RetrogeneDB ID: retro_tnig_2

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: 14:4236783..4237374(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTNIG00000002278
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RHOC (2 of 2)
• Ensembl ID: ENSTNIG00000015041
• Aliases: None
• Description: ras homolog family member C [Source:HGNC Symbol;Acc:669]

Sequence

>retro_tnig_2
ATGGCTGACATACGCAAGAAACTTGTGGTGGTGGGGGACGGCGCAGGTGGGAAGACATGTCTGCTGATCGTCTTCAGCAA
AGACGAGTTTCCTGAGGTGTACGTGCCCACCGTTTTCGAGACGTATGTGGCGGACATCGAGGTGGAAAACAAGCAGGTCC
AGCTGGCGCTGTGGGACACGGCCGGGCAGGAGGACTACGACCGGCTGCGGCCGCTCTCCTACCCGGACACCGACGTCATC
CTCATGTGCTTCTCCGTGGACAGCCCGGACTCTCTGGAGAACATCCCCGAAAAGTGGGTCCCCGAAGTCAAGCACTTCTG
CCCGAATGTCCCCATCATACTGGTGGCCAACAAGAAGGACCTGCGGAACGACGAGAACGTGAAGAACGAGCTGTCCCGGC
TGAAGCTGGAGCCGGTGCGGGCGGAAGATGGCCGAGCCATGGCCATGCGCATCGGCGCCTATGACTATTTGGAGTGCTCG
GCCAAAACGAAGGAGGGTGTCTGGGAGGTGTTCGAGACCGCGACGCGGGCAGCTCTGCAGAAACGAAAAACGCCATCGGG
AGGTTGTCACAGCTGCTGTGTTTTGATGTGA

Alignment

ORF - retro_tnig_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.85 %
• Parental protein coverage: 97.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYIADIEVDGKQVELALWDTAGQEDYDRLR
          MA.IRKKLV.VGDGA.GKTCLLIVFSKD.FPEVYVPTVFE.Y.ADIEV..KQV.LALWDTAGQEDYDRLR
Retrocopy MADIRKKLVVVGDGAGGKTCLLIVFSKDEFPEVYVPTVFETYVADIEVENKQVQLALWDTAGQEDYDRLR

Parental  PLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVR
          PLSYPDTDVILMCFS.DSPDSLENIPEKW.PEVKHFCPNVPIILV.NKKDLRNDE....EL...K.EPVR
Retrocopy PLSYPDTDVILMCFSVDSPDSLENIPEKWVPEVKHFCPNVPIILVANKKDLRNDENVKNELSRLKLEPVR

Parental  SDEGRDMANRISAFGYLECSAKTKDGVREVFEMATRAALQVRKRKRRG
          ...GR.MA.RI.A..YLECSAKTK.GV.EVFE.ATRAALQ.RK....G
Retrocopy AEDGRAMAMRIGAYDYLECSAKTKEGVWEVFETATRAALQKRKTPSGG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tetraodon nigroviridis was not studied using RNA-Seq expression data.

ChIP-Seq

Tetraodon nigroviridis was not studied using ChIP-Seq data.

EST

Tetraodon nigroviridis was not studied using EST data.

TSS

Tetraodon nigroviridis was not studied using FANTOM5 data.

Lab

retro_tnig_2 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_2 has 3 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Gasterosteus aculeatus	retro_gacu_9
Oryzias latipes	retro_olat_13
Takifugu rubripes	retro_trub_19

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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,
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,
Pongo abelii	ENSPPYG00000010686	2 retrocopies	retro_pabe_2013, retro_pabe_2979,
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,