RetrogeneDB ID: retro_xtro_13

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL173263.1:21879..23421(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXETG00000015938
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: cyp1b1
• Ensembl ID: ENSXETG00000025303
• Aliases: None
• Description: cytochrome P450, family 1, subfamily B, polypeptide 1 [Source:Jamboree;Acc:XB-GENE-951460]

Sequence

>retro_xtro_13
GAATGGAAAGACAGTGTCCAACCAGCCCTGGTGTTCTCTTTCTTGATACTCATCTGCCTAGAGGTGTGCCTATGGCTGAG
GAACAATGGGCAGAGGAGGTCTCCCCCTGGACCCTTTCCCTGGCCTGTGGTGGGCAATGCAATGCAACTCGGGCAACTTC
CCCATCTCACCTTTTGTAAAATGTCTCAGAAATATGGCAACGTATTCCAGATCAGACTGGGTACCCAAGACATTGTGGTG
CTGAATGGAGATTCCACCATAAGGGAAGCTCTGGTGAAGCATAGCAAGGAATTTGCTGGGAGACCCAACTTCTCCTCCTT
CCAGCTTATCTCTGGGGGCAAAAGCATTGCTTTTGGGGGCTATTCTACTCTCTGGAAGGCTCAAAAGAAAATTGCTCACT
CAACCCTTAGAGCGTTTTCTACTGTCAACAGCAAAACGCAGAAGCTATTTGAGAAGCATGTGGTGGCAGAGGCGCAGGAC
CTCATTGACGTTTTTCTGCGCTTGACCTCTGAGGAGGAATATTTTGATCCTACACGTGAGTGCACGGTGGCCGCTGCCAA
TGTCATCTGTGCCTTGTGCTTTGGCAAACGTTACAGCCACGATGATGAGGAGTTCAAAGCCCTGATTGGGAGAAATGACA
AGTTTGGCCAAACCGTGGGCGCTGGTAGCCTTGTAGACATCATGCCCTGGCTTCTAACTTTCCCAAACCCAGTGCGCAGC
CTCTATCAGAGCTTCAAAGATCTCAACTGGGAATTTTATGGTTTTGTCAAGGAGAAGGTAAGCCACCACCGGCAAACCTA
CAACCCAGAGATCACCAGGGACATGAGTGATGCCTTCATCAGTCATATAGACAATGCAGAAGGGATAGAAGCAGGTGATG
GTCTGAGCAAGGACTATGTGGAAAGCATTGTCAATGATATCCTGGGCGCAGGGCAAGACACCACTGCTACTGCCCTCACC
TGGATTCTGCTCTTACTCATTAAATACCCTGACATTCAGCAGAAGCTGCAGGAAGAGATAGACCTGGTGGTGGGACCCAA
CCGACTTCCCACAGCAGATGACAAAGTTCAGCTCCCCTATGTCCAAGCCTTTATCTATGAAGCCCTGCGTTTCAGCAGCT
TCGTGCCAGTCACTATCCCGCACTCTACCACCAGTGATGTGGTCATTGATGGCTTCTACATTCCCAAGGACACGGTGGTC
TTTGTTAACCAGTGGTCAGTCAACCATGATGAATCCAAATGGAAAAACCCAGATGTTTTTGACCCCAGCAGGTTTTTGGA
TGAAGAGGGTCAGCTGGACAGAGATGCTGCTTTCGGGGTGATGATCTTCTCCGTGGGCAAAAGGAGATGTATTGGGGACC
AGCTATCTATGCTACAGATATTTCTATTCACGGCCATCTTTCTCCACCAGTGCACCCTCCATGGCAACCCTAAGGAGATA
CCCACCATGGACTGTATCAGTGGCTTATCTCTCAAACCACTGCCCTATGGGATGTCCGTTAGAGCCAGAGTTGGTAGAAC
AACCATGAAAGAACCTGTCTGA

Alignment

ORF - retro_xtro_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.64 %
• Parental protein coverage: 91.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WIRSS----QPPGPFPWPLFGNALQMGSYPHLAFIDLAKRYGNIFQIKLGSQKIVVLNGDLVIRHALLHK
          W.R.......PPGPFPWP..GNA.Q.G..PHL.F......YGN.FQI.LG.Q.IVVLNGD..IR.AL...
Retrocopy WLRNNGQRRSPPGPFPWPVVGNAMQLGQLPHLTFCKMSQKYGNVFQIRLGTQDIVVLNGDSTIREALVKH

Parental  GEDFAGRPKFTSYQFVSGGRSLAFGCYTEKWKAHRKLAHSTVRAFSTGNPQTKRCLAENVLKEARDLIAL
          ...FAGRP.F.S.Q..SGG.S.AFG.Y...WKA..K.AHST.RAFST.N..T.......V..EA.DLI..
Retrocopy SKEFAGRPNFSSFQLISGGKSIAFGGYSTLWKAQKKIAHSTLRAFSTVNSKTQKLFEKHVVAEAQDLIDV

Parental  FSELGQGGKYFYPGRHTVVSVANVMSAVCFGRRYQHGDLEFQSLLSNNDKFTRSVGAGSLVDVMPWLQRF
          F..L.....YF.P.R...V..ANV..A.CFG.RY.H.D.EF..L...NDKF...VGAGSLVD.MPWL..F
Retrocopy FLRLTSEEEYFDPTRECTVAAANVICALCFGKRYSHDDEEFKALIGRNDKFGQTVGAGSLVDIMPWLLTF

Parental  PNPVRSVFRSFQQVNYEFYDFVYKKFLLHRNTANQAVTRDMMDAFIHILITKEG----KSLEAEHVPSTV
          PNPVRS...SF...N.EFY.FV..K...HR.T.N...TRDM.DAFI......EG......L....V.S.V
Retrocopy PNPVRSLYQSFKDLNWEFYGFVKEKVSHHRQTYNPEITRDMSDAFISHIDNAEGIEAGDGLSKDYVESIV

Parental  TDIFGASQDTLSTALQWVIFFLVRYPEIQTKLQDEMDRVIGKDRLPCIEDQPKLPYLMAFLYEFMRFSSF
          .DI.GA.QDT..TAL.W....L..YP.IQ.KLQ.E.D.V.G..RLP...D...LPY..AF.YE..RFSSF
Retrocopy NDILGAGQDTTATALTWILLLLIKYPDIQQKLQEEIDLVVGPNRLPTADDKVQLPYVQAFIYEALRFSSF

Parental  VPITIPHATTKNTTIMGYQIPKDTVVFVNQWSVNHDPQKWSNPGEFNPSRFLDDNGLINKDLVSNIMIFS
          VP.TIPH.TT....I.G..IPKDTVVFVNQWSVNHD..KW.NP..F.PSRFLD..G....D.....MIFS
Retrocopy VPVTIPHSTTSDVVIDGFYIPKDTVVFVNQWSVNHDESKWKNPDVFDPSRFLDEEGQLDRDAAFGVMIFS

Parental  VGKRRCIGEELSKIQLFMFSSILLHQCIFTALPADNLNPKGDYGLSIKPKPFRISMTLRHG
          VGKRRCIG..LS..Q.F.F..I.LHQC.....P..........GLS.KP.P...S...R.G
Retrocopy VGKRRCIGDQLSMLQIFLFTAIFLHQCTLHGNPKEIPTMDCISGLSLKPLPYGMSVRARVG

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	5.47 RPM	1.04 RPM
SRP007412_heart	6.33 RPM	0.00 RPM
SRP007412_kidney	6.33 RPM	0.00 RPM
SRP007412_liver	20.82 RPM	0.00 RPM
SRP007412_skeletal_muscle	3.88 RPM	0.00 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_13 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_13 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Xenopus tropicalis	ENSXETG00000025303	1 retrocopy	retro_xtro_13 ,