RetrogeneDB ID: | retro_ocun_684 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 14:6090815..6092930(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | STT3A | ||
| Ensembl ID: | ENSOCUG00000014677 | ||
| Aliases: | None | ||
| Description: | STT3A, subunit of the oligosaccharyltransferase complex (catalytic) [Source:HGNC Symbol;Acc:6172] |
Retrocopy-Parental alignment summary:
>retro_ocun_684
ATGACTAAGCTTGGATTTTTGCGGTTGTCCTATGAGAAGCAGGACACACTTCTGAAGCTTCTCATTCTGCCAATGGCTGC
TGTGTTATCTTTCTCCACTCGTCTCTTTGCTGTCCTGAGATTTGAAAGTGTTATCCATGAATTTGATCCGTACTTTAATT
ATCGGACTACCCGGTTCCTGGCCGAGGAGGGGTTTTATAAATTCCATAACTGGTTTGATGACCGGGCCTGGTACCCTTTG
GGACGAATCATAGGAGGAACAATATACCCAGGCTTAATGATTACCTCTGCTGCAATCTACCATGTGCTGCACTTTTTCCA
CATCACCATTGACATTCGGAATGTCTGTGTGTTCCTGGCCCCTCTCTTCTCCTCCTTCACTACCATCGTCACGTACCACC
TTACCAAAGAGCTCAAGGATGCAGGGGCTGGGCTGCTTGCTGCTGCCATGATAGCTGTTGTCCCTGGATATATCTCCTGA
TCTGTGGTTGGCTCCTATGATAATGAAGGGATTGCCATTTTTTGTATGCTGCTTACCTACTACATGTGGATCAAGGCAGT
AAAGACTGGTTCTATCTATTGGGCAGCCAAGTGTGCCCTTGCTTATTTCTATATGGTCTCTTCATGGGGGGGTTATGTGT
TCCTGATCAACTTGATCCCGCTCCACGTCCTGGTGCTGATGCTCACAGGCCGTTTCTCCCATCGAATCTACGTGGCTTAC
TGTACCGTCTACTGCCTGGGTACCATACTTTCCAAGCAGATCTCCTTTGTGGGTTTCCAGCCTGTCCTTTCGTCGGAGCA
CATGGCAGCCTTTGGGGTCTTTGGCCTCTGCCAGATACATGCCTTTGTGGATTACCTGCGCAGCAAGTTGAACCCACAGC
AATTTGAAGTTCTTTTCCGCAGTGTCATCCCCTTGGTGGGCTTTGTCCTTCTCACAATGGGAGCTCTCCTCATGCTGACA
GGAAAAATATCTCCCTGGACGGGCCGTTTCTACTCACTGCTGGATCCTTCTTATGCTAAGAACAACATCCCCATCATTGC
ATCTGTATCTGAGCATCAGCCCACAACCTGGTCCTCCTACTATTTTGACTTGCAGCTCCTCGTCTTCATGTTTCCAGTTG
GCCTCTATTACTGCTTTAGCAACCTGTCTGATGCCCGGATTTTTATCATCATGTATGGTGTGACCAGCATGTACTTTTCA
GCTGTGATGTGCGTCTGATGTTGGTGTTGGCGCCTGTTATGTGCATTCTTTCTGGCATTGGAGTTTCCCAGGTGCTATCC
ACATATATGAAGAATCTGGACATAAGTCGTCCAGACAAGAAGAGCAAGAAGCAACAGGATTCTACATACCCTATTAAGAA
TGAAGTGGCAAGTGGGATGATATTGGTCATGGCCTTCTTTCTCATTACCTACACCTTTCATTCAACCTGGGTGACCAGTG
AGGCCTACTCTTCTCCCTCCATTGTGCTGTCTGCCCGGGGTGGGGATGGCAGTAGGATCATTTTTGATGACTTCCGAGAA
GCGTATTATTGGCTTCGTCACAATACTCCAGAGGATGCAAAAGTCATGTCATGGTGGGATTACGGCTACCAGATTACAGC
TATGGCAAATCGGACAATTTTAGTGGACAACAACACATGGAATAATACCCATATTTCTCGAGTAGGGCAGGCAATGGCAT
CCACAGAAGAAAAAGCCTATGAAATCATGAGGGAGCTTGATGTCAGCTATGTGTTGGTCATTTTTGGAGGCCTCACTGGG
TATTCCTCTGATGATATCAACAAATTTCTTTGGATGGTTCGGATTGGAGGCAGCACAGACACAGGCAAACATATCAAGGA
GAATGACTATTATACTCCAACTGGGGAATTCCGTGTGGGACCGTGAGGGTTCTCCAGTGCTGCTCAACTGTCTCATGTAC
AAGATGTGTTACTACCGCTTTGGACAGGTCTACACAGAAGCTAAGCGTCCACCAGGCTTTGACCGTGTCCGAAATGCTGA
GATTGGGAATAAAGACTTTGAGCTTGATGTGCTGGAGGAGGCATATACCACAGAACACTGGCTGGTCAGGATATACAAGG
TAAAGGACCTGGATAATCGAGGCTTGTCAAGGACA
ORF - retro_ocun_684 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.87 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MTKLGFLRLSYEKQDTLLKLLILSMAAVLSFSTRLFAVLRFESVIHEFDPYFNYRTTRFLAEEGFYKFHN |
| MTKLGFLRLSYEKQDTLLKLLIL.MAAVLSFSTRLFAVLRFESVIHEFDPYFNYRTTRFLAEEGFYKFHN | |
| Retrocopy | MTKLGFLRLSYEKQDTLLKLLILPMAAVLSFSTRLFAVLRFESVIHEFDPYFNYRTTRFLAEEGFYKFHN |
| Parental | WFDDRAWYPLGRIIGGTIYPGLMITSAAIYHVLHFFHITIDIRNVCVFLAPLFSSFTTIVTYHLTKELKD |
| WFDDRAWYPLGRIIGGTIYPGLMITSAAIYHVLHFFHITIDIRNVCVFLAPLFSSFTTIVTYHLTKELKD | |
| Retrocopy | WFDDRAWYPLGRIIGGTIYPGLMITSAAIYHVLHFFHITIDIRNVCVFLAPLFSSFTTIVTYHLTKELKD |
| Parental | AGAGLLAAAMIAVVPGYISRSVAGSYDNEGIAIFCMLLTYYMWIKAVKTGSIYWAAKCALAYFYMVSSWG |
| AGAGLLAAAMIAVVPGYIS.SV.GSYDNEGIAIFCMLLTYYMWIKAVKTGSIYWAAKCALAYFYMVSSWG | |
| Retrocopy | AGAGLLAAAMIAVVPGYIS*SVVGSYDNEGIAIFCMLLTYYMWIKAVKTGSIYWAAKCALAYFYMVSSWG |
| Parental | GYVFLINLIPLHVLVLMLTGRFSHRIYVAYCTVYCLGTILSMQISFVGFQPVLSSEHMAAFGVFGLCQIH |
| GYVFLINLIPLHVLVLMLTGRFSHRIYVAYCTVYCLGTILS.QISFVGFQPVLSSEHMAAFGVFGLCQIH | |
| Retrocopy | GYVFLINLIPLHVLVLMLTGRFSHRIYVAYCTVYCLGTILSKQISFVGFQPVLSSEHMAAFGVFGLCQIH |
| Parental | AFVDYLRSKLNPQQFEVLFRSVISLVGFVLLTVGALLMLTGKISPWTGRFYSLLDPSYAKNNIPIIASVS |
| AFVDYLRSKLNPQQFEVLFRSVI.LVGFVLLT.GALLMLTGKISPWTGRFYSLLDPSYAKNNIPIIASVS | |
| Retrocopy | AFVDYLRSKLNPQQFEVLFRSVIPLVGFVLLTMGALLMLTGKISPWTGRFYSLLDPSYAKNNIPIIASVS |
| Parental | EHQPTTWSSYYFDLQLLVFMFPVGLYYCFSNLSDARIFIIMYGVTSMYFSAVM-VRLMLVLAPVMCILSG |
| EHQPTTWSSYYFDLQLLVFMFPVGLYYCFSNLSDARIFIIMYGVTSMYFSAVM.VRLMLVLAPVMCILSG | |
| Retrocopy | EHQPTTWSSYYFDLQLLVFMFPVGLYYCFSNLSDARIFIIMYGVTSMYFSAVM<VRLMLVLAPVMCILSG |
| Parental | IGVSQVLSTYMKNLDISRPDKKSKKQQDSTYPIKNEVASGMILVMAFFLITYTFHSTWVTSEAYSSPSIV |
| IGVSQVLSTYMKNLDISRPDKKSKKQQDSTYPIKNEVASGMILVMAFFLITYTFHSTWVTSEAYSSPSIV | |
| Retrocopy | IGVSQVLSTYMKNLDISRPDKKSKKQQDSTYPIKNEVASGMILVMAFFLITYTFHSTWVTSEAYSSPSIV |
| Parental | LSARGGDGSRIIFDDFREAYYWLRHNTPEDAKVMSWWDYGYQITAMANRTILVDNNTWNNTHISRVGQAM |
| LSARGGDGSRIIFDDFREAYYWLRHNTPEDAKVMSWWDYGYQITAMANRTILVDNNTWNNTHISRVGQAM | |
| Retrocopy | LSARGGDGSRIIFDDFREAYYWLRHNTPEDAKVMSWWDYGYQITAMANRTILVDNNTWNNTHISRVGQAM |
| Parental | ASTEEKAYEIMRELDVSYVLVIFGGLTGYSSDDINKFLWMVRIGGSTDTGKHIKENDYYTPTGEFRV-DR |
| ASTEEKAYEIMRELDVSYVLVIFGGLTGYSSDDINKFLWMVRIGGSTDTGKHIKENDYYTPTGEFRV.DR | |
| Retrocopy | ASTEEKAYEIMRELDVSYVLVIFGGLTGYSSDDINKFLWMVRIGGSTDTGKHIKENDYYTPTGEFRV>DR |
| Parental | EGSPVLLNCLMYKMCYYRFGQVYTEAKRPPGFDRVRNAEIGNKDFELDVLEEAYTTEHWLVRIYKVKDLD |
| EGSPVLLNCLMYKMCYYRFGQVYTEAKRPPGFDRVRNAEIGNKDFELDVLEEAYTTEHWLVRIYKVKDLD | |
| Retrocopy | EGSPVLLNCLMYKMCYYRFGQVYTEAKRPPGFDRVRNAEIGNKDFELDVLEEAYTTEHWLVRIYKVKDLD |
| Parental | NRGLSRT |
| NRGLSRT | |
| Retrocopy | NRGLSRT |
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 .22 RPM | 19 .54 RPM |
| SRP017611_kidney | 0 .61 RPM | 53 .11 RPM |
| SRP017611_liver | 1 .39 RPM | 60 .12 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_684 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_684 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_684 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 | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000014677 | 1 retrocopy |
retro_ocun_684 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000020526 | 1 retrocopy |