RetrogeneDB ID: | retro_cjac_3189 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 9:19884283..19885498(+) | ||
| Located in intron of: | ENSCJAG00000005332 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PRPF38B | ||
| Ensembl ID: | ENSCJAG00000002510 | ||
| Aliases: | None | ||
| Description: | PRP38 pre-mRNA processing factor 38 (yeast) domain containing B [Source:HGNC Symbol;Acc:25512] |
Retrocopy-Parental alignment summary:
>retro_cjac_3189
TTATCCTCAACCTGAAAGCAAGTGATGGGTCTTATAACACACACAGACCCTCCATATATTAGAGCACTTGGATTGATGTA
TATAAGATATACACAGCCCACTACAGATCTATGGGACTGGTTTGAATCCTTCCTTGATGATGAAGAGGACCTAGAAGTGA
AGGCTGGTGGAGGCTGTGTGATGACCATTGGAGAAATGCTACCATCTTTTCTCACAAAACTGGAACGGTTTTCTACCTTG
TTTCCAAGAATTCCAGTTCCAGTTCAAAAGAATATTGATCAACAGATTAAAACCCGACCTAGAAAAATTAAGAAAGAAGG
GAAGGAAGGCGTTGAGGAAATAGACAGACATGTTAAACGCAGAAGTTCAAGGTCTCCAAGGAGATCTCTGAGTCCACGGA
GGTCCCCAAGAAGATCAAGAAGTAGAAGTCATCATTGAGAGGGCCATGGGTCTTCTAGTTTTGACAGAGCATTAGAAAGA
ATTTGACAGAGAAAGAACGTCAGCGACTAGAGCGTGAAGCCAAAGAAAGGGAGAAAGAACGCCGAAGATCTCGAGGTATT
GATCGGGGGTTAGAACAGCAGAAGCAGAAAAAGGCACAGAAGTCGCAGCCGGAGTCATGATAGGAAAGGGGATAGAAGGG
ACAGGGATCGGGAAAGAGAAAAAGAAAGTGAGAGAGGTAGAAGACGAGATCGTGACTATGATAAGGAAAGAGGAAACGAC
CGAGAAAGAGAGAGCGATCAAGAGAACTGTCCACGGAACAGAGAAGTAGGGGAGAGGTAGAAGACAAGAAACATAAAGAA
GACAAAGATGACAGGCGGCACAGAGACGACAAAAAAGATTCCAAGAAAGAAAAAACACAGGAGAAGCAGAAGCAGAGAAA
GGAAACACAGAAGTAGGAGTCGAAGTAGAAATGCAGGGAAACGAAGTAGTAGAAGCAAAAAGAAATGAAGTAAACATAAA
AATGAAAGTAAAGAAAAATCAAATAAACGAAGTAGAAGTGGCAGTCAAGGAAGAACTGACAGTCTCGAAAAATCAAAACC
ATGGGAACATAGCCCCAGCAAAGAAAAATCTACAAAGCGCAGTGGAAGCAAAGAACGTTCCCACAAACGAGATCACAGTG
ATAGTAAGGACCAGTCAGACAAACATGATCGTCGAAGGAGCCAAAGTATAGAACGAGAGAGCCAAGAAAAACAACACAAA
AACGAAGAGGAGACT
ORF - retro_cjac_3189 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.15 % |
| Parental protein coverage: | 74.73 % |
| Number of stop codons detected: | 9 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | LKLTRKQVMGLITHTDSPYIRALGFMYIRYTQPPTDLWDWFESFLDDEEDLDVKAGGGCVMTIGEMLRSF |
| L..T.KQVMGLITHTD.PYIRALG.MYIRYTQP.TDLWDWFESFLDDEEDL.VKAGGGCVMTIGEML.SF | |
| Retrocopy | LSST*KQVMGLITHTDPPYIRALGLMYIRYTQPTTDLWDWFESFLDDEEDLEVKAGGGCVMTIGEMLPSF |
| Parental | LTKLEWFSTLFPRIPVPVQKNIDQQIKTRPRKIKKEGKEGIEEIDRHVERRRSRSPRRSLSPRRSPRRSR |
| LTKLE.FSTLFPRIPVPVQKNIDQQIKTRPRKIKKEGKEG.EEIDRHV.RR.SRSPRRSLSPRRSPRRSR | |
| Retrocopy | LTKLERFSTLFPRIPVPVQKNIDQQIKTRPRKIKKEGKEGVEEIDRHVKRRSSRSPRRSLSPRRSPRRSR |
| Parental | SRSHHREGHGSSSFDRELEREKERQRL-EREAKE-REKE--RRRSRSIDRGLERRHSRSRERHRSRSRSR |
| SRSHH.EGHGSSSFDR.LER...R.....R...E..E.E..RRRSR.IDRGLE...........S...S. | |
| Retrocopy | SRSHH*EGHGSSSFDRALERI*QRKNV<QRLEREAKEREKERRRSRGIDRGLEQQ--KQKKAQKSQPES* |
| Parental | DRKGDRRDRDREREKENER-GRRRDRDYDKERGNDREKERERSR-ERSKE-QRSRGEVEEKKHKEDKDDR |
| ...G........R....ER..RR.DRDYDKERGNDRE.E.......R..E..R...E....K...D..DR | |
| Retrocopy | *ERG*KGQGSGKRKRK*ER>RRR-DRDYDKERGNDRERESDQENCPRNRE<SRGEVEDKKHKEDKD--DR |
| Parental | RHRDDKKDSKKEKKHSRSRSRERKHRSRSR-SRNAGKRSRSRSKEKSSKHKNESKEKSNKRSRSGSQGRT |
| RHRDDKKDSKKEK.......R.......S.........SRS....K.SKHKNESKEKSNKRSRSGSQGRT | |
| Retrocopy | RHRDDKKDSKKEKTQEKQKQRKETQK*ESK>RNAGKRSSRSK--KK*SKHKNESKEKSNKRSRSGSQGRT |
| Parental | DSLEKSKKWEHSPSKEKSRKRSGSKERSHKRDHSDSKDQSDKHDRRRSQSIEQESQEKQHKNKEET |
| DSLEKSK.WEHSPSKEKS.KRSGSKERSHKRDHSDSKDQSDKHDRRRSQSIE.ESQEKQHKN.EET | |
| Retrocopy | DSLEKSKPWEHSPSKEKSTKRSGSKERSHKRDHSDSKDQSDKHDRRRSQSIERESQEKQHKNEEET |
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 |
|---|---|---|
| SRP051959_colon | 0 .24 RPM | 18 .84 RPM |
| SRP051959_heart | 0 .37 RPM | 24 .31 RPM |
| SRP051959_kidney | 0 .20 RPM | 29 .62 RPM |
| SRP051959_liver | 0 .39 RPM | 20 .60 RPM |
| SRP051959_lung | 0 .36 RPM | 39 .04 RPM |
| SRP051959_lymph_node | 0 .27 RPM | 47 .92 RPM |
| SRP051959_skeletal_muscle | 0 .09 RPM | 19 .22 RPM |
| SRP051959_spleen | 1 .83 RPM | 39 .54 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3189 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3189 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3189 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000002510 | 1 retrocopy |
retro_cjac_3189 ,
|
| Nomascus leucogenys | ENSNLEG00000001645 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000006479 | 1 retrocopy |