RetrogeneDB ID: retro_xtro_26

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL173171.1:785294..786320(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSXETG00000033657
• Aliases: None
• Description: None

Sequence

>retro_xtro_26
ATTAAAGAGGAGGTGGCTTCATGTGAAGGGGGAAACCAATCAGATTGCAGCATTAATCCCCTTACAGAACAGATACAGGG
AACAGACACACCTACTCCTATCATAGGAAACACTCTTGATGATACTTTGCCAGAAAGCCAAAACAATGGCAGAAGATCTA
ATAATAGGAGAAGAACGGGAGCGTTACAGAGGATGTATAAGTGCTCTGAGTGCCACAGAAAGTTTAGTAGCAAAGGCACA
TTTGTCAGGCATCAAAGAAGCAGCCACAAAATAGAAAAATGGGTTTCTCCCTCCAAAGATGGGAAATTAATGGCACGGCG
CTCAGACCAAGTGGGATGTAAAAGCAATGGAGACAAATCCATTACGTGTTCTGAATGCGGGAAAAGTTTTACACGACGTT
CAAGCTTTAATGTGCATCGCAGGGTTCACACAGGGGAGAAACCGTTTGCTTGTTCCGAGTGCGGAAAGTGTTTTAGGAAA
GCGTCAGACCTTCATTTACACAACAGGATTCACACAGGAGAGAAACCATTCACTTGTTCCGAATGTGGGAAACGCTTCAC
GCGGAGCTCACACCTGCGTTCCCATCTGAGAACTCACCTAGGGCCGAAGCCGTACTCCTGTTCCGAATGTGGGAAATCTT
TTACACAACGTTCCGCCCTTTATGCGCATTACAAAAGTCACACCGGAGAGAAACTATTTTCTTGTTCTGAGTGCGGCCAA
AGCTTTATGCAACTGTTGGACCTTATTGTACACAGCAGGACTCACCAAGAAAAAACGTTCTCGTGTCCCGAATGCGGGAA
ACGTTTCATCAACCGCGCACTCCTTAGGAGACATCATCAAATTCACACGGGAGAGAAGCCATTCACGTGTTTACAGTGTG
GGAAAGCTTTCACCTATAGGTCGGACCGTAACAGGCATCAAAAATGTCACTTGGGAGAGAAACCGTTTTGTTGTTCTCAG
TGTGGGAAACGTTTTACACGTCAGTCAGACCTTAAGAGACATCACAGGAGTCACGCGGGAGAAAAG

Alignment

ORF - retro_xtro_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.8 %
• Parental protein coverage: 51.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IKEEEVSCEEDNQSDCSINPLTEQTQGTDTPTPIIGNSLNDNLSEIQNSSRKSYN--RMGVLQGMYKCSE
          IKEE..SCE..NQSDCSINPLTEQ.QGTDTPTPIIGN.L.D.L.E.QN..R.S.N..R.G.LQ.MYKCSE
Retrocopy IKEEVASCEGGNQSDCSINPLTEQIQGTDTPTPIIGNTLDDTLPESQNNGRRSNNRRRTGALQRMYKCSE

Parental  CHKRFSSKSTFVRHQR-IHTGEKPYSCSECGKCFTQRSHLSAHLKSHTGEKPFTCSECGKCFTHLGDLKR
          CH..FSSK.TFVRHQR..H..EK..S.S..GK....RS......KS..G.K..TCSECGK.FT.......
Retrocopy CHRKFSSKGTFVRHQRSSHKIEKWVSPSKDGKLMARRSD-QVGCKSN-GDKSITCSECGKSFTRRSSFNV

Parental  HLRSHTGEKPFTCSQCGKAFIRRAHLSRHQKCHLGEKPFSCSQCGKCFTQRTHLERHHRSHTGEKPFSCC
          H.R.HTGEKPF.CS.CGK.F.....L..H...H.GEKPF.CS.CGK.FT...HL..H.R.H.G.KP.S.C
Retrocopy HRRVHTGEKPFACSECGKCFRKASDLHLHNRIHTGEKPFTCSECGKRFTRSSHLRSHLRTHLGPKPYS-C

Parental  SDCGKCFKQRSKLYIHCRTHTGEKPYACSVCGKRFIQVPELNIHYRIHTGEKPFSCSECGKCFTQRAHLS
          S.CGK.F.QRS.LY.H...HTGEK...CS.CG..F.Q...L..H.R.H..EK.FSC.ECGK.F..RA.L.
Retrocopy SECGKSFTQRSALYAHYKSHTGEKLFSCSECGQSFMQLLDLIVHSRTHQ-EKTFSCPECGKRFINRALLR

Parental  MHRRVHSGDKPFSCTECGKCFKQRSDLHKHHRSHTGEKPFACTECEKRFVHRSDLTAHNRIHTGEK
          .H...H.G.KPF.C..CGK.F..RSD...H...H.GEKPF.C..C.KRF...SDL..H.R.H.GEK
Retrocopy RHHQIHTGEKPFTCLQCGKAFTYRSDRNRHQKCHLGEKPFCCSQCGKRFTRQSDLKRHHRSHAGEK

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	3.88 RPM	10.73 RPM
SRP007412_heart	1.65 RPM	6.65 RPM
SRP007412_kidney	1.65 RPM	6.65 RPM
SRP007412_liver	0.63 RPM	8.84 RPM
SRP007412_skeletal_muscle	0.25 RPM	4.69 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_26 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_26 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	ENSXETG00000033657	1 retrocopy	retro_xtro_26 ,