RetrogeneDB ID: | retro_itri_478 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393294.1:13612765..13613494(+) | ||
| Located in intron of: | ENSSTOG00000012335 | ||
Retrocopy information | Ensembl ID: | ENSSTOG00000022019 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PDGFC | ||
| Ensembl ID: | ENSSTOG00000001652 | ||
| Aliases: | None | ||
| Description: | platelet derived growth factor C [Source:HGNC Symbol;Acc:8801] |
Retrocopy-Parental alignment summary:
>retro_itri_478
ATGCTCCTCTTCAGGCTTCTCCTGCTGACATCTGCCCTGGCCGGCCAGATTCACGGGACTCAGGCTGAGTCCAACCTGAG
TAGTAAATTCCAGTTCTCCAGCAACAAGGAACAGAACGGAGTACAAAATCCCCATCATGAGAGAATTATTACTGTGTCTA
CAAATGGGAGTATTCACAGCCCAAGGTTTCCTCATACTTACCCAAGAAATATGGTCTTGGTATGGAGATTGGTAGCAGAG
GAAAATGTGTGGATACAACTTAAATTTGATGAAAGATTTGGGCCGGAAGACCCAGAAGATGACATTTGCAAGTATGATTT
TGTAGAAGTTGAGGAACCCAGTGATGGAACTGTATTATGGTGCTGGTGTGATTCTGGTCCTGTACCAGGAAAACAGATTT
CCAAAGGAAATCAAATCAGAATAAGATTTGTATCTGAGTATTTTTCTTCTGAACCCGGATTCTGCATCCACTACAACATT
GTTATGCCACAACTCACAGAAGCTGTGAGTCCTTCAGTGTTACCCCCTTCAGCTTTGCCACTGGACCTGCTTAATAATGC
TGTAACCGCCTTTAGTACTTTGGAGGATCTTATTCACTATCTTGAACCAGATAGATGGCAGCTGGACTTAGAAGATCTAT
ACAGGCCAACATGGCAACTTCTTGGCAAAGCTTTTGTTTTTGGAAGAAAATCTAGAGTGGTGGATCTGAACCTTCTAAAA
GAGGAGGTT
ORF - retro_itri_478 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.9 % |
| Parental protein coverage: | 70.93 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MLLFGLLLLTSALAGQIHGTQAESNLSSKFQFSSNKEQNGVQNPQHERIITVSTNGSIHSPRFPHTYPRN |
| MLLF.LLLLTSALAGQIHGTQAESNLSSKFQFSSNKEQNGVQNP.HERIITVSTNGSIHSPRFPHTYPRN | |
| Retrocopy | MLLFRLLLLTSALAGQIHGTQAESNLSSKFQFSSNKEQNGVQNPHHERIITVSTNGSIHSPRFPHTYPRN |
| Parental | MVLVWRLVAEENVWIQLTFDERFGLEDPEDDICKYDFVEVEEPSDGTVLGRWCGSGPVPGKQISKGNQIR |
| MVLVWRLVAEENVWIQL.FDERFG.EDPEDDICKYDFVEVEEPSDGTVL..WC.SGPVPGKQISKGNQIR | |
| Retrocopy | MVLVWRLVAEENVWIQLKFDERFGPEDPEDDICKYDFVEVEEPSDGTVLWCWCDSGPVPGKQISKGNQIR |
| Parental | IRFVSDEYFPSEPGFCIHYNIVMPQLTEAVSPSVLPPSALPLDLLNNAVTAFSTLEDLIRYLEPDRWQLD |
| IRFVS.EYF.SEPGFCIHYNIVMPQLTEAVSPSVLPPSALPLDLLNNAVTAFSTLEDLI.YLEPDRWQLD | |
| Retrocopy | IRFVS-EYFSSEPGFCIHYNIVMPQLTEAVSPSVLPPSALPLDLLNNAVTAFSTLEDLIHYLEPDRWQLD |
| Parental | LEDLYRPTWQLLGKAFVFGRKSRVVDLNLLKEEV |
| LEDLYRPTWQLLGKAFVFGRKSRVVDLNLLKEEV | |
| Retrocopy | LEDLYRPTWQLLGKAFVFGRKSRVVDLNLLKEEV |
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_478 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_478 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 | ENSSTOG00000001652 | 1 retrocopy |
retro_itri_478 ,
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