RetrogeneDB ID: retro_xtro_67

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL185543.1:6030..7227(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: nfs1
• Ensembl ID: ENSXETG00000007430
• Aliases: None
• Description: NFS1 nitrogen fixation 1 homolog [Source:Jamboree;Acc:XB-GENE-1010917]

Sequence

>retro_xtro_67
CCCATCTATCTCGACTATGGTGCAACCACTCCCGTGGATCCGCGCGTGGTGGACGCCATGATTCCCTGGTTGCGCGAGCA
TTTCGGCAACGCCGCCTCACGCAGCCATGCCTGGGGCTGGGAGGCGGAAGAGGCCATCGAAAAGGCCCGAGGGCAGGTGG
CGGATCTGATTGGCGCGGATCCCCGCGAGATCGTCTGGACCAGCGGCGCCACCGAATCCATCAACTTGGCCATCAAGGGC
GCGGCCCACTTCTATCAAGGCAAGGGCAAGCACCTGATCACGCTCAAGACCGAGCACAAGGCCGTGCTCGACACCATGCG
GGAGCTGGAGCGCCAGGGCTTCGAAGTGACCTACATGGACGTGCAGCCCGATGGCCTGCTCGACGTCGAGGCGTTCAAGG
CCGCGTTGCGCCCTGACACCATTCTGGTCAGCGTGCTGTTCGTGAACAACGAAATTGGCGTGATCCAGGACATCCCCGCC
ATCGGCGCGCTGTGCCGCGAGAAGGGCATTCTGTTCCATGTGGATGCAGCCCAGGCCACGGGCCGCGTCGAGATCAACAT
GGCGAAGATGCCCATCGATCTGATGAGCATGACCGCGCACAAGACCTACGGCCCCAAGGGGGTGGGCGCCTTGTATGTGC
GGCGCAAGCCCCGCGTGCGCCTGGAGGCGCAGATCCATGGCGGCGGCCATGAGCGCGGCATGCGCTCGGGCACGCTGCCC
ACGCACCAGATCGTTGGCATGGGCGAGGCTTTTTCCATCGCCAAGGCGGAGATGGCCGAGAGCAATGCCAAGGCCTATGC
CTTGCAGCAGCGCCTGCTCAACGGCCTCAAGGACCTGGAGCAGGTGTTCATCAACGGCAGCATGGAGCACCGCGTGCCGC
AGAACCTGAACATGAGCTTCAACTTCGTCGAGGGCGAGTCGCTGATCATGGGCATCAAGGGTCTGGCGGTGTCGTCCGGC
TCGGCATGCACGTCGGCCAGCCTGGAGCCCAGTTACGTGTTGCGCGCCCTGGGCCGCAGCGACGAACTGGCGCACAGCAG
CCTGCGCATGACCATCGGCCGCTTCACGACCGAGGAAGAAATCGATTACGCGATCAGCACCATCCGCAGCAATGTGGTCA
AGCTGCGCGAGCTCAGCCCGCTGTGGGAGATGTTCAAAGACGGCATCGACATCAGCACTATTCAATGGGCGGCACAC

Alignment

ORF - retro_xtro_67 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.98 %
• Parental protein coverage: 98.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PLYMDVQATTSLDPRVLDRMLPYMVNYYGNPHSRTHAYGWETEKAVEKAREQVASLIGADSREIIFTSGA
          P.Y.D..ATT..DPRV.D.M.P......GN..SR.HA.GWE.E.A.EKAR.QVA.LIGAD.REI..TSGA
Retrocopy PIYLDYGATTPVDPRVVDAMIPWLREHFGNAASRSHAWGWEAEEAIEKARGQVADLIGADPREIVWTSGA

Parental  INPIMSLHYVKGVAKFYKSRKRHILTTQTEHKCVLDSCRSLEAEGFQVTYLPVQKNGLVDLKVLEDSIRP
          ...I......KG.A.FY.....H..T..TEHK.VLD..R.LE..GF.VTY..VQ..GL.D........RP
Retrocopy TESINLA--IKGAAHFYQGKGKHLITLKTEHKAVLDTMRELERQGFEVTYMDVQPDGLLDVEAFKAALRP

Parental  DTSLVSIMAVNNEIGVKQPIQEIGQICSSRKIFFHTDAAQAVGKIPLNVNQMKIDLMSISGHKIYGPKGV
          DT.LVS...VNNEIGV.Q.I..IG..C....I.FH.DAAQA.G....N...M.IDLMS...HK.YGPKGV
Retrocopy DTILVSVLFVNNEIGVIQDIPAIGALCREKGILFHVDAAQATGRVEINMAKMPIDLMSMTAHKTYGPKGV

Parental  GAIYVRRRPRVRMEALISGGGQERGLRSGTVPAPLVVGLGAACKVSQEELEYDHRRISALAKRLTQNIMS
          GA.YVRR.PRVR.EA.I.GGG.ERG.RSGT.P....VG.G.A......E.........AL..RL..N...
Retrocopy GALYVRRKPRVRLEAQIHGGGHERGMRSGTLPTHQIVGMGEAFSIAKAEMAESNAKAYALQQRLL-NGLK

Parental  QIPEVVLNGDAEHRYPGCINLSFAYVEGESLLMALKDVALSSGSACTSASLEPSYVLRAIGADEDLAHSS
          ....V..NG..EHR.P...N.SF..VEGESL.M..K..A.SSGSACTSASLEPSYVLRA.G....LAHSS
Retrocopy DLEQVFINGSMEHRVPQNLNMSFNFVEGESLIMGIKGLAVSSGSACTSASLEPSYVLRALGRSDELAHSS

Parental  IRFGIGRFTTEEEVDYTVKKCVEEVKRLREMSPLWEMVQDGIDLKSIKWTQH
          .R..IGRFTTEEE.DY........V..LRE.SPLWEM..DGID...I.W..H
Retrocopy LRMTIGRFTTEEEIDYAISTIRSNVVKLRELSPLWEMFKDGIDISTIQWAAH

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	17.72 RPM
SRP007412_heart	0.00 RPM	20.76 RPM
SRP007412_kidney	0.00 RPM	20.76 RPM
SRP007412_liver	0.02 RPM	13.87 RPM
SRP007412_skeletal_muscle	0.00 RPM	19.05 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_67 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_67 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000010393	1 retrocopy	retro_lafr_141,
Oryctolagus cuniculus	ENSOCUG00000017050	1 retrocopy	retro_ocun_1214,
Tarsius syrichta	ENSTSYG00000005561	1 retrocopy	retro_tsyr_412,
Xenopus tropicalis	ENSXETG00000007430	1 retrocopy	retro_xtro_67 ,