RetrogeneDB ID: | retro_itri_1045 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393362.1:5615008..5615629(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | C4orf17 | ||
| Ensembl ID: | ENSSTOG00000013616 | ||
| Aliases: | None | ||
| Description: | chromosome 4 open reading frame 17 [Source:HGNC Symbol;Acc:25274] |
Retrocopy-Parental alignment summary:
>retro_itri_1045
TTGAATAACATTCTTATTGTACTGTGAATGACCGTGAGACTGAACTCAGAACATAGTGAGGCATTAGCCAGTTTAACCCC
TTAGAGAAGGATGAGATACCCCTTACAAAATGTATGACCCACCCCAACAGAGCAGCTCTGGAGAGTCCTGTTAGAGGATT
GTCACTAGCCCCAAACAATGTCAAAATGCCCCCTTTGACCTCGTTTAGAGCCCAGCAGGAAAATCAGAGTGCTTCAAAAT
TCCCAGTGAGAATCTCTTCTTAATTAAAAAGGAAGAAATCAAGGCTAAAAATCCACCATCACCTCCAACTTCATCCTCTA
CTGCTGGCTCCCATTCTTCAGAGGGGATGAGAACCAAAACTGACATCAAAGAGTACACCATTTGCCTACCAAACTATCCA
GATCAAGAAAGAAAGATCCTATCAAAGCTCGGTGGCATTTTATGCACTGATTCCCTTGTAGAAGTTACACAGCGGCTGCT
TCATGCAAAGAAAAGGAAAAATAAGGGGTCTCAGCTTTGATTCATTCTGAGTGGGCTGAGATGAACTTGTTGATCCTCCC
CAGAAGAAACACCTCTGTGGAACCAGCAGCCGAGACTGGGAAGCCACTCCCAATCAAATCA
ORF - retro_itri_1045 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.32 % |
| Parental protein coverage: | 57.14 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | LNNIPI-CTVNDDELALGALYGVSQFDQLEKDEIPFAKCNYPPSPAAPESPVREVSPAQSRV-KMPPRPH |
| LNNI.I.CTVND.E..L....G.SQF..LEKDEIP..KC...P..AA.ESPVR..S.A...V.K.P..P. | |
| Retrocopy | LNNILI<CTVNDRETELRT**GISQFNPLEKDEIPLTKCMTHPNRAALESPVRGLSLAPNNV>KCPL*PR |
| Parental | SE-PCRKFNECFKTSSENPLVIKKEEIKVKKSPSPPNACYTAGSCSSEAMSTKADVKENTVCIPNYLDQE |
| .E.P..K..ECFK..SEN...IKKEEIK.K..PSPP....TAGS.SSE.M.TK.D.KE.T.C.PNY.DQE | |
| Retrocopy | LE>PAGK-SECFKIPSENLFLIKKEEIKAKNPPSPPTSSSTAGSHSSEGMRTKTDIKEYTICLPNYPDQE |
| Parental | IKILAKLCDILHTDSLAEVTQWLLHA-STKEKEWISALIHSELAEIHLLSRHRRNTPVEPAGETGKPSAV |
| .KIL.KL..IL.TDSL.EVTQ.LLHA...KEK...SALIHSE.AE..LL...RRNT.VEPA.ETGKP... | |
| Retrocopy | RKILSKLGGILCTDSLVEVTQRLLHA<KEKEK*GVSALIHSEWAEMNLLILPRRNTSVEPAAETGKPLPI |
| Parental | KS |
| KS | |
| Retrocopy | KS |
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_1045 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1045 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 | ENSSTOG00000013616 | 1 retrocopy |
retro_itri_1045 ,
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