RetrogeneDB ID: | retro_itri_522 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393298.1:15210271..15210723(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RMDN1 | ||
| Ensembl ID: | ENSSTOG00000005267 | ||
| Aliases: | None | ||
| Description: | regulator of microtubule dynamics 1 [Source:HGNC Symbol;Acc:24285] |
Retrocopy-Parental alignment summary:
>retro_itri_522
AAAAGTGAGTCAAGTTTTGCTGCAATCTGCATTAGAAAGATTTAGCTGCATAATGTTGCTGATTATGAAGCCATCAATAT
TAAAATTTGCAAATGCCTACACTAACTAGGAGCATATTGAGAAACAAATTAAACTGAACCCTAAAGATTCTACCTCCATT
CGCCTTAAGAGTACAGGGTGCTACACATTTGTTCAAATGTCTTGGTACCAAAAAATAATTACTAAAATTGCTGTTTGCAA
CTCCTTCAAGCTCCATCTAGAAGGAGGACTTGACCAACTTTCATGGAGAAAAACAAATGGATCCAATCTTCCAGAGAAAA
AACTTGGCTTCTTTCAGGAAAGACATACATGAAGTTAAACAATAAAAACTTGCTGCTTTCTGGCTGATGAAAGCTAAGGC
CTTCCCAGCACACACAAAGGAGATGCAGACAGAAGCTGCTCAGTTGCTTTCA
ORF - retro_itri_522 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.24 % |
| Parental protein coverage: | 66.23 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | KNESSFAAHKWYAICISDVGDYEGIKVKI-ANAYIIKEHFEKAIELNPKDATSVHLMGIWCYTFAEMPWY |
| K.ESSFAA.....I....V.DYE.I..KI.ANAY...EH.EK.I.LNPKD.TS..L....CYTF..M.WY | |
| Retrocopy | KSESSFAAICIRKI*LHNVADYEAINIKI>ANAYTN*EHIEKQIKLNPKDSTSIRLKSTGCYTFVQMSWY |
| Parental | QRRIAK-MLFATPPSSTYEEALGYFHRAEQVDPNFYSKNL-LLLGKTYLKLKNK-KLAAFWLMKAKDYPA |
| Q..I.K..LFATP.SS...E.L..FH...Q.DP.F..KNL.LL.GKTY.KL.NK.KLAAFWLMKAK..PA | |
| Retrocopy | QKIITK>LLFATPSSSI*KEDLTNFHGEKQMDPIFQRKNL>LLSGKTYMKLNNK<KLAAFWLMKAKAFPA |
| Parental | HTEEDKQVQTEATQLLT |
| HT...K..QTEA.QLL. | |
| Retrocopy | HT---KEMQTEAAQLLS |
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_522 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_522 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 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ictidomys tridecemlineatus | ENSSTOG00000005267 | 2 retrocopies |
retro_itri_522 , retro_itri_525,
|
| Tursiops truncatus | ENSTTRG00000002271 | 1 retrocopy |