RetrogeneDB ID: | retro_xtro_42 | ||
Retrocopy location | Organism: | Xenopus (Xenopus tropicalis) | |
| Coordinates: | GL175336.1:2626..3832(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | gcdh | ||
| Ensembl ID: | ENSXETG00000007932 | ||
| Aliases: | None | ||
| Description: | glutaryl-CoA dehydrogenase [Source:Jamboree;Acc:XB-GENE-1016447] |
Retrocopy-Parental alignment summary:
>retro_xtro_42
CACTGACTGGAGACACCGATGGCCCATGCCCCCTTCCACTGGGAAGACCCGTTCCTGCTCGACCAACAGCTCAGCGCCGA
CGAGCGCGCCATCCGCGACGCCGCCGCCGCTTACTGCCAGGGCCAGTTGGCCCCGCGCGTGCGGGACATGTTCCGCCACG
AGAAGACCGATACCGCCATCTTCCGTGAGATGGGCGCGCTCGGCCTGCTCGGGCCCACGATTCCCGAGGCCTACGGCGGC
GCGGGTCTGAATTACGTCAGCTACGGCCTGATCGCGCGCGAGATCGAGCGCGTGGATTCGGGCTACCGCTCCATGGCGTC
CGTGCAGTCGTCGCTGGTGATGGTGCCGATCCACACCTTCGGCACCGAGGCGCAGAAGCAGAAGTACCTGCCCGGACTGG
CTTCGGGCGCGCTCATCGGCTGCTTCGGCCTGACGGAGCCGGATCATGGCTCCGATCCGGGCAGCATGGCCGCGCGCGCC
ACCAAGGTGGCTGGCGGCTACCGGCTCAAGGGCAGCAAGATGTGGATCACCAATTCACCGGTGGCGGATGTGTTCGTGGT
CTGGGCCAAGGAAGTGAGCGAGGGCGGCGCCGTGGGCCCGATCCGCGGCTTCGTGCTGGAGAAGGGCTGGAAGGGGCTTG
CCGCCCCGGCCATCCATGGCAAGGTGGGGCTGCGCACCAGTATCACGGGCGAGATCGTCATGGACGATGTGTTCGTGCCC
GAGGAAAACGCCTTTCCCGAGGTGCACGGCCTCAAGGGCCCGTTCACCTGCCTGAACAGCGCGCGCTATGGCATTGCCTG
GGGCGCCATGGGTGCGGCCGAGTTCTGCTGGCACACCGCCCGCCAGTACACGCTGGAGCGCCAGCAGTTCGGTCGCCCGC
TGGCGGCCAACCAGCTCGTGCAGAAAAAGCTGGCCGATATGCAGACCGAGATCGCCCTGGGCCTGCAGGCCGCGCTGCGC
TTCGGCCGCATGAAGGATGAAGGTATCGCCGCCGTGGAGGGCACTTCGCTCATCAAGCGCAACAACTGCGGCAAGGCCCT
GGACATCGCCCGTCTGGCGCGCGACATGCTCGGCGGCAACGGCATCAGCGACGAGTTCGGCGTGGCGCGCCATCTGGTGA
ATCTGGAGGTGGTCAATACCTACGAGGGCACGCATGACGTGCACGCGCTCATCCTGGGGCGGGCGCAGACGGGTATCGCA
GCATTC
ORF - retro_xtro_42 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.88 % |
| Parental protein coverage: | 90.45 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | HEKKSSKSRVQFDYQDALSLDSQLTEDEIMIRDSFRAYCQEKLMPRILMANRKEVFERDIISEMGELGVL |
| H..........F...D...LD.QL..DE..IRD...AYCQ..L.PR.....R.E.....I..EMG.LG.L | |
| Retrocopy | H*LETPMAHAPFHWEDPFLLDQQLSADERAIRDAAAAYCQGQLAPRVRDMFRHEKTDTAIFREMGALGLL |
| Parental | GSTI-KGYGCAGTSYVAYGLLAREVERVDSSYRSVMSVQSSLVMHPIAAYGSEEQKQKYLPRLASGEWLG |
| G.TI...YG.AG..YV.YGL.ARE.ERVDS.YRS..SVQSSLVM.PI...G.E.QKQKYLP.LASG...G | |
| Retrocopy | GPTIPEAYGGAGLNYVSYGLIAREIERVDSGYRSMASVQSSLVMVPIHTFGTEAQKQKYLPGLASGALIG |
| Parental | CFGLTEPNHGSDPAGMETRARYNPSSKTYTLNGAKTWITNSPIADLCVVWA--ICEDGKV---RGFLIER |
| CFGLTEP.HGSDP..M...AR.......Y.L.G.K.WITNSP.AD..VVWA....E.G.V...RGF..E. | |
| Retrocopy | CFGLTEPDHGSDPGSMA--ARATKVAGGYRLKGSKMWITNSPVADVFVVWAKEVSEGGAVGPIRGFVLEK |
| Parental | GTKGLSTPKIEGKFSLRASATGMILLEDVEIPEENLLPNVSGLGGPFGCLNNARYGISWGALGAAEFCFH |
| G.KGL..P.I.GK..LR.S.TG.I...DV..PEEN..P.V.GL.GPF.CLN.ARYGI.WGA.GAAEFC.H | |
| Retrocopy | GWKGLAAPAIHGKVGLRTSITGEIVMDDVFVPEENAFPEVHGLKGPFTCLNSARYGIAWGAMGAAEFCWH |
| Parental | TARQYTLDRIQFGVPLARNQLIQKKLADMLTDITIGLQACLRLGRLKDEEKATPEMISMLKRNSCGKALD |
| TARQYTL.R.QFG.PLA.NQL.QKKLADM.T.I..GLQA.LR.GR.KDE..A..E..S..KRN.CGKALD | |
| Retrocopy | TARQYTLERQQFGRPLAANQLVQKKLADMQTEIALGLQAALRFGRMKDEGIAAVEGTSLIKRNNCGKALD |
| Parental | IARQARDMLGGNGISDEYHIIRHVMNLESVNTYEGTHDVHALILGRAITGLQAF |
| IAR.ARDMLGGNGISDE....RH..NLE.VNTYEGTHDVHALILGRA.TG..AF | |
| Retrocopy | IARLARDMLGGNGISDEFGVARHLVNLEVVNTYEGTHDVHALILGRAQTGIAAF |
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 | 43 .27 RPM |
| SRP007412_heart | 0 .00 RPM | 49 .81 RPM |
| SRP007412_kidney | 0 .00 RPM | 49 .81 RPM |
| SRP007412_liver | 0 .02 RPM | 142 .45 RPM |
| SRP007412_skeletal_muscle | 0 .00 RPM | 65 .96 RPM |
Xenopus tropicalis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_xtro_42 retrocopy.
Xenopus tropicalis was not studied using FANTOM5 data.
retro_xtro_42 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 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Xenopus tropicalis | ENSXETG00000001085 | 1 retrocopy | |
| Xenopus tropicalis | ENSXETG00000007932 | 1 retrocopy |
retro_xtro_42 ,
|
| Xenopus tropicalis | ENSXETG00000016078 | 1 retrocopy |