RetrogeneDB ID: | retro_mdom_1139 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 3:222404495..222405122(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TMEM42 | ||
| Ensembl ID: | ENSMODG00000029706 | ||
| Aliases: | None | ||
| Description: | transmembrane protein 42 [Source:HGNC Symbol;Acc:28444] |
Retrocopy-Parental alignment summary:
>retro_mdom_1139
ATGGCACCGCATGGGCGTGGTTGCCCCAGCAGGTGAAGTGCAGGCAGGGACCCTGGGAAAGGTTCTGATTTTGCCTCAGC
TCGCGGTTCAGGCAGGGGCCCCATTGCCCTGCCGCGACTGCTCCAGTTCCCATTTCTGGTGCCGGAAGGGATGGCGGGCA
TTCTGAGGCCCAACGCCCTGATTCAACTCTGCTGGGGCTCAGCTTTTTCATCCTTCTCAGCCGGCAGCATGGGTGCCTTC
AAGGCCACCTTCACCAAACTGGCTCTAAAACCCACAGTGTCCCAGGCACCATAGGAGGACATCGAGGGGCAGGAACAACC
TTACTGGCCAGCCATGCAGGCCTGGCTGACCTTTATGTTTGGACTGATGGCCTTTTCATTGATGATTGTTAGCAACTCGC
TGATGTGGGCCTTCTTTTCCAAAGGACTCAGCATTTCTTCTTCTGCTACAGCATCACAGACAATGACTCCTCCTAACATC
ACTGACTCTGCCTTCCTGTGTTACCTGTTTTATGGAGAATACTATGCCATGATGTGGCAGGCTGGTGTCCTCCTGACCCT
CAATGGACTTGCACTGATGCACATAAGCCTGCTGGTCCATGAGGAGGTCGAGGAGAAGAAGAATCAG
ORF - retro_mdom_1139 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.58 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAPRGRGCRSRRGESRDPGKGSGSASDRGSGSSPIALPLPLQFPFPVPEAMAAVLGPNALARLRWGSAFC |
| MAP.GRGC.SR....RDPGKGS..AS.RGSG..PIALP..LQFPF.VPE.MA..L.PNAL..L.WGSAF. | |
| Retrocopy | MAPHGRGCPSR*SAGRDPGKGSDFASARGSGRGPIALPRLLQFPFLVPEGMAGILRPNALIQLCWGSAFS |
| Parental | SIAAGGLGAFAAAFAKLALKPTVSQAPEEEEDVEGQEQPYPPAMQAWLTLMFRLMAFSLMIVSNSLMWAF |
| S..AG..GAF.A.F.KLALKPTVSQAP...ED.EGQEQPY.PAMQAWLT.MF.LMAFSLMIVSNSLMWAF | |
| Retrocopy | SFSAGSMGAFKATFTKLALKPTVSQAP--*EDIEGQEQPYWPAMQAWLTFMFGLMAFSLMIVSNSLMWAF |
| Parental | FSKALSISSSSATASLTMTASNIIASAFLGYLLYGEYCAVMWWAGVVLILYGLALMHISSTADEELEEKK |
| FSK.LSI.SSSATAS.TMT..NI..SAFL.YL.YGEY.A.MW.AGV.L.L.GLALMHIS....EE.EEKK | |
| Retrocopy | FSKGLSI-SSSATASQTMTPPNITDSAFLCYLFYGEYYAMMWQAGVLLTLNGLALMHISLLVHEEVEEKK |
| Parental | NQ |
| NQ | |
| Retrocopy | NQ |
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_1139 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1139 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 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000029706 | 3 retrocopies |
retro_mdom_1139 , retro_mdom_1400, retro_mdom_406,
|
| Tursiops truncatus | ENSTTRG00000004623 | 1 retrocopy |