RetrogeneDB ID: | retro_mdom_1611 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 6:149224572..149224983(+) | ||
| Located in intron of: | ENSMODG00000016624 | ||
Retrocopy information | Ensembl ID: | ENSMODG00000016623 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSMODG00000021343 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_mdom_1611
GTGGATTTTAAAACCTATGTGGACCAAGCATGTAGAGCTGCTGAAGAATTTGCCAATATCTACTATGACACCATTGATAA
AAGGAGAAGAGTGCTTACTAGACTATACTTGGACAGCGCCACTTTGATTTGGAATGGAAACGCTGTTTCTGGACAAGATG
CCTTGAATGAATTTTTTGAGATGTTGCCTTCCAGCGAGTTCCACATCAATGTATTAGATTGCCAACCTGTTCATGAGCAA
GCTACTCAGAGCCAAACAACCATCCTCGTGGTGGCCTGTGGGACTGTGAAGTTCGATGGAAATAAACAGCGCTATTTCCA
TCAGAACTTCCTGTTGACAGCACAGGTCACACCCAACAACACAGTATGGAAGATTGCAAGTGATTGCTTCCGTTTCCAGG
ATTGATCTACT
ORF - retro_mdom_1611 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.94 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MDFKTHADQACRAAEEFVNIYYDTIDKRRRVLTRLYLDTATLIWNGNPISGLNALTEFFETLPSSEFQIS |
| .DFKT..DQACRAAEEF.NIYYDTIDKRRRVLTRLYLD.ATLIWNGN..SG..AL.EFFE.LPSSEF.I. | |
| Retrocopy | VDFKTYVDQACRAAEEFANIYYDTIDKRRRVLTRLYLDSATLIWNGNAVSGQDALNEFFEMLPSSEFHIN |
| Parental | VVDCQPVHEQATQSQTTVLVVTCGAVKFDGNKQRYFNQNFLLTAQVMPNSTVWKIASDCFRFQDWSS |
| V.DCQPVHEQATQSQTT.LVV.CG.VKFDGNKQRYF.QNFLLTAQV.PN.TVWKIASDCFRFQD.S. | |
| Retrocopy | VLDCQPVHEQATQSQTTILVVACGTVKFDGNKQRYFHQNFLLTAQVTPNNTVWKIASDCFRFQD*ST |
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_1611 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1611 was not experimentally validated.