RetrogeneDB ID: | retro_mdom_1959 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | Un:30144804..30145950(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMODG00000006247 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BSPRY | ||
| Ensembl ID: | ENSMODG00000004402 | ||
| Aliases: | None | ||
| Description: | B-box and SPRY domain containing [Source:HGNC Symbol;Acc:18232] |
Retrocopy-Parental alignment summary:
>retro_mdom_1959
GACCAAGCGCCACGATGTCCCGAGCATGACCTGGAGCTGAAATGGTTCTGCAGCGCCGAGGGGCCTGTTGTGTGCACCAG
CTGCAAGGGTCTGGGGGGGCCCTGCCGAGAGCACCATGTCCGGAGGGAGGAGGAGCGGGCAGAGGAGTTGCAGAACAAGG
TCCTGGATCAGTGTGAGAAGCTGCAGCTACAGAGTGCTGGCATCACCAAATAAATGGCTGAAGTCTTGCTTCGGAAAAAC
CAAAATGCAGCGACCTTAGCCAGTGGGGCCCGGGAGATAGTGATCCAGCGGCTGGGCCTGGTGAAGAATGTGTGTGAGAG
TGAGGAGCAGAGGCTGCTGGAACAGGTTCACAGGGAGGAGGAGCGAGCCCACCAGAGCATCCTGACCCAGCGATCCATTG
GACCGAGGCCTTACAGAAGCTCAGCACCAACCTAGTGAGCATGCTCACTGATCTGGATGACCTCAGCCTTGTTCAATCAG
TGGGGAGATTTTTGAGAGGACTGAGGAAGCTGAGGGAGTCTTGGATCTCCAGGAATCTGAGAAGTTACATTTTAATCAGA
AATGTGTTTGGAGCCCATTATTGACCCAGCTCTGGGCATCGGCTGTTCTCTGCTGTCTATCAGGTACTGAGGACATGCAG
GTGGATGAGAGGACCATCAGTCCCTTTCTCCGACTGTCAGAGGACAGGAAGACCTTAACCTTCAGTGCCAAGAAGTCTAA
GGCCTATGCAGATGGCCCGGAACCCTTTGACCACTGGCCCAATGCCCTGGCTTCAACCTCCTTCCAGGGTGGCCTTCGTG
CCCGGATAGTGAATGTAGAGAACAGCTGTGCCCATAAGGTGGGAGTCTCCTCGAGCCAGCTGCCCCAAAAGGGTTCTGGC
AGTGACACCCGCCTTGGCCACAATGCTTCTTCCTGGGTTTTCTCTCGCTATGACCAGGAATTCCGGTTCCTGCACTATGG
TCAGTACCAGCCTTTGGCGCTGCTGCACTGGCCAGACTGCATTGGGGTGTGTTGGACTTGGCAGTGGGCGAGCTGCTGTT
CTATGAGCCCACCTCAGGGACCCTCTCGTGTTCCTGCCATGCCCAGTTGGAGGGCCCTATCTTTCCCATCTTTGCTGTGG
CTGACCAGAACATCTCCATTGTTCAG
ORF - retro_mdom_1959 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.92 % |
| Parental protein coverage: | 96.5 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | DSAPRCPEHDLELKWFCSSERRLVCASCKGLGGPCREHHVRRAEERAEELRNKIVDQCEKLQLQSAGITK |
| D.APRCPEHDLELKWFCS.E...VC.SCKGLGGPCREHHVRR.EERAEEL.NK..DQCEKLQLQSAGITK | |
| Retrocopy | DQAPRCPEHDLELKWFCSAEGPVVCTSCKGLGGPCREHHVRREEERAEELQNKVLDQCEKLQLQSAGITK |
| Parental | YMAEVLPRKNQNAATLASGAREIVIQRLGLVKNVCESEEQRLLEQVHTEEERAHQSILTQRS-HWTEALQ |
| .MAEVL.RKNQNAATLASGAREIVIQRLGLVKNVCESEEQRLLEQVH.EEERAHQSILTQRS.HWTEALQ | |
| Retrocopy | *MAEVLLRKNQNAATLASGAREIVIQRLGLVKNVCESEEQRLLEQVHREEERAHQSILTQRS<HWTEALQ |
| Parental | KLSTIRTNLVSMLTDLDDRSLVQS-EREIFERTEEAEGILDPQESEKLNFNQKCVRSPLLTQLWASAVLC |
| KLS...TNLVSMLTDLDD.SLVQS...EIFERTEEAEG.LD.QESEKL.FNQKCV.SPLLTQLWASAVLC | |
| Retrocopy | KLS---TNLVSMLTDLDDLSLVQS<SGEIFERTEEAEGVLDLQESEKLHFNQKCVWSPLLTQLWASAVLC |
| Parental | CLSGTEDIQVDERTISPFLRLSEDRKTLTFNPKKSKAYADGPERFDHWPNALASTSFQGGLHAWIVNVEN |
| CLSGTED.QVDERTISPFLRLSEDRKTLTF..KKSKAYADGPE.FDHWPNALASTSFQGGL.A.IVNVEN | |
| Retrocopy | CLSGTEDMQVDERTISPFLRLSEDRKTLTFSAKKSKAYADGPEPFDHWPNALASTSFQGGLRARIVNVEN |
| Parental | SCAYKVGVSSSQLPRKGSGSDTRLGHNAFSWVFSRYDQEFRFLHCGQYQPLALLRCPDRIGV-LLDLAAG |
| SCA.KVGVSSSQLP.KGSGSDTRLGHNA.SWVFSRYDQEFRFLH.GQYQPLALL..PD.IGV..LDLA.G | |
| Retrocopy | SCAHKVGVSSSQLPQKGSGSDTRLGHNASSWVFSRYDQEFRFLHYGQYQPLALLHWPDCIGV<VLDLAVG |
| Parental | ELLFYEPTSGALLCSYHAQFEGPIFPVFAVADQKISIVQ |
| ELLFYEPTSG.L.CS.HAQ.EGPIFP.FAVADQ.ISIVQ | |
| Retrocopy | ELLFYEPTSGTLSCSCHAQLEGPIFPIFAVADQNISIVQ |
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 | 108 .83 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 25 .79 RPM |
| SRP007412_heart | 0 .00 RPM | 8 .37 RPM |
| SRP007412_kidney | 0 .00 RPM | 38 .19 RPM |
| SRP007412_liver | 0 .00 RPM | 2 .01 RPM |
| SRP007412_testis | 0 .00 RPM | 8 .84 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1959 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1959 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 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000004402 | 1 retrocopy |
retro_mdom_1959 ,
|
| Tupaia belangeri | ENSTBEG00000003560 | 1 retrocopy |