RetrogeneDB ID: retro_xtro_15

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL172736.1:1735509..1736100(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXETG00000026772
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: rhoc
• Ensembl ID: ENSXETG00000006898
• Aliases: None
• Description: ras homolog gene family, member C [Source:Jamboree;Acc:XB-GENE-941426]

Sequence

>retro_xtro_15
ATGGCCGCGATACGCAAGAAGCTGGTGGTGGTCGGGGACGGAGCTTGCGGCAAAACCTGCCTCCTCATCGTCTTCAGCAA
GGACGAGTTCCCCGAGGTGTACGTTCCCACCGTGTTCGAGAACTACGTGGCCGATATCGAGGTGGACGTGAAGCAGGTGG
AGCTGGCCCTGTGGGACACGGCGGGGCAGGAGGACTACGACCGGCTGCGGCCTCTCTCCTACCCCGACACGGACGTCATC
CTCATGTGCTTCTCCGTGGACAGCCCGGACTCGCTGGAGAACATCCCGGAGAAGTGGGTGCCCGAGGTGAAGCACTTCTG
CCCCAGCGTCCCCATCATCCTGGTGGCCAACAAGAAGGACCTGAGGAACGACGAGCACGTCCGCAACGAGCTGGCCCGCA
TGAAGCAGGAGCCGGTCCGCACCGAGGACGGCAGGGCCATGGCCGTGAGGATTAACGCCTTCGAGTACCTGGAGTGCTCG
GCCAAGACCAAGGAAGGGGTCCGGGAGGTGTTCGAAACGGCCACTAGGGCGGCGCTGCAGAAGAAACACGGCCGGAGCGG
TGAATGTATGAGCTGCTGTAAGCTCCTCTGA

Alignment

ORF - retro_xtro_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.32 %
• 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.ADIEVD.KQVELALWDTAGQEDYDRLR
Retrocopy MAAIRKKLVVVGDGACGKTCLLIVFSKDEFPEVYVPTVFENYVADIEVDVKQVELALWDTAGQEDYDRLR

Parental  PLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELTKMKQEPVK
          PLSYPDTDVILMCFS.DSPDSLENIPEKW.PEVKHFCP.VPIILV.NKKDLRNDEH.R.EL..MKQEPV.
Retrocopy PLSYPDTDVILMCFSVDSPDSLENIPEKWVPEVKHFCPSVPIILVANKKDLRNDEHVRNELARMKQEPVR

Parental  PEDGREMANRINAFGYLECSAKTKDGVREVFEMATRAALQVRKHRKKQRC
          .EDGR.MA.RINAF.YLECSAKTK.GVREVFE.ATRAALQ..KH.....C
Retrocopy TEDGRAMAVRINAFEYLECSAKTKEGVREVFETATRAALQ-KKHGRSGEC

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
SRP007412_brain	66.95 RPM	133.14 RPM
SRP007412_heart	38.93 RPM	46.14 RPM
SRP007412_kidney	38.93 RPM	46.14 RPM
SRP007412_liver	24.75 RPM	69.76 RPM
SRP007412_skeletal_muscle	17.32 RPM	20.28 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_15 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_15 was not experimentally validated.

Homology

Retrocopy orthology:

Xenopus tropicalis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,