RetrogeneDB ID: | retro_mdom_570 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 1:338883385..338884575(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LACTB | ||
| Ensembl ID: | ENSMODG00000011098 | ||
| Aliases: | None | ||
| Description: | lactamase, beta [Source:HGNC Symbol;Acc:16468] |
Retrocopy-Parental alignment summary:
>retro_mdom_570
CAAGGTTTAGGTTATATTGATGTAAAAAACAGAATTCCATGTAAACCAGAAACAGTGATGAGAATTGCTAGCATCAGCAA
AAGTCTTACCATGGTGACCATTGCCAAATTATGGGAAGAGGGCAGATTGGATGTTGATATTCCAGGACAGAAATATGTTC
TTGAATTTCCAGAGAAATAATATGAAGGTGAAAAAGTTTCTGTCACTACAAAATTAATGATTTCTCATTTAAGTGGAATT
TGCCACTATGAAAAGGATATGAAAAAAGTAAAAGAAGAGAAGGCTTATAAAGCTTTGAAGATGATGAAAGAAACAATGGA
ATTTAACCAAGACAAAGACTTGAAAGAAACAGGAGGCAAAAGTAATGAAAAGAATGACTTTGCCAAAGTTAAGATACAGC
AAGATAGTGAAGGCAAAGGCTGAAATTCCAAACCTGTCAAGAAGATGAATGATTTTGAACAAGATGAATTATATTTGAAA
GAAAATTTGAAAATTAAATTTAGTTTCTAAGATTATTTTAAAATGATCCTCTGTTCTTTAAACCATGTAGTCAGTTTTTG
TACTCAACTTTTGGATATAGTCTACTGGCATCTGTCATAGAAAGAGCTTCAGGACAGACATTTTTGGACACTATGCAGAA
AATATTCCATGATGTGGATGTGGTGATGACTGTGCAAGAAGAAAATGAGCCAATGATTTACAAGAGAGCAAGGTTTTATG
TTTACAATAAAAAAGGATGTCTTGTCAATACTCCTTATGTGGACAACTTTTATAAATGGGTCATTGGTGCATTTCTTTCT
ATAGTTGGTGATTTTCTTAAATTTGGGAATGTAATACTCTATGGTGACCAAATTGGAATGATTAAAATCTTAAGTGAGAA
GCTTTTGCCAGGGTACCTCAAGCCAGAAACCATGGTCATGATTTGGACTCCTGTGCCAAACACAGAGATGTCTTGGGATA
GAGAAGAAAAATACTCAATGGCCTGGGGTGTGGTGGAAAAGAAGCAGATATATAGCTTCTGTTGGCAACAGCAACATTAT
GCTTCTCACAGTGGAGGGGCAGTGGGTACTAATAATGTCCTGCTAATTCTTCCTGAAGATTTGGAGGTAGAAACTATAGA
TAACAGAATAGCTATTCCCCCAAGAGGAGTGATCATTACCATCATATGTAATATGTAGTCTGTTGGCCTC
ORF - retro_mdom_570 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.42 % |
| Parental protein coverage: | 71.53 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | EGLGYADVENRVPCKPETVMRIASISKSLTMVAIAKLWEEGRLDLDIPVQKYVPEFPEKEYEGEKVSVTT |
| .GLGY.DV.NR.PCKPETVMRIASISKSLTMV.IAKLWEEGRLD.DIP.QKYV.EFPEK.YEGEKVSVTT | |
| Retrocopy | QGLGYIDVKNRIPCKPETVMRIASISKSLTMVTIAKLWEEGRLDVDIPGQKYVLEFPEK*YEGEKVSVTT |
| Parental | RLLISHLSGIRHYEKDMKKVKEEKAYKALKMTKEAMEFNQDKGLKEIGGKSNEKNDIAKVKIEQDSEGKG |
| .L.ISHLSGI.HYEKDMKKVKEEKAYKALKM.KE.MEFNQDK.LKE.GGKSNEKND.AKVKI.QDSEGKG | |
| Retrocopy | KLMISHLSGICHYEKDMKKVKEEKAYKALKMMKETMEFNQDKDLKETGGKSNEKNDFAKVKIQQDSEGKG |
| Parental | RNSKPGKKKNDFEQDELYLKE-KFENSIESLRLFKNDPLFFKPGSQFLYSTFGYSLLAAVIERASGQKFL |
| .NSKP.KK.NDFEQDELYLKE.KFEN.I..LRLF.NDPLFFKP.SQFLYSTFGYSLLA.VIERASGQ.FL | |
| Retrocopy | *NSKPVKKMNDFEQDELYLKE<KFEN*I*FLRLF*NDPLFFKPCSQFLYSTFGYSLLASVIERASGQTFL |
| Parental | DYMQKIFHDLDMVTTVQEENEPMIYNRARFYVYNKKGRLVNTPYVDNSYKWAGGGFLSTVGDLLKFGNAM |
| D.MQKIFHD.D.V.TVQEENEPMIY.RARFYVYNKKG.LVNTPYVDN.YKW..G.FLS.VGD.LKFGN.. | |
| Retrocopy | DTMQKIFHDVDVVMTVQEENEPMIYKRARFYVYNKKGCLVNTPYVDNFYKWVIGAFLSIVGDFLKFGNVI |
| Parental | LYGYQIGMIKNLSEKLLPGYLKPETMVMIWTPVPNTEMSWDREGKYAMAWGVVEKKQTHGSCRQQRHYAS |
| LYG.QIGMIK.LSEKLLPGYLKPETMVMIWTPVPNTEMSWDRE.KY.MAWGVVEKKQ....C.QQ.HYAS | |
| Retrocopy | LYGDQIGMIKILSEKLLPGYLKPETMVMIWTPVPNTEMSWDREEKYSMAWGVVEKKQIYSFCWQQQHYAS |
| Parental | HTGGAVGASSVLLILPEDLEVETTDNRMTIPPRGVIVTIICNMQSVGL |
| H.GGAVG...VLLILPEDLEVET.DNR..IPPRGVI.TIICNM.SVGL | |
| Retrocopy | HSGGAVGTNNVLLILPEDLEVETIDNRIAIPPRGVIITIICNM*SVGL |
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 | 32 .30 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 24 .16 RPM |
| SRP007412_heart | 0 .00 RPM | 41 .07 RPM |
| SRP007412_kidney | 0 .00 RPM | 60 .57 RPM |
| SRP007412_liver | 0 .00 RPM | 43 .30 RPM |
| SRP007412_testis | 0 .00 RPM | 23 .18 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_570 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_570 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 | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000017373 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000011098 | 1 retrocopy |
retro_mdom_570 ,
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