RetrogeneDB ID: | retro_ocun_1616 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | GL018717:3830271..3830799(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSOCUG00000021310 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | STX3 | ||
| Ensembl ID: | ENSOCUG00000013382 | ||
| Aliases: | None | ||
| Description: | syntaxin 3 [Source:HGNC Symbol;Acc:11438] |
Retrocopy-Parental alignment summary:
>retro_ocun_1616
CGGCTGGAGCAGCTGAAGGCCAAGCAGCTGACACAGGATGATGACACTGATGAGGTCGAGATCGCTATTGACAACACAGC
TTTCATGGATGAGGTCTTCTCAGAGATTGAAGAAACTCGGCTCAACATTGACAAGATCTCAGAGCACGTGGAGGAGGCCA
AGAAACTCTACAGTATCATTTTTTCTGCACCAATTCCAGAGCCAAAAACCAAGGATGACCTAGAGCAGCTCACAACTGAG
ATCAAGAAAAGAGCCAACAACGTCCGGAACAAGCTGAAGAGCATGGAGAGGCACATTGAAGAAGATGAGGTCTGGTCATC
TGCAGACCTTCGAATTAGGAAATCTCAGCACTCTGACCTCTCCCGGAAGTTTGTGGAGGTGATGACCAAATACAACGAAG
CTCAGGTGGACTTCCGGGAACGCAGCAAAGGGAGAATCCAGCGGCAGCTTGAAATCACTGGCAAAAAGACAACAGATGAG
GAACTGGAGGAGATATTAGAGAGTGGCAACCCAGCCATCTTACTTTCC
ORF - retro_ocun_1616 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.23 % |
| Parental protein coverage: | 61.03 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RLIKLPVKQLTQDDDTDEVEIAIDNTAFMDEFFSEIEETRLNIDKISEHVEEAKKLYSIILSAPIPEPRK |
| RL..L..KQLTQDDDTDEVEIAIDNTAFMDE.FSEIEETRLNIDKISEHVEEAKKLYSII.SAPIPEP.K | |
| Retrocopy | RLEQLKAKQLTQDDDTDEVEIAIDNTAFMDEVFSEIEETRLNIDKISEHVEEAKKLYSIIFSAPIPEP-K |
| Parental | MVSKSVLLVVTIKEQFGKTFLSFPGMERHIEEDEVRSSADLRIRKSQHSVLSRKFVEGMTKYNEAQVDFR |
| .......L...IK............MERHIEEDEV.SSADLRIRKSQHS.LSRKFVE.MTKYNEAQVDFR | |
| Retrocopy | TKDDLEQLTTEIKKRANNVRNKLKSMERHIEEDEVWSSADLRIRKSQHSDLSRKFVEVMTKYNEAQVDFR |
| Parental | ERSKGRIQRQLEITGKKTTDEELEEMLESGNPAIFTS |
| ERSKGRIQRQLEITGKKTTDEELEE.LESGNPAI..S | |
| Retrocopy | ERSKGRIQRQLEITGKKTTDEELEEILESGNPAILLS |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP017611_brain | 1 .71 RPM | 14 .51 RPM |
| SRP017611_kidney | 2 .94 RPM | 18 .14 RPM |
| SRP017611_liver | 0 .31 RPM | 2 .54 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1616 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1616 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1616 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Myotis lucifugus | ENSMLUG00000026681 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000013382 | 1 retrocopy |
retro_ocun_1616 ,
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