RetrogeneDB ID: retro_cfam_1152

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 24:35234409..35234810(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOC
• Ensembl ID: ENSCAFG00000013413
• Aliases: None
• Description: ras homolog family member C [Source:HGNC Symbol;Acc:669]

Sequence

>retro_cfam_1152
GCCCCAGCCATGGCTGCGATCAGAAAGAAGCTAGTGATTGTGGGAGATGGAGCCTGTGGGAAGACCTGCCTCCTCATCGT
CTTCAGCAAGGATCAGTTCCCAGAGGTCTGTGTCCCCACTGTCTTTGAGAACTACGTCACGGACATAGAGGTGGACGGCA
AGCAGGGGGAACTGGCTCTATGGGACACGGCTGGGCAGGAAGACTATGATCGCCTACGGCCTCTCTCCTACCCGGACACT
GATGTCATCCTCATGTGCTTCTCCATCAACAGCCCCGACAGCCTGGAAAACATTCCTGAGAAATGGACCCCAGAGGTGAA
GCATTCCTGCCCCAACGTGCCCATCACCGCAGTGGGGAACAGGAGAGAGCTGGCCAAGATGAAGCAGGAGCCCGTGCGAT
C

Alignment

ORF - retro_cfam_1152 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 65.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  APAMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYIADIEVDGKQVELALWDTAGQEDYD
          APAMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEV.VPTVFENY..DIEVDGKQ.ELALWDTAGQEDYD
Retrocopy APAMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVCVPTVFENYVTDIEVDGKQGELALWDTAGQEDYD

Parental  RLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLR-QDEHTRREL
          RLRPLSYPDTDVILMCFSI.SPDSLENIPEKWTPEVKH.CPNVPI..VGN...L..QDE...R..
Retrocopy RLRPLSYPDTDVILMCFSINSPDSLENIPEKWTPEVKHSCPNVPITAVGNRRELA<QDEAGARAI

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
SRP012049_cerebellum	0.71 RPM	9.20 RPM
SRP017611_brain	0.32 RPM	9.21 RPM
SRP017611_kidney	6.67 RPM	147.39 RPM
SRP017611_liver	1.52 RPM	38.14 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1152 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1152 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1152 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014299	1 retrocopy	retro_btau_1171,
Canis familiaris	ENSCAFG00000013413	1 retrocopy	retro_cfam_1152 ,
Canis familiaris	ENSCAFG00000023066	2 retrocopies	retro_cfam_1652, retro_cfam_186,
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,