RetrogeneDB ID: | retro_acar_95 | ||
Retrocopy location | Organism: | Anole lizard (Anolis carolinensis) | |
| Coordinates: | 2:161187711..161188292(-) | ||
| Located in intron of: | ENSACAG00000011884 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SUSD3 | ||
| Ensembl ID: | ENSACAG00000001297 | ||
| Aliases: | None | ||
| Description: | sushi domain containing 3 [Source:HGNC Symbol;Acc:28391] |
Retrocopy-Parental alignment summary:
>retro_acar_95
TCCAATCCAAGAGGACAATGCAACCAGATATTGGCATCTCACCTTGACATGCCTGAGATCATCCATGGTAATGGCATCAT
TGTGGGCACAGTCATTACATTTGAGTGTTCTGCAGAACACCAACTGGTTGGACAGGGAGTCGTCACATGAATTTGGGAAG
GCAATAGCACCCAGCAGACAGCAGATATCCCTTCATGTAAATCTATATCCAAATATGAAACCTTTGGATTTAAAGTTACA
ATGATTGCCTCCATTGTGAACTGTGCAATTATTCTGCTGATGTCTATAGCTTTTTTAACCTGCTGTTTCATGTGTTAAGA
AAAGTGAGAAAAGGAGAAAGAGCTCAAAGGGATATGGAACTGTGGTACCAGCTTAAAAGTGAAGAACTGGAAAGCATGCA
AGCAGCTTATTTTGGTTATAAAGGAAGAAATAACAACAATAAACATATCAAGCATAAGGCAGCATTTGATGGTGGCTGTC
ATATGGCATATGATAACCAAGGCTTCTGCAGCTTCCATGAAGAATGCAGGAACTGAGTGTTATGGAGAAAATTATTTACA
AAGGAATTCAGCCAAAACCAT
ORF - retro_acar_95 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.08 % |
| Parental protein coverage: | 70.91 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | SNYTGQCNQIFAPHLGMSEIIHGNGTTVGTVITFRCSAEHQLVGQGVVTCIWKGNSTQWTADIPSCKPIS |
| SN..GQCNQI.A.HL.M.EIIHGNG..VGTVITF.CSAEHQLVGQGVVT.IW.GNSTQ.TADIPSCK.IS | |
| Retrocopy | SNPRGQCNQILASHLDMPEIIHGNGIIVGTVITFECSAEHQLVGQGVVT*IWEGNSTQQTADIPSCKSIS |
| Parental | KYETFGFKIAVIASIVSCAIILLMSMAFLTCCLIKCVKK-SERRRAQR-DMQLWYQLRSEELESMQAAYF |
| KYETFGFK...IASIV.CAIILLMS.AFLTCC...C..K...RR.....DM.LWYQL.SEELESMQAAYF | |
| Retrocopy | KYETFGFKVTMIASIVNCAIILLMSIAFLTCCFM-C*EK>EKRRKSSK>DMELWYQLKSEELESMQAAYF |
| Parental | GYKGRNNNNNKNIKNKAAFDRGSHMAYDNQGFCSFHEECNGDITGTECYGENYLQRN |
| GYKGR.NNNNK.IK.KAAFD.G.HMAYDNQGFCSFHEEC...............Q.. | |
| Retrocopy | GYKGR-NNNNKHIKHKAAFDGGCHMAYDNQGFCSFHEECRN*VLWRKLFTKEFSQNH |
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 |
|---|---|---|
| SRP009831_adrenal | 0 .00 RPM | 60 .26 RPM |
| SRP009831_brain | 0 .05 RPM | 3 .98 RPM |
| SRP009831_dewlap | 0 .04 RPM | 36 .07 RPM |
| SRP009831_embryo | 0 .00 RPM | 3 .47 RPM |
| SRP009831_heart | 0 .00 RPM | 4 .20 RPM |
| SRP009831_liver | 0 .00 RPM | 9 .45 RPM |
| SRP009831_lung | 0 .00 RPM | 2 .17 RPM |
| SRP009831_ovary | 0 .00 RPM | 27 .37 RPM |
| SRP009831_skeletal_muscle | 0 .00 RPM | 0 .47 RPM |
Anolis carolinensis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_acar_95 retrocopy.
Anolis carolinensis was not studied using FANTOM5 data.
retro_acar_95 was not experimentally validated.
Retrocopy orthology:
Anolis carolinensis 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 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Anolis carolinensis | ENSACAG00000001297 | 1 retrocopy |
retro_acar_95 ,
|
| Ochotona princeps | ENSOPRG00000005344 | 2 retrocopies | |
| Rattus norvegicus | ENSRNOG00000016525 | 1 retrocopy |