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 summary: | ||
| Parental gene symbol: | enosf1 | ||
| Ensembl ID: | ENSXETG00000003158 | ||
| Aliases: | None | ||
| Description: | enolase superfamily member 1 [Source:Jamboree;Acc:XB-GENE-940740] |
Retrocopy-Parental alignment summary:
>retro_xtro_44
ACAATCCGTTCGCTGCGCGTCCACGACGTGCGCTTTCCGACGTCCAGCCAGCTGGATGGCTCGGACGCCATGAACCCGGA
CCCGGACTATTCCGCCGCCTACGTGGTGCTGGAAACCGACAACCCGACCCTGGAAGGCCACGGCCTGACCTTCACCATTG
GCCGCGGCAACGAAGTCTGCTGCGCCGCCATCAAGGCCCTGGCTCCCCGCGTGGAAGGTCTGAACCTGGACTGGGTGGCC
GAGGACATGGGCCGCTTCTGGCGCCACATCACGGCCGACAGCCAGCTGCGCTGGATCGGCCCGGACAAGGGCGCCATGCA
CCTGGCCACCGGCGCCGTGGTCAACGCCATGTGGGACTTGTGGGCCAAGTCGGTGGGCAAGCCCGTGTGGCAGCTGGTAG
CCGACATGGGTCCCGAGGAACTGGTGCGCCTGATCGACTTCCGCTACATCACCGACTGCATCACGCCAGAAGAAGCGCTG
GCGCTGCTGCGCGAACGCGCCCAGGGCAAAGAAGAGCGCCGCGCCGACCTGCTGGCCCATGGCTATCCCTGCTACACCAC
CTCGGCCGGCTGGCTGGGCTATGGCGACGACAAGCTGCGCCGTCTGGCCCAGGAGGCGGTGGACGAAGGCTTCACGCACA
TCAAACTCAAGGTCGGCCGCGACCTGCAGGACGACATCCGCCGCTTGCGCATCGCCCGCGAAGTGCTGGGCCCGGAGCGC
CAGCTGATGATCGACGCCAACCAGGTCTGGGAAGTCGACCAGGCACTGGAATGGCTGCCGCACCTGGCCTTTGCCAAGCC
CTGGTTCATCGAAGAGCCAACCAGCCCGGACGACATCGAAGGCCATCGCCGCATCCGCGAAGCCATGCAAGGCTCCATGC
AGGTGGCGACCGGCGAAATGTGCCAGAACCGCATCATCTTCAAGCAGCTCATCATGCGCGGCGCCATCGACGTAGTGCAG
ATCGACGCCTGCCGTCTGGGCGGCGTCAACGAAGTGCTGGCCGTCATGCTGATGGCTGCCAAGTACGGCCTCAAGGTCTG
CCCGCACGCGGGCGGCGTGGGACTGTGCGAGTACGTGCAGCACCTCTCCATGATCGACTACCTGTGCATCGCTGGCACCA
AGGAGGGCCGCGTCATCGAGTACGTGAACCATCTGCACGAGCACTTCATCGCCCCCTGCGTGGTACGCAACGCGGCCTAC
ATGCCGCCCAAGCTGCCGGGCTACTCCATCGAGATGAAGGCGGCCTCGCTGGCAGCGCACGAATTCAAGGGCTGATCAGC
ATGG
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 |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
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 |
Xenopus tropicalis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_xtro_44 retrocopy.
Xenopus tropicalis was not studied using FANTOM5 data.
retro_xtro_44 was not experimentally validated.
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.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 ,
|