RetrogeneDB ID: retro_xtro_64

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL184637.1:0..1473(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSXETG00000032691
• Aliases: None
• Description: None

Sequence

>retro_xtro_64
ATGCATCTAAAAAGAAGGAATTTCTCAGCAAGAAGCAGACTGGCTTTATTCTTCATTGTACAAATGGCTGCTGATTTTGT
TCTGTGCCAGCTCCATTACATGATTCCTGAGGAATCCAAACACGGCACCTTTGTTGGGAGAATTGCTCAGGACCTGGGGC
TACAGATCAGTGACATTAACTCCAGAAGGCTAAGGATTTCCTCTAAGGATGGATCAGATTATTTCCAGGTAAATCTGAAA
AATGGAATTTTATTTGTCAATAGAATGATAGACAGGGAAGCTCTGTGTCCTGAAATCAGTGTTTGTATTGTGCAACTGGA
AGTTATAGTTGATAAACCTGTACAGATTCACCATGTAGATGTAGAGATTGAAGATATAAATGACAATTATCCAATATTCC
CTGCTAAAGAATATAAACTGCTAATTGCTGAATCAAGGCTGCCAGGATCACGCTTTCCACTAGAGGGAGCAGTTGATTCT
GATGTTGGAACTAATTCTGTTACTGGCTATGAACTCAGCTCAAATGATAATTTTGCATTAGACGTTCAGTCATATACACA
TGAAAGCAAATCTGTTCAACTTGTATTAAAGAAGTCTCTGGACAGAGAGCAAATACCATTTCACAATATAACGCTTATTG
CATTTGATGGAGGAAAACCAAAATTAAATGGCTCTGCCCAGCTTCTGATTACAGTGCAAGATGTTAATGATAATGCCCCA
GTGTTTGAACAATCAATTTATAGAGCCAGTTTGTTGGAAAATGCTCTTGTGGGAACATTTGTCATCAAGGTAAATGCAAC
AGATTTGGATGAGGGAGAAAATGGCAAACTTAAATATTCTTTTAATAAGTTGGTTCCACCACAAACTAGATCAGTTTTTA
ACATAGAGGAGCACACTGGTATAATTCGAAGTTTTGGAGAGGTTGACTATGAAAAGAAAAGCCTGTATGAAATTGAAGTT
GATGCCATTGATAAAGGTCCATATGCCATAGCCGGACATTGCAAGGTTATCGTAAATATAGTGGATGTAAATGATAATCC
ACCAGAGATGACTGTAACATCACTAAATGTTCCTGTTCCTGAGGATTCACCTACTGGAACGGTAGTTGCAGTTATCAGTG
TCCATGACAGAGATTCAGATCAGAATGGAAAAGTCACTTGTCATATTTCTAAAAATATTCCCTTCAAGATATCTCCTACG
CTAAGAGAATATTACTCACTGACCGTGGATGGACCTTTAGATCGTGAAAGAACATCAGAATATGAACTGGATATAACAGC
TACAGATGGAGGTGCTCCAGCTCTCTCAGTTACCAAATCTATTAAGGTTCAGATAAGTGATGTGAACGACAATCCACCTT
CTTTTCAAAAATCTTCAGAGATAATTTCTGTTAAGGAAAACAACCCACCAGGATCTCACGTCTATACAGTATCAGCCTCT
GATTCAGATACTGGCCAGAATTCCTTTATTACA

Alignment

ORF - retro_xtro_64 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.32 %
• Parental protein coverage: 61.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHLKRRNFSARSRLALFFIVQMAADFVLCQLHYMIPEESKHGTFVGRIAQDLGLQISDINSRRLRISSKD
          MHLKRRNFSARSRLALFFIVQMAADFVLCQLHYMIPEESKHGTFVGRIAQDLGLQISDINSRRLRISSKD
Retrocopy MHLKRRNFSARSRLALFFIVQMAADFVLCQLHYMIPEESKHGTFVGRIAQDLGLQISDINSRRLRISSKD

Parental  GSDYFQVNLKNGILFVNRMIDREALCPEISVCIVQLEVIVDKPVQIHHVDVEIEDINDNYPIFPAKEYKL
          GSDYFQVNLKNGILFVNRMIDREALCPEISVCIVQLEVIVDKPVQIHHVDVEIEDINDNYPIFPAKEYKL
Retrocopy GSDYFQVNLKNGILFVNRMIDREALCPEISVCIVQLEVIVDKPVQIHHVDVEIEDINDNYPIFPAKEYKL

Parental  LIAESRLPGSNFPLEGAVDSDVGTNSVTVYELSSNDNFALDVQSYTHESKSVNLVLRKPLDREQIPLHNI
          LIAESRLPGS.FPLEGAVDSDVGTNSVT.YELSSNDNFALDVQSYTHESKSV.LVL.K.LDREQIP.HNI
Retrocopy LIAESRLPGSRFPLEGAVDSDVGTNSVTGYELSSNDNFALDVQSYTHESKSVQLVLKKSLDREQIPFHNI

Parental  TLIAFDGGKPKLSGTTQLLITVQDINDNAPVFNEEIYRASLLENALKGTIVIKVNATDLDEGENSKLTYA
          TLIAFDGGKPKL.G..QLLITVQD.NDNAPVF...IYRASLLENAL.GT.VIKVNATDLDEGEN.KL.Y.
Retrocopy TLIAFDGGKPKLNGSAQLLITVQDVNDNAPVFEQSIYRASLLENALVGTFVIKVNATDLDEGENGKLKYS

Parental  FNRLVPQHVRTIFSIEENTGIIR-LGEVDFEKKNLYEIEVNAIDRGHRAMVGHCKVLVNVLDVNDNPPEM
          FN.LVP...R..F.IEE.TGIIR..GEVD.EKK.LYEIEV.AID.G..A..GHCKV.VN..DVNDNPPEM
Retrocopy FNKLVPPQTRSVFNIEEHTGIIRSFGEVDYEKKSLYEIEVDAIDKGPYAIAGHCKVIVNIVDVNDNPPEM

Parental  SITSLNLPVSEDSKVGTVVAIINVHDKDSGQNGKVKCQISTNVPFKIASTLREYYSLIVDGPLDHESISE
          ..TSLN.PV.EDS..GTVVA.I.VHD.DS.QNGKV.C.IS.N.PFKI..TLREYYSL.VDGPLD.E..SE
Retrocopy TVTSLNVPVPEDSPTGTVVAVISVHDRDSDQNGKVTCHISKNIPFKISPTLREYYSLTVDGPLDRERTSE

Parental  YNFDIIAIDEGFPSLSVTKSIKIQISDVNDNRPSFHQGAETIFIKENNPPGSHVYTVTASDADTGQNSFI
          Y..DI.A.D.G.P.LSVTKSIK.QISDVNDN.PSF....E.I..KENNPPGSHVYTV.ASD.DTGQNSFI
Retrocopy YELDITATDGGAPALSVTKSIKVQISDVNDNPPSFQKSSEIISVKENNPPGSHVYTVSASDSDTGQNSFI

Parental  T
          T
Retrocopy T

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	1.11 RPM	2.22 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_skeletal_muscle	0.00 RPM	0.00 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_64 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_64 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000008368	2 retrocopies	retro_mputfur_472, retro_mputfur_473,
Tarsius syrichta	ENSTSYG00000004901	2 retrocopies	retro_tsyr_692, retro_tsyr_867,
Xenopus tropicalis	ENSXETG00000032691	1 retrocopy	retro_xtro_64 ,