RetrogeneDB ID: retro_xtro_44

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL175759.1:9711..10995(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: enosf1
• Ensembl ID: ENSXETG00000003158
• Aliases: None
• Description: enolase superfamily member 1 [Source:Jamboree;Acc:XB-GENE-940740]

Sequence

>retro_xtro_44
ACAATCCGTTCGCTGCGCGTCCACGACGTGCGCTTTCCGACGTCCAGCCAGCTGGATGGCTCGGACGCCATGAACCCGGA
CCCGGACTATTCCGCCGCCTACGTGGTGCTGGAAACCGACAACCCGACCCTGGAAGGCCACGGCCTGACCTTCACCATTG
GCCGCGGCAACGAAGTCTGCTGCGCCGCCATCAAGGCCCTGGCTCCCCGCGTGGAAGGTCTGAACCTGGACTGGGTGGCC
GAGGACATGGGCCGCTTCTGGCGCCACATCACGGCCGACAGCCAGCTGCGCTGGATCGGCCCGGACAAGGGCGCCATGCA
CCTGGCCACCGGCGCCGTGGTCAACGCCATGTGGGACTTGTGGGCCAAGTCGGTGGGCAAGCCCGTGTGGCAGCTGGTAG
CCGACATGGGTCCCGAGGAACTGGTGCGCCTGATCGACTTCCGCTACATCACCGACTGCATCACGCCAGAAGAAGCGCTG
GCGCTGCTGCGCGAACGCGCCCAGGGCAAAGAAGAGCGCCGCGCCGACCTGCTGGCCCATGGCTATCCCTGCTACACCAC
CTCGGCCGGCTGGCTGGGCTATGGCGACGACAAGCTGCGCCGTCTGGCCCAGGAGGCGGTGGACGAAGGCTTCACGCACA
TCAAACTCAAGGTCGGCCGCGACCTGCAGGACGACATCCGCCGCTTGCGCATCGCCCGCGAAGTGCTGGGCCCGGAGCGC
CAGCTGATGATCGACGCCAACCAGGTCTGGGAAGTCGACCAGGCACTGGAATGGCTGCCGCACCTGGCCTTTGCCAAGCC
CTGGTTCATCGAAGAGCCAACCAGCCCGGACGACATCGAAGGCCATCGCCGCATCCGCGAAGCCATGCAAGGCTCCATGC
AGGTGGCGACCGGCGAAATGTGCCAGAACCGCATCATCTTCAAGCAGCTCATCATGCGCGGCGCCATCGACGTAGTGCAG
ATCGACGCCTGCCGTCTGGGCGGCGTCAACGAAGTGCTGGCCGTCATGCTGATGGCTGCCAAGTACGGCCTCAAGGTCTG
CCCGCACGCGGGCGGCGTGGGACTGTGCGAGTACGTGCAGCACCTCTCCATGATCGACTACCTGTGCATCGCTGGCACCA
AGGAGGGCCGCGTCATCGAGTACGTGAACCATCTGCACGAGCACTTCATCGCCCCCTGCGTGGTACGCAACGCGGCCTAC
ATGCCGCCCAAGCTGCCGGGCTACTCCATCGAGATGAAGGCGGCCTCGCTGGCAGCGCACGAATTCAAGGGCTGATCAGC
ATGG

Alignment

ORF - retro_xtro_44 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.19 %
• Parental protein coverage: 97.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TITSLHVTDVRFPTSLDQHGSDAMHTDPDYSAAYIVIETDAADGLKGHGLTFTLGKGTEIVVCAVRALSR
          TI.SL.V.DVRFPTS....GSDAM..DPDYSAAY.V.ETD....L.GHGLTFT.G.G.E....A..AL..
Retrocopy TIRSLRVHDVRFPTSSQLDGSDAMNPDPDYSAAYVVLETDNPT-LEGHGLTFTIGRGNEVCCAAIKALAP

Parental  HVIGKALGDIVNNFRDFYRQLTSDGQLRWIGPEKGAVQLATAAVLNAVWDLWAKKEKKPLWKLLVDMDPH
          .V.G..L.........F.R..T.D.QLRWIGP.KGA..LAT.AV.NA.WDLWAK...KP.W.L..DM.P.
Retrocopy RVEGLNLDWVAEDMGRFWRHITADSQLRWIGPDKGAMHLATGAVVNAMWDLWAKSVGKPVWQLVADMGPE

Parental  QLVSCIDFRYITDALTEEEALEILQNGKQGQRDREEHMLRSGYPAYTTSCAWLGYSDEQLKKLCSDALKE
          .LV..IDFRYITD..T.EEAL..L....QG...R....L..GYP.YTTS..WLGY.D..L..L...A..E
Retrocopy ELVRLIDFRYITDCITPEEALALLRERAQGKEERRADLLAHGYPCYTTSAGWLGYGDDKLRRLAQEAVDE

Parental  GWTRFKVKVGADLKDDIRRCELIRGMIGPDNIMMLDANQRWDVQEAISWVKDLAKYKPLWIEEPTSPDDI
          G.T..K.KVG.DL.DDIRR....R...GP....M.DANQ.W.V..A..W...LA..KP..IEEPTSPDDI
Retrocopy GFTHIKLKVGRDLQDDIRRLRIAREVLGPERQLMIDANQVWEVDQALEWLPHLAFAKPWFIEEPTSPDDI

Parental  LGHATISKALSPLNIGVATGEQCHNRVMFKQFLQANALQYLQIDSCRLGSVNENLSVLLMSKKFNVPVCP
          .GH..I..A.......VATGE.C.NR..FKQ.....A....QID.CRLG.VNE.L.V.LM..K....VCP
Retrocopy EGHRRIREAMQG-SMQVATGEMCQNRIIFKQLIMRGAIDVVQIDACRLGGVNEVLAVMLMAAKYGLKVCP

Parental  HAGGVGLCELVQHLILFDYISVSGSLDNRMCEYVDHLHEHFMYPVIISRAAYMPPKDPGYSTEMKDESVL
          HAGGVGLCE.VQHL...DY....G....R..EYV.HLHEHF..P.....AAYMPPK.PGYS.EMK..S..
Retrocopy HAGGVGLCEYVQHLSMIDYLCIAGTKEGRVIEYVNHLHEHFIAPCVVRNAAYMPPKLPGYSIEMKAASLA

Parental  QYQFPDGEIW
          ...F.....W
Retrocopy AHEFKG*SAW

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	2.98 RPM
SRP007412_heart	0.00 RPM	9.56 RPM
SRP007412_kidney	0.00 RPM	9.56 RPM
SRP007412_liver	0.00 RPM	16.07 RPM
SRP007412_skeletal_muscle	0.00 RPM	4.07 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_44 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_44 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Xenopus tropicalis	ENSXETG00000003158	3 retrocopies	retro_xtro_34, retro_xtro_36, retro_xtro_44 ,