RetrogeneDB ID: | retro_xtro_10 | ||
Retrocopy location | Organism: | Xenopus (Xenopus tropicalis) | |
| Coordinates: | GL180905.1:10429..11581(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSXETG00000031141 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | acadl | ||
| Ensembl ID: | ENSXETG00000001085 | ||
| Aliases: | None | ||
| Description: | acyl-CoA dehydrogenase, long chain [Source:Jamboree;Acc:XB-GENE-958719] |
Retrocopy-Parental alignment summary:
>retro_xtro_10
GCCACACCCATGCAAGACCTGAGCCAACGCACCGTCTACCGCGAAGACCACGAACAATTCCGCACGCAGGTACGCCGCTT
CTTCGAGCGCGAAATCGTGCCCTTCCACGCCCAGTGGGAACGCGACGGCATCGTGCCCAAGGAAGTGTGGCGCAAGGCCG
GACGCGAGGGCCTGCTCAACACCATGCTGCCCGAGCCCTACGGCGGCGGTGGCGACTTCGGCCACGCGGCGGTGCTGATC
GAGGAAGTGGCACGCACGGGCGCCAGCGGCCTGGGTTTTCCGCTGCACTCCGACATCGTCGCGCCCTACATCCACGCCTA
CGGCAGCACGGCGCAGAAAGACCGCTGGCTACCGCACATGGCCGCAGGCGCGCTGATCGGCGCCATCGCCATGACCGAGC
CCGGCGCGGGCAGCGACCTGAAATCGGTACGCACCACGGCACGGCGCGAAGGCGACCACTACGTCATCAACGGCGCCAAG
ACCTTCATCACCAACGGCATCAACGCCGGACTCGTCATCGTCGTGTGCAAGACCGCACCCGAGCTGGGCGCCAAAGGCGT
GTCGCTGATCGTGGTGGAGGAGGGCACACCGGGCTTCAGCAAAGGCCGCAAACTCGAAAAAATCGGCCTCATGGCGCAAG
ACACCTCCGAACTGTTCTTCGACCACGCCAAAGTACCCGCAGGGCATCTGCTGGGCGAGGAGAACCAGGGCTTCAAGTAC
CTGATGAAGGAACTCGCGCAAGAGCGTCTGGTGGTTGCAGTGCGCGCTGCCGCCTCCATCGAAGCCATGCTGCACCAAAC
CGTGGCCTACACACGCGAGCGCCGCGCCTTCGGCCAAACGGTGTTCGAATTCCAGAACACGCGCTTCAAGCTCGCCGAAG
CCAAGGCCCAGGCCACCATGCTGCGCGTGTTCGTAGACGACTGCATCGCCCTGCACCTGCGCCGCGCCCTCACACCCGAA
CGCGCCGCCATGGTCAAACTCAACGCCACAGCGTTGCAAAACCGCCTGCTCGACGAATTCCTGCAACTGCACGGCGGCTA
CGGCTACATGACCGAATACCAAGTGGGCCGCGCCTGGACCGATGCACGCATAGGCCGCATCTACGGCGGCAGCGACGAGA
TCATGAAAGAAATCATCGCCCGCACGCTGTAA
ORF - retro_xtro_10 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 50.52 % |
| Parental protein coverage: | 86.94 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | AKSLMDIGTRRIFSSDHDIFRESARKFFQQEVVPYHAEWEKAGQVSRNLWEKAGQQGLLGTSTPEEHGGI |
| A....D...R.....DH..FR...R.FF..E.VP.HA.WE..G.V....W.KAG..GLL.T..PE..GG. | |
| Retrocopy | ATPMQDLSQRTVYREDHEQFRTQVRRFFEREIVPFHAQWERDGIVPKEVWRKAGREGLLNTMLPEPYGG- |
| Parental | GGDILSSAIVWEEQMYVNCTGPGFSLHSDIVMPYISRYGSKSQVEKYIPQMTAGKCIGAIAMTEPGAGSD |
| GGD....A...EE.......G.GF.LHSDIV.PYI..YGS..Q.....P.M.AG..IGAIAMTEPGAGSD | |
| Retrocopy | GGDFGHAAVLIEEVARTGASGLGFPLHSDIVAPYIHAYGSTAQKDRWLPHMAAGALIGAIAMTEPGAGSD |
| Parental | LQGVRTNAKKDGSDWILNGSKVFITNGWMSDVVIVVAVTNREARTPAHGISLFLVDNGTKGFVKGRKLEK |
| L..VRT.A...G.....NG.K.FITNG.....VIVV..T..E....A.G.SL..V..GT.GF.KGRKLEK | |
| Retrocopy | LKSVRTTARREGDHYVINGAKTFITNGINAGLVIVVCKTAPELG--AKGVSLIVVEEGTPGFSKGRKLEK |
| Parental | IGLKAQDTAELFFEDVRLPADALLGQENKGFYYLMAELPQERLLIADMALASCEFMFEETRNYVKQRKAF |
| IGL.AQDT.ELFF.....PA..LLG.EN.GF.YLM.EL.QERL..A..A.AS.E.M...T..Y...R.AF | |
| Retrocopy | IGLMAQDTSELFFDHAKVPAGHLLGEENQGFKYLMKELAQERLVVAVRAAASIEAMLHQTVAYTRERRAF |
| Parental | GKTIAHLQTVQHKLAELKTQICIGRTFLDNCLQLHAEKRLDSATASMAKYWASDLQNSVATQCVQLHGGW |
| G.T....Q....KLAE.K.Q....R.F.D.C..LH....L....A.M.K..A..LQN.......QLHGG. | |
| Retrocopy | GQTVFEFQNTRFKLAEAKAQATMLRVFVDDCIALHLRRALTPERAAMVKLNATALQNRLLDEFLQLHGGY |
| Parental | GYMWEYPIAKAYVDSRVQPIYGGTNEIMKELIARDI |
| GYM.EY....A..D.R...IYGG..EIMKE.IAR.. | |
| Retrocopy | GYMTEYQVGRAWTDARIGRIYGGSDEIMKEIIARTL |
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 | 15 .85 RPM |
| SRP007412_heart | 0 .00 RPM | 307 .24 RPM |
| SRP007412_kidney | 0 .00 RPM | 307 .24 RPM |
| SRP007412_liver | 0 .00 RPM | 101 .13 RPM |
| SRP007412_skeletal_muscle | 0 .00 RPM | 314 .83 RPM |
Xenopus tropicalis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_xtro_10 retrocopy.
Xenopus tropicalis was not studied using FANTOM5 data.
retro_xtro_10 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 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Echinops telfairi | ENSETEG00000000487 | 1 retrocopy | |
| Xenopus tropicalis | ENSXETG00000001085 | 1 retrocopy |
retro_xtro_10 ,
|
| Xenopus tropicalis | ENSXETG00000007932 | 1 retrocopy | |
| Xenopus tropicalis | ENSXETG00000016078 | 1 retrocopy |