RetrogeneDB ID: | retro_mdom_1829 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 8:31701554..31702771(+) | ||
| Located in intron of: | ENSMODG00000025237 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PRCC | ||
| Ensembl ID: | ENSMODG00000016779 | ||
| Aliases: | None | ||
| Description: | papillary renal cell carcinoma (translocation-associated) [Source:HGNC Symbol;Acc:9343] |
Retrocopy-Parental alignment summary:
>retro_mdom_1829
AGTCTGGCTGAAGCTGCAGGGGGTAGGCAAGGGGCTGGGGCTGGGGCTGCCCCTGCCACCAGCCACAGGCCTCAGCTTGG
CCCCTGCTATCGGTGGTGCCAGCCCCCTCTGGCCCTCCCCAAGTCTAAGAAGATGGCAACACAGTTCGCGCTGATTGAGG
TGCCGGAGCTGCATCAGGGGGATTCAGATTCAGAGGAAGATGAATCTACAAAGAAGAAAACTTTTCTTCAGCGATCTGGT
GAAGGAACAGGTTTATCAGCTTTTCTTGCCCAACCCAAAAACCTTACTACAAAAGAGACTAACCTATTTCTCTGGCCCTA
TACTTTCTCTTGAAAACCCACAGATGTCTCTGCTTACACCAAGCTCTCCAAATCAGTCCCCAAGACCAAATATGCTTCTT
TTATTTCCTTTTCTACCCCCTGTTATTGGTGCAACCACTACTACCTCCATCTCCCTCAGTCATCAAAGCAGCTGCCAAGA
GTGCTGCTCTACAGGTGACAAAGCACTTCACACAAGAGGAGGATGACAGTGATGAAGAAGTAGCCCCTGAGAACTTCTTC
CATCCAGATGAGGTTGAGCCTCCTGGAACTGAACCATACCCTTACCTTGTCCCTGTTGCCTCTGAAGAGCAATCCCACCT
CTGGCATAGAGCCATATCCCACCTTCTAGGAAAATGCAGCCAATGTTCCCCTTGAATTCAAGAAGGTGACTGGATCAAGT
GGGACTCCTTGGGTGCCTAAGCCTGGGGAGGACGACAACAGTCATCCTTATTATCAGTTCCCTACATATGGTGATGCTAA
TACCAGTGGCATTTACTATCATAATTATTGTAGTAGTGGCTACTACCCTGAATCTGATCCAGCCTTAGCTTTCTCCAAGA
GATTACTCCAGACACCTCTTTCGTGGATGACTAAGCATTCAAGGGGCTTCAGGGAAAGAAGAACCAACCAAGGAAGAGAG
GAGATAAAATTTGTAGAGATCAAAGGGGATGACCAGCTCAATGGGGGCCAGCAGTGGATGACCAAGTCCTTGAGAGAAGA
AAAAAACCATGAAGTTATTCAGCAAGAAGAAAGGTCAATAGTCAACAGGCCAGCAGAGGAAAAAACACCAAACCACATTA
TATGATTCCCCTGACTAAGGAGTGAGAATTGGAGCTAAAGAATACTTGGTCAGAGAACAAGTTCAGCCACTGGCAGATGC
AAGCCAAATATAGATTC
ORF - retro_mdom_1829 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.63 % |
| Parental protein coverage: | 80.76 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | SLAEAAG-VGEGLGLGLPLPRAPGLSLPPPVGGAGP-PLGLPKPKKRTTEPVRIAAPELHQGDSDSEEEE |
| SLAEAAG.VG.GLGLGLPLP.A.GLSL.P..GGA.P.PL.LPK.KK..T....I..PELHQGDSDSEE.E | |
| Retrocopy | SLAEAAG>VGKGLGLGLPLPPATGLSLAPAIGGASP<PLALPKSKKMATQFALIEVPELHQGDSDSEEDE |
| Parental | PTKKKTVLQGSGEGTGLSALLPQPKNLTTKETNRLLLPYAFSRKPTDGSADTKLSKPAPKTKSASSISSS |
| .TKKKT.LQ.SGEGTGLSA.L.QPKNLTTKETN..L.PY.FS.KPTD.SA.TKLSK..PKTK.AS.IS.S | |
| Retrocopy | STKKKTFLQRSGEGTGLSAFLAQPKNLTTKETNLFLWPYTFS*KPTDVSAYTKLSKSVPKTKYASFISFS |
| Parental | TP-VVGATTTT-PSPSAIKAAAKSAALQVTKQITQEEDDSDEEVAPENFFSLPDKAEPPGAEPYPYPVPV |
| TP.V.GATTTT.PSPS.IKAAAKSAALQVTK..TQEEDDSDEEVAPENFF..PD..EPPG.EPYPY.VPV | |
| Retrocopy | TP>VIGATTTT>PSPSVIKAAAKSAALQVTKHFTQEEDDSDEEVAPENFFH-PDEVEPPGTEPYPYLVPV |
| Parental | -ASEE-PPPGTEPDPTFQDDAANAPLEFKMVAGSSGAPWVPKPGEDYSSQPYNQFPTYGDANATGVYYQD |
| ...E..P..G.EP.PTF...AAN.PLEFK.V.GSSG.PWVPKPGED..S.PY.QFPTYGDAN..G.YY.. | |
| Retrocopy | ASEEQ>PTSGIEPYPTF*ENAANVPLEFKKVTGSSGTPWVPKPGEDDNSHPYYQFPTYGDANTSGIYYHN |
| Parental | YYSSGYYPESDPALAPSQE-ITPDASFIDDEAFKRLQGKRNRGREEINFVEIKGDDQLSGAQQWMTKSLT |
| Y.SSGYYPESDPALA.S........S..............N.GREEI.FVEIKGDDQL.G.QQWMTKSL. | |
| Retrocopy | YCSSGYYPESDPALAFSKRLLQTPLSWMTKHSRGFRERRTNQGREEIKFVEIKGDDQLNGGQQWMTKSLR |
| Parental | EE-KTMKSFSKKKGEQPTGQQRRKHQIT-YLIHQAKERELELKNTWSENKLSRRQTQAKYGF |
| EE.KTMK.FSKKKG...TGQQR.KHQ.T.Y.I...KE.ELELKNTWSENK.S..Q.QAKY.F | |
| Retrocopy | EE>KTMKLFSKKKGQ*STGQQRKKHQTT>YMIPLTKE*ELELKNTWSENKFSHWQMQAKYRF |
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_1829 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1829 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 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Macropus eugenii | ENSMEUG00000016202 | 2 retrocopies | |
| Monodelphis domestica | ENSMODG00000016779 | 1 retrocopy |
retro_mdom_1829 ,
|
| Otolemur garnettii | ENSOGAG00000024539 | 1 retrocopy |