RetrogeneDB ID: | retro_mdom_673 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 2:62056023..62057179(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
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_673
CACTGTAAAGCTCTAGCACATGAGTATGCCAAGGCAGCTGGAAAATTGAAGGCTGAAGGTTCTAAAATCAGATTGGCCAA
AGTAGATGCCACTGAAGAATCTGATCCCGCATGGCAATATGGGGTTCGGGGGTACCCTATCAAATTTTTTAAGAATGGAG
ATACAACTTCTCCTAAAGAGTATACAGCTGGTAGAGAAGCTGAAGACATTGTGAACTGGCTGAAGAAACGGACTAGTCCA
GCGGTCACTGTCCTGGGAGATGTTGCTGCTGCTGAGTCCTTGGTGGATTCCAGTGAAGTTGCTGTTATTGGTTTATTCAA
GGATGTAGATTCAGAATCTGTCAAACAGTTCACATTGGCTGCAGAGTCCATCGATGATATCCCATTTGGAATTTCTTCCA
ACAGTGATGTGTATTCCAAATATCAAATGGATAAAGATGGCATTATCCTCCTTAAGAAGTTTGATGAAGGTAGAAACAAC
TATGATGGAGAGATTACCAAGGAGAACCTAATGAATTTTGTTAATTATCACCGGCTGCCCTTAATCATTGAGTTCACAGA
ACCCCCAATTTTTTGGAGGTGAAATCAAGACTCATATTCTGCTGTTCCTGCCAAAGAGTGTTTCTGACTATGATGACAAA
CTGAGTAACTTCAAAAAAGCAGCAGAAAGCTTCAAAGGGAAGATCCTATTTATCTTCATTGATAGTGACCACACTGACAA
CCAGAGGATCCTTGAGTTCTTTGGCTTAAAGAAAGAGGAATGCCCAGCTGTCCATCTCATCACTTTGGAAGAGGAGATGA
CCAAGTACAAGCCTGAGTCAGATGAATTAACAGCAGAAAAGATAAAAGAATTCTGTGACCGATTTTTGGAGGGCAAAGTC
AAGCCTCATTTAATGAGCCAGGACCTACCTGATGACTGGGACGAGCAGCCTGTTAAAGTACTAGTTGGGAAGAACTTTGA
GGAAGTTGCTTTTGATGAAAAAAAGAATGTCTTTGTGGAATTTTATGCTCCCTGATGTGGTCACTGCAAACAGCTGGCTC
CCATTTGGGAAAAATTGGGAGAGGCTTATAAGGATCATGAAAGTATAGTCATTGCCAAGATGGACTCAACAGCTAATGAA
GTAGTTTCTCTACGTTATTCTTCCCTGCAAGTGCTG
ORF - retro_mdom_673 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.56 % |
| Parental protein coverage: | 76.27 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | HCKALAPEYAKAAGKLKAEGSKIRLAKVDATEESDLARQYGVRGYPTIKFFKNGDTTSPKEYTAGREAED |
| HCKALA.EYAKAAGKLKAEGSKIRLAKVDATEESD.A.QYGVRGYP.IKFFKNGDTTSPKEYTAGREAED | |
| Retrocopy | HCKALAHEYAKAAGKLKAEGSKIRLAKVDATEESDPAWQYGVRGYP-IKFFKNGDTTSPKEYTAGREAED |
| Parental | IVNWLKKRTSPAVTVLRDVAAAESLVDSSEVAVIGLFKDVDSEFVKQFTLAAESIDDIPFGISSSNDVYS |
| IVNWLKKRTSPAVTVL.DVAAAESLVDSSEVAVIGLFKDVDSE.VKQFTLAAESIDDIPFGISS..DVYS | |
| Retrocopy | IVNWLKKRTSPAVTVLGDVAAAESLVDSSEVAVIGLFKDVDSESVKQFTLAAESIDDIPFGISSNSDVYS |
| Parental | KYQMDKDGIILLKKFDEGRNNYDGEITKENLMDFVNYHRLPLVIEFTEQTAPKIF-GGEIKTHILLFLPK |
| KYQMDKDGIILLKKFDEGRNNYDGEITKENLM.FVNYHRLPL.IEFTE...P.IF.GGEIKTHILLFLPK | |
| Retrocopy | KYQMDKDGIILLKKFDEGRNNYDGEITKENLMNFVNYHRLPLIIEFTE---PPIF>GGEIKTHILLFLPK |
| Parental | SVSDYDDKLSNFKKAAESFKGKILFIFIDSDHTDNQRILEFFGLKKEECPAVRLITLEEEMTKYKPESDE |
| SVSDYDDKLSNFKKAAESFKGKILFIFIDSDHTDNQRILEFFGLKKEECPAV.LITLEEEMTKYKPESDE | |
| Retrocopy | SVSDYDDKLSNFKKAAESFKGKILFIFIDSDHTDNQRILEFFGLKKEECPAVHLITLEEEMTKYKPESDE |
| Parental | LTAEKIKEFCDRFLEGKVKPHLMSQDLPDDWDKQPVKVLVGKNFEEVAFDEKKNVFVEFYAPWCGHCKQL |
| LTAEKIKEFCDRFLEGKVKPHLMSQDLPDDWD.QPVKVLVGKNFEEVAFDEKKNVFVEFYAP.CGHCKQL | |
| Retrocopy | LTAEKIKEFCDRFLEGKVKPHLMSQDLPDDWDEQPVKVLVGKNFEEVAFDEKKNVFVEFYAP*CGHCKQL |
| Parental | APIWDKLGETYKDHESIVIAKMDSTANEVEAVKVHSFPTL |
| APIW.KLGE.YKDHESIVIAKMDSTANEV......S...L | |
| Retrocopy | APIWEKLGEAYKDHESIVIAKMDSTANEVVSLRYSSLQVL |
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 .00 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 | 0 .00 RPM | 0 .00 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_673 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_673 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 |