RetrogeneDB ID: | retro_itri_384 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393288.1:10118322..10119337(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MARK3 | ||
| Ensembl ID: | ENSSTOG00000009776 | ||
| Aliases: | None | ||
| Description: | MAP/microtubule affinity-regulating kinase 3 [Source:HGNC Symbol;Acc:6897] |
Retrocopy-Parental alignment summary:
>retro_itri_384
ATCATCATGTAGTATGCAAGTGGAGGTGAATTTTTTTGACTATGTGATTGCACACAGAAGAATGAAGAAAAAAAGAAGCA
AGAGCTAAATTTAGACAAATCGTGTCTGCAGTACAGTATTGCCATCAAAAGAGATTGTTCACAGAGACCTCAAGGCAGAA
AATCTGTTGTTAGATGCAGATATGAACATTAAAATAGCAGATTTTTGTTTTAGCAATGAGTTTACTTTGGTCACTAAACT
AGATCCATTTTGTGGGAGTCCTCCATATGCAGCCCAAGAATTCTCCCAGAGCTAGAAGTACCATGAGCTGGACGTAGATG
AGTGGAGTCTTGGAATTATTCTGTACACTCTAGTCAACCAGTTGCTTTCCTCTGGGGGGATAGAATCTTGGAAGGAACTT
AGAGAGTTTTGAGGGAAATACAGAATCCTTTTCTACATATCCACAGGCTATGAAAAGCTGCTCAAATGCTTTCTGGTGCT
AAACCCAATTAAGCTAGGCATTCCAGAGCAAATCACGAAGGACGGGTGGCTCAACGCAGGGCATGAGGAAGATGAACTTG
AACCCTTTGTTGAACCAGAGCTGGACTAGAAGAGAATAGATATTATGGTAGGAGTGGGATATTCACAGGAAGAAATTCAA
GAATCTCTCAGTAAAAGGAAATATGATGAAATCACAGCTACATAATTATTGTTGTGGAGAAAATCTGCAGAGCTGAACAC
TAGTGACTCCAATTCTAACAGCAATTTTTCACTTGCTAAGGTGAGGCCAAGCAGTGACCTCAGCAACAGCACCAGACAGT
CTCCTCCCCACAAAGTGCAGAGAAGCTTTTCTTCAATCCAGAAGCAGAGAGCCTACAGTGATCATGCTGGACCAGCTATT
CCTTCAGTTGGGGCATATACCAAGAGGAGTCAGATAAGCATTGCTATTAGTGACCTCAAAGAAGATGGAATTCCCTCCAA
GAAATAAGGTTGCAGTGCAGTGGGAGGAGAGGCAGTTGCTCAAGCCAGTCCAATG
ORF - retro_itri_384 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.72 % |
| Parental protein coverage: | 72.61 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | LIMEYASGGEVF-DYLVAHGRMKEK-EARAKFRQIVSAVQYCHQKR-IVHRDLKAENLLLDADMNIKIAD |
| .IM.YASGGE.F.DY..AH.RMK.K.EARAKFRQIVSAVQYCHQKR.IVHRDLKAENLLLDADMNIKIAD | |
| Retrocopy | IIM*YASGGEFF>DYVIAHRRMKKK>EARAKFRQIVSAVQYCHQKR<IVHRDLKAENLLLDADMNIKIAD |
| Parental | FGFSNEFTLGSKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDG-QNLKELRERV |
| F.FSNEFTL..KLD.FCGSPPYAA.E..Q..KY....VD.WSLG.ILYTLV...L...G....KELRE.. | |
| Retrocopy | FCFSNEFTLVTKLDPFCGSPPYAAQEFSQS*KYHELDVDEWSLGIILYTLVNQLLSSGGIESWKELRE-- |
| Parental | LRGKYRIPFYMSTDCENLLKRFLVLNPIKRGTLEQIMKDRWINAGHEEDELKPFVEPELDISDQKRIDIM |
| ..GKYRI.FY.ST..E.LLK.FLVLNPIK.G..EQI.KD.W.NAGHEEDEL.PFVEPEL...D.KRIDIM | |
| Retrocopy | F*GKYRILFYISTGYEKLLKCFLVLNPIKLGIPEQITKDGWLNAGHEEDELEPFVEPEL---D*KRIDIM |
| Parental | VGMGYSQEEIQESLSKMKYDEITATYLLLGRKSSELDASDSSSSSNLSLAKVRPSSDLSNSTGQSPHHKV |
| VG.GYSQEEIQESLSK.KYDEITAT.LLL.RKS.EL..SDS.S.SN.SLAKVRPSSDLSNST.QSP.HKV | |
| Retrocopy | VGVGYSQEEIQESLSKRKYDEITAT*LLLWRKSAELNTSDSNSNSNFSLAKVRPSSDLSNSTRQSPPHKV |
| Parental | QRSVSSSQKQRRYSDHAGPAIPSVVAYPKRSQTSTADSDLKEDGIPSRKSGGSAGGGKGIAPASPM |
| QRS.SS.QKQR.YSDHAGPAIPSV.AY.KRSQ.S.A.SDLKEDGIPS.K.G.SA.GG...A.ASPM | |
| Retrocopy | QRSFSSIQKQRAYSDHAGPAIPSVGAYTKRSQISIAISDLKEDGIPSKK*GCSAVGGEAVAQASPM |
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_384 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_384 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 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ictidomys tridecemlineatus | ENSSTOG00000009776 | 2 retrocopies |
retro_itri_1792, retro_itri_384 ,
|