RetrogeneDB ID: | retro_ocun_1878 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | X:29001252..29001922(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ALKBH3 | ||
| Ensembl ID: | ENSOCUG00000016359 | ||
| Aliases: | None | ||
| Description: | alkB, alkylation repair homolog 3 (E. coli) [Source:HGNC Symbol;Acc:30141] |
Retrocopy-Parental alignment summary:
>retro_ocun_1878
ACCTGGTCAGACCTGGAGAAGGAGCATCATCTGAAAGAGTCTGTGTTCAAAGAATCAAACAAGTAGTACATAGCCTTCCA
GAGCCACAAATGATTAATAGGGAGGGAGGTCATAAAATCAGCCTGTTACCCACAAGTCTATCTAGGGAGCATTTGTACCC
TGGCATTGTTGATTTAAAAGAAGCCAACTGGGCATTTAAACAAGTTTGTCAGGATGTTCCCTGGAAACAGAAGACAGCAT
CAAAGAGGATATAATTTATCAACAACCAAGACTTGTAGCATGGGCATGGAGAACTTCCTTATACCTATTCAAGAATCCCT
ATGCAACCAAATTCTCATTATCAGCCTGTGCTGAGCACATTGAAGAACCACATCAAAGAGAACACCAGATACATGTTTAA
CAACTTACCCTGCAATCTTTACTGAAATAACAACAGTGGAGACTGGTATAGCAATGAGTAACCCTTATCAGGGAGGTGCC
CCATCATTGCCTTGCTCAATTTGGATGCCATATGTACTTCTGAGATGAGGAAGAAGCCCCCACCAGAAGAGAGCAGAAAC
CACACATATGAGGAGAGAGTTAAGATACCTCTGATCACAGGACTGCATTAATCACAGAGGGATCTGTACAAGCTAACTGG
CAGCATCGAGGGCCCAAAGAAAACCACTCT
ORF - retro_ocun_1878 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.74 % |
| Parental protein coverage: | 78.82 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | TWRSKEHPLPDREFVFREP-QQVVRPVPEPRVIDREGVYEISLSPTGVSTSRVRLYPGFIDLKEADWMLE |
| TW...E......E.VF.E...QVV...PEP..I.REG...ISL.PT..S.SR..LYPG..DLKEA.W... | |
| Retrocopy | TWSDLEKEHHLKESVFKES<KQVVHSLPEPQMINREGGHKISLLPT--SLSREHLYPGIVDLKEANWAFK |
| Parental | RLCQDVPWKQRTG-IRENITYQQPRLTAW-YGELPYTYSRITMEPNPHWHPVLSTLKRRIEENTGYSFNS |
| ..CQDVPWKQ.T..I.E.I.YQQPRL.AW..GELPYTYSRI.M.PN.H..PVLSTLK..I.ENT.Y.FN. | |
| Retrocopy | QVCQDVPWKQKTA<IKEDIIYQQPRLVAW>HGELPYTYSRIPMQPNSHYQPVLSTLKNHIKENTRYMFNN |
| Parental | LLCNLYRNEKDSVDWHSDDEPSLGRCPVIASLSFGATRTFEMRKKPSVEENGDYTYVERVKIPL-DHGTL |
| L.CNLY.N...S.DW.S...P..GRCP.IA.L...A..T.EMRKKP..EE....TY.ERVKIPL.DH.T. | |
| Retrocopy | LPCNLY*N-NNSGDWYSNE*PLSGRCPIIALLNLDAICTSEMRKKPPPEESRNHTYEERVKIPL<DHRTA |
| Parental | LIMEGATQADWQHRVPKEYHS |
| LI.EG..QA.WQHR.PKE.HS | |
| Retrocopy | LITEGSVQANWQHRGPKENHS |
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 | 0 .00 RPM | 6 .46 RPM |
| SRP017611_kidney | 0 .00 RPM | 5 .07 RPM |
| SRP017611_liver | 0 .00 RPM | 4 .93 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1878 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1878 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1878 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 | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000019863 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000016359 | 1 retrocopy |
retro_ocun_1878 ,
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