RetrogeneDB ID: | retro_mdom_554 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 1:282723063..282724491(-) | ||
| Located in intron of: | ENSMODG00000013060 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | KPNA5 | ||
| Ensembl ID: | ENSMODG00000017826 | ||
| Aliases: | None | ||
| Description: | karyopherin alpha 5 (importin alpha 6) [Source:HGNC Symbol;Acc:6398] |
Retrocopy-Parental alignment summary:
>retro_mdom_554
GAAAGTCCTATTCAGGATCCAGTTATCAGCTCTACTGTACTTGTTCCTGAGGAAGAAGTTATTACTGCTGATATGGTGCA
GATGATTTTCTCTGATGATGCTGACCAACAGCTTACAGCAACACAAAAGTTTTGAAAGTTGCTTTCTAAAGAACCTAACC
AACCTATAGATGAAGTTATACAAAAACCAGGAGTTGTACAGAGATTTGTGAAGTTTCTTGAAAGAAACGAAAATTGTACT
TTGCAGTTTGAAGCTGCATGGGCTTTAACTAATATGGTATCTGGAACATTTCTACTCACCAAAGTGGTAATTCAAATTGG
AGCTGTTCCAATTTTTATCAAACTCCTCAATTCAGAACATGAAGATGTACAGGAACAGGCAGTATGGACACTTGGTAATA
TTGCTAGTGATAATGCAGAATGCAGAGGCTTTGTTCTGAATTGTGGAATTCTTCCCCCTCTTTTAGAATTACTGACAAAT
TCAAAAAGACTTACAACAACTCGAAATGCTGTATAGGCACTCTCAAATTTATGTAGAGGCAAGAACCCACCTCCAGATTT
CAGTAAGGTGTCACCTTGCTTAAATGTCCTGTCAAGATTATTATTTAGCAGTGACCCAGATGTATTAGCAGATGCTTGTT
GGGCCCTTTCTTATCTTTCTGATGGACCCAATGACAAAATCCAAGCAGTCATTGACTCTGGAGTCTGTCAAAGATTGGTG
GAACTTTTGATGCACAATGATTATAAAGTGGTATCACCTGTATTAAGAGCTGTTGGTAATATTGTGAAAGGGGATGATAT
TCAAACACAGGTAATTCTGAATTGTTCTGCTTTACCCTGCCTCTTACATTTACTGAGTAGTCCAAAAGAATCAATTAGAA
AAGAGGCTTGCTGGACTGTATCTAACATTACAGCAGGAAATAGAGCACAGATTCAGGCTGTCATAGATGCAAATATCTTT
CCTGTGTTGATTGAAATTCTTCAGAAAGCTGAATTTCATACCAGAAAAGAGGCAGCATAGGCCATAACCAATGCAACATC
TGGAGGCACTCCAGAACAGATACGGTATCTGGTAGCATTAGGCTGTATTAAACCTCTCTGTGACCTTTTGACTGTGATGG
ATTCCAAAATAGTCCAGGTGGCTTTAAATGGCCTTGAAGATATTTTACGACTTGGAGAGCAAGAATCTAGACAAAATGAA
ATGAACATCAATCCATACTGTGCTCTCATTGAAGAAGCATATGGTCTGGATAAAACTGAGTTTCTTCAAAGCCATGAAAA
TCAAGAGATCTACCAAAAGGCTTTTGATCTAATTGAACACTACTTTGGGGTGGAAGATGAAGATGCCAACATTGTCCCTC
AGGTGGATGAAAACCAGTAACAATTTGTTTTCCAACAGCAGGAAGCACCAATGGAAGGATTTCAGTTA
ORF - retro_mdom_554 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.12 % |
| Parental protein coverage: | 88.31 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ESPIQDPDISSTVPVPEEEVITADMVQMIFSDDADQQLTATQKVKKEHFFKPNPPIDEVIQKPGVVQRFV |
| ESPIQDP.ISSTV.VPEEEVITADMVQMIFSDDADQQLTATQK..K.....PN.PIDEVIQKPGVVQRFV | |
| Retrocopy | ESPIQDPVISSTVLVPEEEVITADMVQMIFSDDADQQLTATQKF*KLLSKEPNQPIDEVIQKPGVVQRFV |
| Parental | KFLERNENCTLQFEAAWALTNIASGTFLHTKVVIETGAVPIFIKLLNSEHEDVQEQAVWALGNIAGDNAE |
| KFLERNENCTLQFEAAWALTN..SGTFL.TKVVI..GAVPIFIKLLNSEHEDVQEQAVW.LGNIA.DNAE | |
| Retrocopy | KFLERNENCTLQFEAAWALTNMVSGTFLLTKVVIQIGAVPIFIKLLNSEHEDVQEQAVWTLGNIASDNAE |
| Parental | CRDFVLNCGILPPLLELLTNSNRLTTTRNAVWALSNLCRGKNPPPDFSKVSPCLNVLSRLLFSSDPDVLA |
| CR.FVLNCGILPPLLELLTNS.RLTTTRNAV.ALSNLCRGKNPPPDFSKVSPCLNVLSRLLFSSDPDVLA | |
| Retrocopy | CRGFVLNCGILPPLLELLTNSKRLTTTRNAV*ALSNLCRGKNPPPDFSKVSPCLNVLSRLLFSSDPDVLA |
| Parental | DACWALSYLSDGPNDKIQAVIDSGVCRRLVELLMHNDYKVVSPALRAVGNIVTGDDIQTQVILNCSALPC |
| DACWALSYLSDGPNDKIQAVIDSGVC.RLVELLMHNDYKVVSP.LRAVGNIV.GDDIQTQVILNCSALPC | |
| Retrocopy | DACWALSYLSDGPNDKIQAVIDSGVCQRLVELLMHNDYKVVSPVLRAVGNIVKGDDIQTQVILNCSALPC |
| Parental | LLHLLSSPKESIRKEACWTVSNITAGNRAQIQAVIDANIFPVLIEILQKAEFRTRKEAAWAITNATSGGT |
| LLHLLSSPKESIRKEACWTVSNITAGNRAQIQAVIDANIFPVLIEILQKAEF.TRKEAA.AITNATSGGT | |
| Retrocopy | LLHLLSSPKESIRKEACWTVSNITAGNRAQIQAVIDANIFPVLIEILQKAEFHTRKEAA*AITNATSGGT |
| Parental | PEQIRYLVALGCIKPLCDLLTVMDSKIVQVALNGLENILRLGEQESRQNEMNINPYCALIEEAYGLDKIE |
| PEQIRYLVALGCIKPLCDLLTVMDSKIVQVALNGLE.ILRLGEQESRQNEMNINPYCALIEEAYGLDK.E | |
| Retrocopy | PEQIRYLVALGCIKPLCDLLTVMDSKIVQVALNGLEDILRLGEQESRQNEMNINPYCALIEEAYGLDKTE |
| Parental | FLQSHENQEIYQKAFDLIEHYFGVEDEDANIVPQVDENQQQFVFQQQEAPMEGFQL |
| FLQSHENQEIYQKAFDLIEHYFGVEDEDANIVPQVDENQ.QFVFQQQEAPMEGFQL | |
| Retrocopy | FLQSHENQEIYQKAFDLIEHYFGVEDEDANIVPQVDENQ*QFVFQQQEAPMEGFQL |
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 .48 RPM | 0 .00 RPM |
| SRP007412_cerebellum | 0 .65 RPM | 0 .00 RPM |
| SRP007412_heart | 0 .20 RPM | 0 .00 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP007412_liver | 0 .50 RPM | 0 .00 RPM |
| SRP007412_testis | 1 .77 RPM | 0 .00 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_554 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_554 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 | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000003897 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000017826 | 1 retrocopy |
retro_mdom_554 ,
|
| Otolemur garnettii | ENSOGAG00000011924 | 1 retrocopy |