RetrogeneDB ID: | retro_mdom_125 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 1:87760615..87762148(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMODG00000008634 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | P4HB | ||
| Ensembl ID: | ENSMODG00000003000 | ||
| Aliases: | None | ||
| Description: | prolyl 4-hydroxylase, beta polypeptide [Source:HGNC Symbol;Acc:8548] |
Retrocopy-Parental alignment summary:
>retro_mdom_125
GCTAACAACTGCGCTCTGCTCTCTCTCGCCCTGGCAGTGTCTACTGAAGTCGCAGATCCTCCTCAAACCAAGGAGGATGA
AGACGATTACGTCCTGGTCTTAAATAATGGCAACATCAATGAGGCACTGAGCACCTATGAATATCTCTTGGTGTTCTTCC
ATGCTCCTTGGTGTCTTCCCTGTCGAGATTTGGCGCCTGAGTATGCCAAGGCAGCGGAACAGTTGAAATCTGAGAGATCT
ATCAAGTTAGCCAAAATAGATGCCACTCAAGAACATGGTCTAGCACGGCAGTTTAGCATTCGACTCTACCCTACTATCAA
GTTATTTAAGCATGGAGATACATCTTCTCCTAAGGAGTATACGGAAGGCAGAGATGCTGAAGATATCGTGAAATGGATGC
AGCTACAACTCCAGCCCGCTGTCATTATCTTGGAAGATGTCCCTACTGTAGAGTCTTTAGTGGATTCCAATGAACTTGTT
GTTTTAGGCATATTCAAAGATGCTCAGTCGGATAATGTTAAGAATTTCACACTGGCTGCAGAGTCCATCGATGGTATCCC
ATTCGGAATCACTTACAACAACGAGGCGTTTTCGAAATATCAACTGGAGAAAGATAGCATTATCCTCTTTAAGAAGTTTG
ATGAAGGTCGAAACAACTTTCATGGAGAGATTTCAAAAATGAACTTAATAAATTTTGTTCATAACCACTGGCTGCCCTTG
GTCACCGAGTACAATGAACATACTGCCCCAAGGATTTTTGAAAGTCAGGTGAAAAATCATCTGCTAATATTCTTGCAAAA
GAGCAATAATGACTTTGAGGACAAAATTAGCAACTTCAAAAAAGCGGCTGAAAGTTACAGGGGGAAAATCCTATATATCC
TCATTGATATTGAATTCAGTGACAACAAGGGGATCCTTAAATTCTTTAGCCTGAAAGAAGAAGAGTGCCCAACGATGCGT
CTCATTAGTATGGAAAGTGACATGACCAAGTACAAGCCAGAGACAAATGAATTAACGATAGAAAAGATAGACGAATTCTG
TAAAAAGTATTTAGAGGAAAAATCCAAGTCCCATCTGATGAGCCAAGATGTGCCTGATGACTGGGATAAAAAGCCTGTTA
AAATATTGGTTGGGAAAAACTTTGAAAAAGTTGCTTTCGATGAGAAAAAGAACGTCTTTGTGAACTTCTATGCTCCTTGG
TGTAGTCAGTGCATAGGGATAGCTCCCATTTGGGATAAACTGGGAGATGTTTACAAGGATCATCAAGATATAGTCATTGC
TAAGATGGACTCATCAGTTAATGAAGTTGATTCAATTACAGTCCATAATTTCCCCACACTGATATACTTCCCTGCAGGTA
CCGACAGAAAAATCATTGAATACCATGGGGCATGGACTCTAGAAAATTTCAGAAAGTTCCTAGACAGCGGTGACTATGAT
AGACCAAAGAAAATAAGTGGCTTAGAGGTCCTAGAAGAAACTGAAGAAATGGAATCACAAGATAGGAAAGAGAGAGGACA
AAGAACTCATTCT
ORF - retro_mdom_125 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.87 % |
| Parental protein coverage: | 97.45 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | NRVLLCLALAVMAGVRADAPK----EEDDVLVLNKSNFGEALKSYEYLLVEFYAPWCGHCKALAPEYAKA |
| N..LL.LALAV...V.AD.P.....E.D.VLVLN..N..EAL..YEYLLV.F.APWC..C..LAPEYAKA | |
| Retrocopy | NCALLSLALAVSTEV-ADPPQTKEDEDDYVLVLNNGNINEALSTYEYLLVFFHAPWCLPCRDLAPEYAKA |
| Parental | AGKLKAEGSKIRLAKVDATEESDLARQYGVRGYPTIKFFKNGDTTSPKEYTAGREAEDIVNWLKKRTSPA |
| A..LK.E.S.I.LAK.DAT.E..LARQ...R.YPTIK.FK.GDT.SPKEYT.GR.AEDIV.W......PA | |
| Retrocopy | AEQLKSERS-IKLAKIDATQEHGLARQFSIRLYPTIKLFKHGDTSSPKEYTEGRDAEDIVKWMQLQLQPA |
| Parental | VTVLRDVAAAESLVDSSEVAVIGLFKDVDSEFVKQFTLAAESIDDIPFGISSSNDVYSKYQMDKDGIILL |
| V..L.DV...ESLVDS.E..V.G.FKD..S..VK.FTLAAESID.IPFGI...N...SKYQ..KD.IIL. | |
| Retrocopy | VIILEDVPTVESLVDSNELVVLGIFKDAQSDNVKNFTLAAESIDGIPFGITYNNEAFSKYQLEKDSIILF |
| Parental | KKFDEGRNNYDGEITKENLMDFVNYHRLPLVIEFTEQTAPKIFGGEIKTHILLFLPKSVSDYDDKLSNFK |
| KKFDEGRNN..GEI.K.NL..FV..H.LPLV.E..E.TAP.IF....K.H.L.FL.KS..D..DK.SNFK | |
| Retrocopy | KKFDEGRNNFHGEISKMNLINFVHNHWLPLVTEYNEHTAPRIFESQVKNHLLIFLQKSNNDFEDKISNFK |
| Parental | KAAESFKGKILFIFIDSDHTDNQRILEFFGLKKEECPAVRLITLEEEMTKYKPESDELTAEKIKEFCDRF |
| KAAES..GKIL.I.ID....DN..IL.FF.LK.EECP..RLI..E..MTKYKPE..ELT.EKI.EFC... | |
| Retrocopy | KAAESYRGKILYILIDIEFSDNKGILKFFSLKEEECPTMRLISMESDMTKYKPETNELTIEKIDEFCKKY |
| Parental | LEGKVKPHLMSQDLPDDWDKQPVKVLVGKNFEEVAFDEKKNVFVEFYAPWCGHCKQLAPIWDKLGETYKD |
| LE.K.K.HLMSQD.PDDWDK.PVK.LVGKNFE.VAFDEKKNVFV.FYAPWC..C...APIWDKLG..YKD | |
| Retrocopy | LEEKSKSHLMSQDVPDDWDKKPVKILVGKNFEKVAFDEKKNVFVNFYAPWCSQCIGIAPIWDKLGDVYKD |
| Parental | HESIVIAKMDSTANEVEAVKVHSFPTLKFFPASADRTVIDYNGERTLEGFKKFLESGGQDGAGDDDDLED |
| H..IVIAKMDS..NEV....VH.FPTL..FPA..DR..I.Y.G..TLE.F.KFL.SG..D.......LE. | |
| Retrocopy | HQDIVIAKMDSSVNEVDSITVHNFPTLIYFPAGTDRKIIEYHGAWTLENFRKFLDSGDYDRPKKISGLEV |
| Parental | LEEAEEPDMEE |
| LEE.EE..... | |
| Retrocopy | LEETEEMESQD |
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 |
|---|---|---|
| SRP007412_brain | 0 .72 RPM | 0 .00 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .00 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .00 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .00 RPM |
| SRP007412_testis | 12764 .20 RPM | 0 .00 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_125 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_125 was not experimentally validated.
Retrocopy orthology:
Monodelphis domestica 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 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000003000 | 2 retrocopies |
retro_mdom_125 , retro_mdom_673,
|
| Sarcophilus harrisii | ENSSHAG00000011040 | 1 retrocopy |