RetrogeneDB ID: | retro_mdom_617 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 1:549533857..549535022(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CNOT2 | ||
| Ensembl ID: | ENSMODG00000020387 | ||
| Aliases: | None | ||
| Description: | CCR4-NOT transcription complex, subunit 2 [Source:HGNC Symbol;Acc:7878] |
Retrocopy-Parental alignment summary:
>retro_mdom_617
ATTCTTACCCTCCCTGCCCAAACTGCAACCCAAACAACAAGCCAAACAGCAGTAATCACAGACAGTTCAATTAAATGCCT
TCCAATGAGGGGAATGAGAAACAATACCCCTCAGTTAAATCACAGCTTATCCCAAGACACTCAGTAACCAAGCCACGTCA
CACCAACAACAGAGGTACCAACAATATCACTTCATATGCTTCCATCTCCAAGCAACCTATGAATCCTAGGAATATGATGA
ACCACTCCCAAGTTTGTCAGGACATTGGAATTGCCAAAAGGACAAATAGCATGAGCAGTTCAGGATTAGGTAACCCTAAC
AGAATTTCACCAAGCATAATATGTATACCAAAGCAGCAACCCTCTAGACAACCTTTTACTGTGAATTGTAGGTCTGGATT
TGGAATGAACAAGAATCAGGCATTCGGAATAAATAATTCTCTATCAAGTAACATTTTAATGGAACAGATGGAAGTGAAAA
TGTGACAGGACTGGACCTTTCAGATTTTCCAGCACTAGCAGATCTAAACAGAAGGGAAGGAAACAGTAACCCAACTCCAT
TAATAAACCCCTTATCTGGAAGAGCTCCTTATGTTGGAATGGTAACAAAACCAGCAAGTGAGCAATCCCAAGATTTCTCA
ATACACAATGAAGATTTTCCAGTATTGTCAGGCTCCAGTTATAAAGATCCAATAACAAATAATGAGGATAGCAAATCTAA
TTTTAATACATCTGGTGAGACATCTTCAAGTACAGATGGACCTAAATTTCCTGGAGACAAAAGTTCAACAGCAAAAATCA
ACAACCAGCAGAAAAAAGGGATCCAGGTATTACCTGATGGTCAAATTACTAACATTCCTCAAGGGATGGTGATGGACCAA
TTTGGAATGATTGGCCTGCTGACATTCATTAGAGCAGCAGAGATAGACCCAGAAATTGTACAGCTTGCATTAAGAAGTCA
CTTAAGAACACTAAGCCTCAATCTCAAATTCCCTGAAAATCTCTATCCCAAATTTGCATCACCTTGGGTGTCTTCATCTT
GTTGACCTGAAGACATAGACTTCCATTTTCCAACTGAATACTTAAGGAACAGTCACATTAGAGATAAGCTGGCTGCAATA
AAATTGGGCTGATATGGAGATCTACTATTCTATTTCTATTACATA
ORF - retro_mdom_617 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.96 % |
| Parental protein coverage: | 70.56 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MLASPSTSGQLSQFGASLYGQQSALGLPMRGMSNNTPQLNRSLSQGTQLPSHVTPTTGVPTMSLHTPPSP |
| .L..P.................S...LPMRGM.NNTPQLN.SLSQ.TQ.PSHVTPTT.VPT.SLH..PSP | |
| Retrocopy | ILTLPAQTATQTTSQTAVITDSSIKCLPMRGMRNNTPQLNHSLSQDTQ*PSHVTPTTEVPTISLHMLPSP |
| Parental | S-RGILPMNPRNMMNHSQVGQGIGIASRTNSMSSSGLGSPNRSSPSIICMPKQQPSRQPFTVNSMSGFGM |
| S.....P.N..N...HSQV.Q.IGIA.RTNSMSSSGLG.PNR.SPSIIC.PKQQPSRQPFTVN..SGFGM | |
| Retrocopy | S<QPMNPRNMMN---HSQVCQDIGIAKRTNSMSSSGLGNPNRISPSIICIPKQQPSRQPFTVNCRSGFGM |
| Parental | NRNQAFGMNNSLSSNI-FNGTDGSENVTGLDLSDFPALADRNRREGSGNPTPLINPLAGRAPYVGMVTKP |
| N.NQAFG.NNSLSSNI.FNGTDGSENVTGLDLSDFPALAD.NRREG..NPTPLINPL.GRAPYVGMVTKP | |
| Retrocopy | NKNQAFGINNSLSSNI<FNGTDGSENVTGLDLSDFPALADLNRREGNSNPTPLINPLSGRAPYVGMVTKP |
| Parental | ASEQSQDFSIHNEDFPALPGSSYKDPTTSNEDSKSNLNTSGKTSSSTDGPKFPGDKSSTTQNNNQQKKGI |
| ASEQSQDFSIHNEDFP.L.GSSYKDP.T.NEDSKSN.NTSG.TSSSTDGPKFPGDKSST...NNQQKKGI | |
| Retrocopy | ASEQSQDFSIHNEDFPVLSGSSYKDPITNNEDSKSNFNTSGETSSSTDGPKFPGDKSSTAKINNQQKKGI |
| Parental | QVLPDGRVTNIPQGMVTDQFGMIGLLTFIRAAETDPGMVHLALGSDLTTLGLNLNSPENLYPKFASPWAS |
| QVLPDG..TNIPQGMV.DQFGMIGLLTFIRAAE.DP..V.LAL.S.L.TL.LNL..PENLYPKFASPW.S | |
| Retrocopy | QVLPDGQITNIPQGMVMDQFGMIGLLTFIRAAEIDPEIVQLALRSHLRTLSLNLKFPENLYPKFASPWVS |
| Parental | SPCRPQDIDFHVPSEYLTNIHIRDKLAAIKLGRYGEDLLFYLYYM |
| S.C.P.DIDFH.P.EYL.N.HIRDKLAAIKLG.YG.DLLFY.YY. | |
| Retrocopy | SSC*PEDIDFHFPTEYLRNSHIRDKLAAIKLG*YG-DLLFYFYYI |
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 | 2 .15 RPM | 0 .00 RPM |
| SRP007412_cerebellum | 0 .33 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_617 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_617 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 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000020387 | 1 retrocopy |
retro_mdom_617 ,
|