RetrogeneDB ID: | retro_itri_657 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393309.1:13440285..13441040(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HSD11B2 | ||
| Ensembl ID: | ENSSTOG00000016446 | ||
| Aliases: | None | ||
| Description: | hydroxysteroid (11-beta) dehydrogenase 2 [Source:HGNC Symbol;Acc:5209] |
Retrocopy-Parental alignment summary:
>retro_itri_657
CTCTTGGTTGCCCATATGCTGCTGTAGTTACTGCGTGTAGACCTGTGACTGGGCTGCCAGTTGCTGGCTGCACTGGTGAA
CTGCTGGCCCCACTAGACTGACTATGCCAGAACCTTCTGCCCATGCTGGCCACACTGGCCATGTTGGCTGCTCCCAGTTG
GATTGCTTGTCCTGCCTAGCACGCCTACTGCGTCTGCCACTGGCTTCTTGCCGAGTGCTCATCACTGGCTGTGACTCTGG
TTTTGTCAAGGAGATGGCCAAGCAATTGGACACCAGGGTCTTCACATGCTGGCTACCATGTTAGAGTTCAAGAACCCCAA
TGCCCTAAAGCTGAGTGCCTGCTGTTTCCTTTGCCTAAGGCTATTGCAGATGGACCTCACTAAACTGCACACATTAGCTT
TGCACTGAAGTTCACTAAGTCCCACACCAACAGCAGTGGTGTGTGAGACCTGGTCAATAATGCAGGCTTCAGTGATGTGA
AGCTGTCTCCAATGGCCACATTCTGCAACTGCATGGAGGTGAACTTCTTTGACGCACTGTAGCTGACCAAGGGCCTCCTG
CAGCTCTCACACCACTCAAAGGGTTGCATTGTGACAGTGGGCAGCCCAGCAGGGGACATGCTATATCCATGCTTGGCAGC
CTATGGGACCTCCAAGGCAACCTTGACACTACTCAAGGAAACATTCAGCTGTAAACTTCTTTCCTGGAGGATCAAAGTCA
GTGTCATCCAGCCTGATTTCTTCAAAACAGTCAGT
ORF - retro_itri_657 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.75 % |
| Parental protein coverage: | 66.32 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | LVAARALLQLLRADLRL-GRPLLAALA-LLAALDWLCQRLLPPPAALAVLAAAGWIA-LSRLARPLRLPV |
| L..A..LL.LLR.DL.L.G.P.......LLA.LD.LCQ.LLP..A.LA.LAA..WIA.LS.LAR.LRLP. | |
| Retrocopy | LLVAHMLL*LLRVDL*L<GLPVAGCTGELLAPLD*LCQNLLPMLATLAMLAAPSWIA<LSCLARLLRLPL |
| Parental | ATRAVLITGCDSGFGKETAKKLDAMGFT-VLATVLELNSPGALELRACCSPRLRLLQMDLTK-PADIRRA |
| A...VLITGCDSGF.KE.AK.LD...FT..LAT.LE...P.AL.L.ACC...LRLLQMDLTK..A.I..A | |
| Retrocopy | ASCRVLITGCDSGFVKEMAKQLDTRVFT<MLATMLEFKNPNALKLSACCFLCLRLLQMDLTK<TAHISFA |
| Parental | LEFTRAHTTSTGLWGLVNNAGFNDIVADVELSPVSTFRTCMEVNFFGALELTKGLLPLLRHSKGRIVTVG |
| L.FT..HT.S.G...LVNNAGF.....DV.LSP..TF..CMEVNFF.AL.LTKGLL.L..HSKG.IVTVG | |
| Retrocopy | LKFTKSHTNSSGV*DLVNNAGFS----DVKLSPMATFCNCMEVNFFDAL*LTKGLLQLSHHSKGCIVTVG |
| Parental | SPAGDMPYPCLAAYGTSKAAMALLMDSFSCELLPWGIKVSVIQPGCFKTES |
| SPAGDM.YPCLAAYGTSKA...LL...FSC.LL.W.IKVSVIQP..FKT.S | |
| Retrocopy | SPAGDMLYPCLAAYGTSKATLTLLKETFSCKLLSWRIKVSVIQPDFFKTVS |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.
Ictidomys tridecemlineatus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_itri_657 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_657 was not experimentally validated.
Retrocopy orthology:
Ictidomys tridecemlineatus 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 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ictidomys tridecemlineatus | ENSSTOG00000016446 | 1 retrocopy |
retro_itri_657 ,
|