RetrogeneDB ID: | retro_itri_930 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393345.1:2804890..2806017(-) | ||
| Located in intron of: | ENSSTOG00000002689 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MAPK4 | ||
| Ensembl ID: | ENSSTOG00000022822 | ||
| Aliases: | None | ||
| Description: | mitogen-activated protein kinase 4 [Source:HGNC Symbol;Acc:6878] |
Retrocopy-Parental alignment summary:
>retro_itri_930
ATGGCAGAGAAATTTGAAAGTCTTATGAACATTCATGGTTTTGATCTGGGCTCTAGGTATATGGACTTAAAACCATTGGG
TTGTGGAGGCAATGGCTTGGTTTTTTCTGCTGTAGACAATGAATGTGACAAAAGAGTAGCCATCAAGAAAATTGTCCTTA
CTGATCCCCAGAGTGTCAAACATGCTCTCCGTGAAATCAAATTATTAGAAGACTTGACCATGATAACATTGTGAAAGTGT
TTAAAATTCTTGGCCCCAGTGGAAGCCAGTTAACAGACGTTGTGGGCTCTCTTACTGAACTGAACAGTGTTTACATTGTT
CAGGAGTACATGGAGACAGACTTGGCTAATGTGCTGGAGCAGGGCCCTTTACTGGAAGAGCATGCCAGGCTTTTCATGTA
TCAGCTGCTACAGGGGCTCAAGTATATTCACTCTGCAAATGTACTGCACAGAGATCTCAAACCAGCTAATCTTTTCATTA
ATACTGAAGACTTGGTGCTGAAGATAGGTGACTTTAGTCTTGCACGGATTATGGATCCTCATTATTCCCATAAGGGTCAG
CTTTCTGAAGGTTTGGTTACTAAATGGTACAGATCTCCACATCTTTTACTTTCTCCTAATAACTATACTAAAGCCATTGA
CATGTGGGCTGCAGGCTGCATCTTTGCTGAAACGCTGACTGGTAAAACCCTCTTTGCAGGTGCACATGAACTTGAACAGA
TGCAACTGATTTTAGAATCTATTCCTGTTGTACATGAGGAAGATCGTTCGGAGCTTCTCAGTGTAATTCCAGTTTACATT
AGAAATGATATGACTGAGCCACACAAACCTTTAACTCAGCTGCTTTCAGGAATTAGTCGAGAAGCACTGGATTTCCTGGA
ACAAATTTTGACATTTAGCCCCATGGATCGATTGACAGCAGAGGAAGCACTCTCTTATCCTTATATGAGTATATATTCTT
TTCCAGTGGATGAGCCAATTTCAAGCCATCCTTTTCACATTGAAGATGAAGTTGATGATATTTTGCTTATGGATGAAACT
CACAGTCACATTTATAACTGGGAAAGGTACCATGATTGTCAGTTTTCAGAGCATGATTGGCCTATACGTAACAACTTCGA
TACTGAT
ORF - retro_itri_930 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 66.58 % |
| Parental protein coverage: | 62.82 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAERGDCFASVYGYDLGGRFVDFQPLGFGVNGLVLSATDSHTCRKVAVKKIALSDARSMKHALREIK-II |
| MAE.........G.DLG.R..D..PLG.G.NGLV.SA.D......VA.KKI.L.D..S.KHALREIK.II | |
| Retrocopy | MAEKFESLMNIHGFDLGSRYMDLKPLGCGGNGLVFSAVDNECDKRVAIKKIVLTDPQSVKHALREIK<II |
| Parental | RRLDHDNIVKVYEVLGPKG---TDLQGELFKFSVAYIVQEYMETDLARLLEQGTLTEEHAKLFMYQLLRG |
| RRLDHDNIVKV...LGP.G...TD..G.L......YIVQEYMETDLA..LEQG.L.EEHA.LFMYQLL.G | |
| Retrocopy | RRLDHDNIVKVFKILGPSGSQLTDVVGSLTELNSVYIVQEYMETDLANVLEQGPLLEEHARLFMYQLLQG |
| Parental | LKYIHSANVLHRDLKPANIFISTEDLVLKIGDFGLARIVDQHYSHKGYLSEGLVTKWYRSPRLLLSPNNY |
| LKYIHSANVLHRDLKPAN.FI.TEDLVLKIGDF.LARI.D.HYSHKG.LSEGLVTKWYRSP.LLLSPNNY | |
| Retrocopy | LKYIHSANVLHRDLKPANLFINTEDLVLKIGDFSLARIMDPHYSHKGQLSEGLVTKWYRSPHLLLSPNNY |
| Parental | TKAIDMWAAGCILAEMLTGRMLFAGAHELEQMQLILETIPVIREEDKDELLRVMPAFV-NSTWEVKRPLR |
| TKAIDMWAAGCI.AE.LTG..LFAGAHELEQMQLILE.IPV..EED..ELL.V.P....N...E...PL. | |
| Retrocopy | TKAIDMWAAGCIFAETLTGKTLFAGAHELEQMQLILESIPVVHEEDRSELLSVIPVYIRNDMTEPHKPLT |
| Parental | KLLPEVNSEAIDFLEKILTFNPMDRLTAEMGLQHPYMSPYSCPEDEPISQHPFRIEDEIDDIVLMAASQS |
| .LL.....EA.DFLE.ILTF.PMDRLTAE..L..PYMS.YS.P.DEPIS.HPF.IEDE.DDI.LM....S | |
| Retrocopy | QLLSGISREALDFLEQILTFSPMDRLTAEEALSYPYMSIYSFPVDEPISSHPFHIEDEVDDILLMDETHS |
| Parental | QLSNWDRYLVC--SSQRYPVSLSSDLE |
| ...NW.RY..C..S....P.....D.. | |
| Retrocopy | HIYNWERYHDCQFSEHDWPIRNNFDTD |
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_930 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_930 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 | ENSSTOG00000022822 | 1 retrocopy |
retro_itri_930 ,
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