RetrogeneDB ID: retro_xtro_33

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL174170.1:37210..38458(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: aldh5a1
• Ensembl ID: ENSXETG00000021961
• Aliases: None
• Description: aldehyde dehydrogenase 5 family, member A1 [Source:Jamboree;Acc:XB-GENE-1013005]

Sequence

>retro_xtro_33
GAGCGCAGCATCCTCCTGCGCAAGTGGTACGACCTGCTGCTGGCCCACCAGGACGACCTGGGCCGCATCATGACCGCCGA
ACAGGGCAAACCCCTGCCCGAAGCCAAGGGCGAAGTAGCCTACGGCGCGAGCTTCGTCGAGTGGTTCGCCGAGGAAGCCA
AGCGCGTCAACGGCGAAACGCTGCCGCAGTTCGACAACAACCGGCGCCTGCTCGTACTCAAGCAGCCCATCGGCGTATGC
GCGGCCATCACGCCCTGGAATTTCCCGCTCGCCATGATCACCCGCAAGGTTGCACCCGCCCTCGCGGCTGGTTGCACCGT
GGTCATCAAACCGGCCGAACTGACCCCGCTCACGGCGCTGGCCGCCGCCGAACTGGCGGTGCGCGCGGGCATCCCGGCCG
GGGTGCTGAACATCCTGAGCGCTGACGGCGCCAACTCCATCGCCATCGGCAAAGTGCTGTGCGCCAGCGACGTGGTGCGC
CACATCAGCTTCACGGGCAGCACGGAAGTCGGCCGCATCCTCATGGCCCAGTCCGCCCCCACGGTAAAGAAAATGTCGCT
GGAACTCGGTGGCAACGCGCCCTTCATCGTGTTCGACGACGCCGATATCGACTCCGCCGTCGAAGGCGCCTTCGCCAGCA
AGTACCGCAACGCAGGCCAGACTTGCGTGTGCACCAACCGTTTTTACGTGCAGGAAGGCGTGTACGACGAATTCGTCGCC
AAATTCGCGGCCAAGGTCAAAACCGCCAAGGTCGGCAACGGCTTCGCGGACGGTGTGAGCCAGGGCCCGCTGATCGAAGA
GGCCGCTATCGAGAAGGTACAGCGCCACGTGCAAGACGCCGTGGCCAAGGGGGGCCAGATCGTCGCGGGCGGCCAGCGTC
TCGCAGCCCTGGGCAGCGGCCAGTTCTTCGAGCCCACGGTCGTCGCGGGCGCCACGGCCGACATGCTGTGCGCGCGCGAG
GAAACCTTCGGCCCCTTTGCGCCTGTGTTCAAGTTCAAGACCGAAGCGGAAGCCATCGCCGCAGCCAACGCCACCGAGTT
TGGCCTCGCCAGCTACTTCTACAGCCGCGACGTGGGCCGCATCTTCCGCGTAAGCGAGGCGCTGGAGTACGGCATGGTAG
GCATCAACGTAGGTATTCTGGCCACCGAACATGTGCCCTTCGGCGGCGTAAAACAGTCCGGCCTAGGCCGCGAAGGCTCA
CACCACGGCATGGACGATTACGTGGAAATCAAATACCTCTGCGTGGGT

Alignment

ORF - retro_xtro_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.71 %
• Parental protein coverage: 85.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERSVLLRRWYDLMIQNKEDLAKIITAENGKPLKEALGEILYAAGFLEWFSEEARRVYGDVIPVAVKDRRA
          ERS.LLR.WYDL......DL..I.TAE.GKPL.EA.GE..Y.A.F.EWF.EEA.RV.G...P.....RR.
Retrocopy ERSILLRKWYDLLLAHQDDLGRIMTAEQGKPLPEAKGEVAYGASFVEWFAEEAKRVNGETLPQFDNNRRL

Parental  VVLKQPVGVAAIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPLSALALAELAQQAGFPAGVYNVVP
          .VLKQP.GV.A.ITPWNFP.AMITRKV..ALAAGCTVV.KPAE.TPL.ALA.AELA..AG.PAGV.N...
Retrocopy LVLKQPIGVCAAITPWNFPLAMITRKVAPALAAGCTVVIKPAELTPLTALAAAELAVRAGIPAGVLNILS

Parental  CSREKTPAVGETLCTDLAVSKISFTGSTATGKILLHHAANSVKRVSMELGGHAPFIVFDSANVDQAVAGA
          .......A.G..LC....V..ISFTGST..G.IL....A..VK..S.ELGG.APFIVFD.A..D.AV.GA
Retrocopy ADGANSIAIGKVLCASDVVRHISFTGSTEVGRILMAQSAPTVKKMSLELGGNAPFIVFDDADIDSAVEGA

Parental  LASKFRNSGQTCVCSNRFLVQKGIHNTFVSKLAALMNKELRIGHGFGDGVTQGPLINEKAVQKVEQHVSN
          .ASK.RN.GQTCVC.NRF.VQ.G....FV.K.AA...K....G.GF.DGV.QGPLI.E.A..KV..HV..
Retrocopy FASKYRNAGQTCVCTNRFYVQEGVYDEFVAKFAAKV-KTAKVGNGFADGVSQGPLIEEAAIEKVQRHVQD

Parental  AVSLGAQIEAGGKR-SAVGK-NFFEPTLLSNVTTDMLCTQEETFGPLAPVIKFDTEEEAVAIANSANVGL
          AV..G.QI.AGG.R..A.G...FFEPT.....T.DMLC..EETFGP.APV.KF.TE.EA.A.AN....GL
Retrocopy AVAKGGQIVAGGQRLAALGSGQFFEPTVVAGATADMLCAREETFGPFAPVFKFKTEAEAIAAANATEFGL

Parental  AGYFYSQDPAQIWRVAERLEVGMVGVNEGLLSSVECPFGGVKQSGIGREGSKYGIDEYLEVKYVCFG
          A.YFYS.D...I.RV.E.LE.GMVG.N.G.L.....PFGGVKQSG.GREGS..G.D.Y.E.KY.C.G
Retrocopy ASYFYSRDVGRIFRVSEALEYGMVGINVGILATEHVPFGGVKQSGLGREGSHHGMDDYVEIKYLCVG

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	0.00 RPM	140.48 RPM
SRP007412_heart	0.00 RPM	24.56 RPM
SRP007412_kidney	0.00 RPM	24.56 RPM
SRP007412_liver	0.00 RPM	102.20 RPM
SRP007412_skeletal_muscle	0.00 RPM	10.85 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_33 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_33 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	ENSXETG00000021961	1 retrocopy	retro_xtro_33 ,