RetrogeneDB ID: | retro_mdom_1075 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 3:526042417..526043707(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RNF38 | ||
| Ensembl ID: | ENSMODG00000002665 | ||
| Aliases: | None | ||
| Description: | ring finger protein 38 [Source:HGNC Symbol;Acc:18052] |
Retrocopy-Parental alignment summary:
>retro_mdom_1075
ATGCAACCATGGAAGATGACATCAAATAGGCAGCCTCCTTCAGTTCGACCCAATCAGCATCATTTCTCAGGGGAATGATG
CAACACACCTGCACGCAACAGAAGTCCTCCTGTTAGGCGCCAGAGAGGAAGGAGGGATCGTCTCTCTCAACATAATTCCA
TTAGTCAGGATGAAATCTATCACCATCTTTCATATGGACAGCAGCAAGCAATAGAGGAACCCCGAGCCTTCCATCCTTCG
AATGTATCCCCACGTATGTTGCATCCTACTGCTCACCCACCACAGCAGAATGCAGTGATGGTTGACATACATGAACAGCT
TCATCAAGGCACAGTCCCAGTTTCTTATACTGTAACAACTGTTGCTCCACATGGGATTCCACTTTGTACTGGTCAGCACA
TCCCTGCTTGTAATATACAGCAGGTTCCAGGATGCTCTGTGGTTTTCAGTGGACAGCACCTCCCAGTCTGTAGTGTGCCT
CCTCCAATGCTTCAGGCATGTTCAGTTCAGCACTTGCCAGTACCATATGCTGCATTCCCACCTCTTATTTCTAGTGATCC
ATTTCTTTTACATCCGCCTCACCTTTCTCCACATCCTCCTCCTCATTTGCCACCACCTGGCCAGTTTGTACCCTTCCAAA
CACAGCAATCACAATCGCCATTACAGAGGATAGAAAATTAAGTTGAACTCTTGGGAGAACACCTTCCTGTAGGAGGCTTT
ACTTATCCTGCATCGGCCCATCCTCCAACATTACCTCCATCAGCCCTTCTCCAGTTCTTAATACACGATCCTTTGCACCA
GGAGGTATCTTTTGGAGTACCTTATCCTCCATTTATGCCTCGAAGACTTACAGGACATAGTAGATATCAATCCCAGCAAC
CAATACCGCCTCCCCCTTATCATCCCAGTCTCCTACCATATGTACTATCAATGCTTCCAGTGCCACCTGCAATAGGTCCA
GCCTTCAGCTTTGAATTGGATGGAGTAGATGGAGAAGTAGAAAATTATGAGGCATTACTAAATCTGGCAGAATGACTAGA
AGCTAAGCCACGTGGATTAACAAAAGCAGATACCGAATAGCTTCCTTCTTACCGGTTCAATCCTATCAACCACCAGTCAG
AGCAGACTTTGTGCGTAGTATGCATGTGTGATTTTGAGTCAAGGCAGCTACTTAGAGTCTTACCCTGTAACCATGAGTTC
CATGCCAAGTATGTTGATAAATGGCTTAAGGCAAATTGTACCTGCCCAATTTGTCGAGCTGATGCATCGGAAGTACATCG
TGATTCAGAA
ORF - retro_mdom_1075 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.21 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MRPWEMTSNRQPPSVRPNQHHFSGERCNTPARNRRSPPVRRQRGRRDRLSRHNSISQDENYHHLSYGQQQ |
| M.PW.MTSNRQPPSVRPNQHHFSGE.CNTPARNR.SPPVRRQRGRRDRLS.HNSISQDE.YHHLSYGQQQ | |
| Retrocopy | MQPWKMTSNRQPPSVRPNQHHFSGE*CNTPARNR-SPPVRRQRGRRDRLSQHNSISQDEIYHHLSYGQQQ |
| Parental | AIEEPRAFHPPNVSPRMLHPAAHPPQQNAVMVDIHEQLHQGTVPVSYTVTTVAPHGIPLCTGQHIPACNT |
| AIEEPRAFHP.NVSPRMLHP.AHPPQQNAVMVDIHEQLHQGTVPVSYTVTTVAPHGIPLCTGQHIPACN. | |
| Retrocopy | AIEEPRAFHPSNVSPRMLHPTAHPPQQNAVMVDIHEQLHQGTVPVSYTVTTVAPHGIPLCTGQHIPACNI |
| Parental | QQVPGCSVVFSGQHLPVCSVPPPMLQACSVQHLPVPYAAFPPLISSDPFLLHPPHLSPHHPPHLPPPGQF |
| QQVPGCSVVFSGQHLPVCSVPPPMLQACSVQHLPVPYAAFPPLISSDPFLLHPPHLSPH.PPHLPPPGQF | |
| Retrocopy | QQVPGCSVVFSGQHLPVCSVPPPMLQACSVQHLPVPYAAFPPLISSDPFLLHPPHLSPHPPPHLPPPGQF |
| Parental | VPFQTQQSRSPLQRIENEVELLGEHLPVGGFTYPASAHPPTLPPSAPLQFLTHDPLHQEVSFGVPYPPFM |
| VPFQTQQS.SPLQRIEN.VELLGEHLPVGGFTYPASAHPPTLPPSA.LQFL.HDPLHQEVSFGVPYPPFM | |
| Retrocopy | VPFQTQQSQSPLQRIEN*VELLGEHLPVGGFTYPASAHPPTLPPSALLQFLIHDPLHQEVSFGVPYPPFM |
| Parental | PRRLTGRSRYRSQQPIPPPPYHPSLLPYVLSMLPVPPAIGPAFSFELDVEDGEVENYEALLNLAERLGEA |
| PRRLTG.SRY.SQQPIPPPPYHPSLLPYVLSMLPVPPAIGPAFSFELD..DGEVENYEALLNLAE.L.EA | |
| Retrocopy | PRRLTGHSRYQSQQPIPPPPYHPSLLPYVLSMLPVPPAIGPAFSFELDGVDGEVENYEALLNLAE*L-EA |
| Parental | KPRGLTKADIEQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPIC |
| KPRGLTKAD.E.LPSYRFNP.NHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAK.VDKWLKAN.TCPIC | |
| Retrocopy | KPRGLTKADTE*LPSYRFNPINHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKYVDKWLKANCTCPIC |
| Parental | RADASEVHRDSE |
| RADASEVHRDSE | |
| Retrocopy | RADASEVHRDSE |
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_1075 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1075 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 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000005519 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000010299 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000002665 | 1 retrocopy |
retro_mdom_1075 ,
|