RetrogeneDB ID: retro_xmac_13

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH556749.1:1674575..1675163(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXMAG00000019632
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: rhoad
• Ensembl ID: ENSXMAG00000008103
• Aliases: None
• Description: ras homolog gene family, member Ad [Source:ZFIN;Acc:ZDB-GENE-040718-144]

Sequence

>retro_xmac_13
ATGGCTGTCCAGCGAAAGAAACTTGTGGTTGTCGGTGACGGCGCTTGTGGGAAAACGTGTCTACTGATCGTTTTCAGCAA
GGACGAGTTTCCCGAGGTCTACGTCCCGACTGTGTTTGAAACCTACGTGGCCGACATAGAGGTTGACAACCAGCAGGTCC
AGCTGGCTCTGTGGGACACGGCCGGACAGGAGGACTACGACCGACTGCGCCCACTCTCCTACCCGGACACTGATGTCATC
CTCATGTGCTACTCCGTGGACAACCCGGACTCGTTGGGGAACATCTCCGAAAAGTGGGTCCCTGAGGTCAAGCACTTTTG
TCCGAACGTGCCAATCATTTTGGTGGCCAACAAGAAAGATCTGCGCAACGACGAGAACACGAAGAACGACCTCTCCCGGA
TGAAACTAGAGCCCGTGAAGGCGGAGGACGGTCGTGCGATGGCCATGCGCATCGGCGCGTATGACTACTTGGAGTGCTCC
GCCAGGACCAAAGAGGGCATCTGGGAGGTGTTCGAGACCGCAACACGGGCTACCCTGCAGAAACGCTCCACACCGGGGGA
TTGTTTCAAATGCTGTGTGATGCTGTGA

Alignment

ORF - retro_xmac_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.89 %
• Parental protein coverage: 90.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYIADIEVDGKQVELALWDTAGQEDYDRLR
          MA..RKKLV.VGDGACGKTCLLIVFSKD.FPEVYVPTVFE.Y.ADIEVD..QV.LALWDTAGQEDYDRLR
Retrocopy MAVQRKKLVVVGDGACGKTCLLIVFSKDEFPEVYVPTVFETYVADIEVDNQQVQLALWDTAGQEDYDRLR

Parental  PLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVK
          PLSYPDTDVILMC.S.D.PDSL.NI.EKW.PEVKHFCPNVPIILV.NKKDLRNDE.T...L..MK.EPVK
Retrocopy PLSYPDTDVILMCYSVDNPDSLGNISEKWVPEVKHFCPNVPIILVANKKDLRNDENTKNDLSRMKLEPVK

Parental  SEEGKDMAQRIGAFGYLECSAKTKDGVREVFEMATRAALQVRKRKKRGGC
          .E.G..MA.RIGA..YLECSA.TK.G..EVFE.ATRA.LQ..KR...G.C
Retrocopy AEDGRAMAMRIGAYDYLECSARTKEGIWEVFETATRATLQ--KRSTPGDC

Legend:

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

Expression

RNA-Seq

Xiphophorus maculatus was not studied using RNA-Seq expression data.

ChIP-Seq

Xiphophorus maculatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xmac_13 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_13 was not experimentally validated.

Homology

Retrocopy orthology:

Xiphophorus maculatus 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 ,