93 RPM	25.14 RPM
SRP021940_embryo	56.95 RPM	118.48 RPM
SRP021940_placental_villous	344.91 RPM	197.30 RPM
SRP021940_synovial_membrane	160.54 RPM	168.39 RPM
SRP021940_testis	18.74 RPM	79.61 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_112 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_112 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_108
Pan troglodytes	retro_ptro_10
Gorilla gorilla	retro_ggor_18
Macaca mulatta	retro_mmul_977
Bos taurus	retro_btau_206
Canis familiaris	retro_cfam_186

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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,