RetrogeneDB ID: | retro_mdom_1703 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 7:913339..913894(+) | ||
| Located in intron of: | ENSMODG00000016811 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | UCP2 | ||
| Ensembl ID: | ENSMODG00000007498 | ||
| Aliases: | None | ||
| Description: | uncoupling protein 2 (mitochondrial, proton carrier) [Source:HGNC Symbol;Acc:12518] |
Retrocopy-Parental alignment summary:
>retro_mdom_1703
TCTGTCAAGCAATTCTACACCAACGGGTCTGAACATGCAGATATTGGAAGTCGCCTCCTGGCAGGCTGTACCACAGGAGC
ACTGGTAGTATGTGTAACCCAATGCATAGATGTGATAAAGGTATGTTTACAGGCCAAGGCTCTTGCAGGGCGCAGCTGGA
GATAACAGGGTGCAGTGCATGCCTATACGACTATCACCTGAGAGGAGGGACTTTGGGGCCTATGGAAAGGAACTTTGTCC
AATGTTGCTCGCGATGCTATTGTCAACTGTGCTGAGCTAGTGATCCATGACCTCATCAGAGATGCCATCCTGAAGGCCCA
CTTCAAGACTGATGACCTTGTATGACCCTTCACTTTAGCCTTTGGGCCTGGCTTCTACACCACCATCATCACCTCCCCTG
TGGATGCGGTCAAGATGAGATACATGAACTCTGCCTCGAGCCGGTATGCCAGTGGAGGCCACTGTACTCTTGCTATGCTT
TAGAAAGAAGGGCCCTAACTTTTCTACAAAGGGTTCATGCCTTCCTTCCTCCACTTGGGCTCCTGGAATATAGTG
ORF - retro_mdom_1703 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.97 % |
| Parental protein coverage: | 58.73 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SVKQFYTKGSEHAGIGSRLLAGCTTGALAVGVAQPTDVVKVRFQAQARAGGSRRYQGTMDAYKTIAREEG |
| SVKQFYT.GSEHA.IGSRLLAGCTTGAL.V.V.Q..DV.KV..QA.A.AG.S.R.QG...AY.TI..EEG | |
| Retrocopy | SVKQFYTNGSEHADIGSRLLAGCTTGALVVCVTQCIDVIKVCLQAKALAGRSWR*QGAVHAYTTIT*EEG |
| Parental | LRGLWKGTSPNVARNAIVNCAELVTYDLIKDALLKAHLMTDDLPCHFTSAFGAGFCTTIIASPVDVVKTR |
| L.GLWKGT..NVAR.AIVNCAELV..DLI.DA.LKAH..TDDL...FT.AFG.GF.TTII.SPVD.VK.R | |
| Retrocopy | LWGLWKGTLSNVARDAIVNCAELVIHDLIRDAILKAHFKTDDLV*PFTLAFGPGFYTTIITSPVDAVKMR |
| Parental | YMNSASGQYASAGHCALTMLRKEGPQAFYKGFMPSFLRLGSWNVV |
| YMNSAS..YAS.GHC.L.ML.KEGP..FYKGFMPSFL.LGSWN.V | |
| Retrocopy | YMNSASSRYASGGHCTLAML*KEGP*LFYKGFMPSFLHLGSWNIV |
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_1703 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1703 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 4 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Echinops telfairi | ENSETEG00000014773 | 1 retrocopy | |
| Macropus eugenii | ENSMEUG00000011481 | 2 retrocopies | |
| Monodelphis domestica | ENSMODG00000007498 | 2 retrocopies |
retro_mdom_1122, retro_mdom_1703 ,
|
| Otolemur garnettii | ENSOGAG00000001700 | 1 retrocopy |