RetrogeneDB ID: | retro_mdom_821 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 2:88951980..88952733(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMODG00000011894 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SH3GLB1 | ||
| Ensembl ID: | ENSMODG00000008125 | ||
| Aliases: | None | ||
| Description: | SH3-domain GRB2-like endophilin B1 [Source:HGNC Symbol;Acc:10833] |
Retrocopy-Parental alignment summary:
>retro_mdom_821
TTAGCAAACAAAGCTGAATGCACCAAACAATGGATAGAAAAAAAAATGATGAGGCCAACAGAGATGCTGTCCAGCCAAAT
CCTAATTCTAGAATGGAAGAATTTGTTTATGAGAAATTGGATAAAAAAGCTCCAACTCGTAGAAACAACCAAGAACTCTT
GGGGCAATCCATGATTGATGCAGGGAATGAGTTTGGCACAGGAATTGCTTATGGTAATGCCCTCATCAAATGTGGAGAAA
CACATAAACGAATTGGAACTGCAGACAGAGAACTGGTTCAGACAGCTGCAATAAACTTTCCGTACTCCTTGAAGAAACTT
TATAGAAATAGATTAAAAAACAATTGCTAAAGAAAGGAAACTACTGCAAAATAAGAACCTTGATTTGGATGCGGCAAAGA
CTAGACTGAAAAAAGGCAAAAATCGCAGAGAAAAGAGCACTATCTGAACAGGAATTAAGAATAACTCGAAGTGAATTTGA
CCACCAAGCAGAGATTACCGGACTCCTTCCGGAAGGGATCAGCAGCACCTATGCACATGCACACCACCTTCACTGCCTGA
AGGACTTTGTGGAAGTCCAAATGACTTACTATGCTCAGGGCTACCAGTACATAGTGGACCGGCAAAAACAACTCAGGAGT
TTCCCATCTGTCGTTGTATGACAAATGGTCGATCTTCCACAATCTCCACGTCATCTTCTGGAGTTTTCACCTCTCTGTTG
CCTTTAACAAGTGGCACAGCTCTTATTCCTGCC
ORF - retro_mdom_821 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.9 % |
| Parental protein coverage: | 66.49 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | LLSKAECTKQWTEKM-MRQTEVL-LQPNPNARIEEFVYEKLDRKAPTRINNQELLGQYMIDAGNDFGPGT |
| L..KAECTKQW.....MR.TE.L..QPNPN.R.EEFVYEKLD.KAPTR.NNQELLGQ.MIDAGN.FG.G. | |
| Retrocopy | LANKAECTKQWIXXXXMRPTEML<VQPNPNSRMEEFVYEKLDKKAPTRRNNQELLGQSMIDAGNEFGTGI |
| Parental | AYGNALIKCGETQKRIGTADRELVQTAAINF-LTPLRNFIEGDYKTITKERKLLQNKRLDLDAAKTRL-K |
| AYGNALIKCGET.KRIGTADRELVQTAAINF..TP.RNFIE.D.KTI.KERKLLQNK.LDLDAAKTRL.K | |
| Retrocopy | AYGNALIKCGETHKRIGTADRELVQTAAINF>RTP*RNFIEID*KTIAKERKLLQNKNLDLDAAKTRL>K |
| Parental | KAKIAETRALSEQELRITQSEFDRQAEITRLLLEGISST--HAHHLRCLNDFVEAQMTYYAQCYQYMLDL |
| KAKIAE.RALSEQELRIT.SEFD.QAEIT.LL.EGISST..HAHHL.CL.DFVE.QMTYYAQ.YQY..D. | |
| Retrocopy | KAKIAEKRALSEQELRITRSEFDHQAEITGLLPEGISSTYAHAHHLHCLKDFVEVQMTYYAQGYQYIVDR |
| Parental | QKQLGSFPSVFV-SNNSQSST--TSMSNISTSSSGIT--TSLLPS |
| QKQL.SFPSV.V...N..SST..TS.S...TS....T..T.L.P. | |
| Retrocopy | QKQLRSFPSVVV<MTNGRSSTISTSSSGVFTSLLPLTSGTALIPA |
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_821 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_821 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 | ENSMODG00000000931 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000008125 | 1 retrocopy |
retro_mdom_821 ,
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