RetrogeneDB ID: | retro_cfam_2148 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | X:39995026..39996283(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SF1 | ||
| Ensembl ID: | ENSCAFG00000014239 | ||
| Aliases: | None | ||
| Description: | splicing factor 1 [Source:HGNC Symbol;Acc:12950] |
Retrocopy-Parental alignment summary:
>retro_cfam_2148
CCTGACCCTGAGCCCATCTACAATAGGGAGGCAAAGAGGCTTAACACCTGGGAGTTCTGCACCAGCAAAACGCTTGAAGA
AGAGCAGCACAATCTCACCGGAGATGGTTGCCCTCAACCCTGATTTTGAGCCTCCTGCAGATGACAAACTTCCAGCAACA
TGTGTGAGCCATAAAGTAGTGAGTCCACAAGATGAGTATCCAGAAATCAACTTCTTGGGGCTGCTGATTGGGCCCAGTGG
GAACATCTTGAGGAACATAAAGAAGGAATGTAATGTCAAGATTGTGATCGGGGGAAATGGGTCTGTCAAGGAAAAGCAGG
GAGCAAAGATGGCCAGATGTTGCCCAGAGAAGGTGAGCCACGTCATGCCCTAGCTTCTGCCAACACCATGGAAAATGTGA
AGAAAGCCCTGGAACAGATAAGAAGCATCCAGAAACAGGCTATTGAGACCCCTGCAGATCAGGATGATCTATGGAAGATG
CAGCTTCGGTAGTTGGCTTGCCTGAATAGGACTCTTCAGGAATATGATAACAGGATCTTAAGACCCTGGCAGAGCTCAGA
GACTCACAACATTGCCAATACCACAGTGCACACCAAGTGTGGTCACAAAGCTTTTGATTGCAAATTCCAAAGGCCTGATG
ACACCCAGTCAGCTCAAGATAAAGCATGGATGGATAAAGAATCTTTGTCCCTTAGGGCTGAACTTGGTGAAGCACCTATG
GACTCTACCTCTGGGCCCACCACCACGCCCCTGGACAGTGCACCTTGGCCTGCTGCTCCCACCAACAATCCACCTCCACC
ATCTCTCATGGCCACTACCCAGAGCTGCCCACTCTAGATGATGAATTTTGGCACTTCAGAGAGTTGGCCCTACCATGGCA
TGCACAGAGGTGGTCTTGGTGGGCCTGGAGGTGGCCCCCACAGCCTCCCACACCCATTACCCAGCCTGACAGGTAGGCAT
GCTGGACATCCCATGCAGCATAACCTTAATGGACCCCCACTTCCTTGAATGCAGCCACTACCACCACAGATGGACCAGGG
CCCCACCCACCTGGGTACCATTGCCCTCTTCCAGTGGATCAGTAACTGGGAAGTATGCCTGTGGGTTCTGGGGTCTCTTG
CTTGCTTCAAGGAAAAGATATGATGCCATCTATGGGTGTGATGCTGGCACCATGCCCTCTTTCTTCCCCCATGGCAGCAG
CAGCCTCCATCACCCTGTCTGCCCAACAGCAGTATGGCTTCCAGGAGCCCCTTGCCA
ORF - retro_cfam_2148 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.59 % |
| Parental protein coverage: | 67.24 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | PSPEPIYNSEGKRLNTREFRTRKKLEEERHNLIT-EMVALNPDFKPPADYKPPATRVSDKVMIPQDEYPE |
| P.PEPIYN.E.KRLNT.EF.T.K.LE.E.....T.EMVALNPDF.PPAD.K.PAT.VS.KV..PQDEYPE | |
| Retrocopy | PDPEPIYNREAKRLNTWEFCTSKTLE-EEQHNLT>EMVALNPDFEPPADDKLPATCVSHKVVSPQDEYPE |
| Parental | INFVGLLIGPRGNTLKNIEKECNAKIMI-RGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKA |
| INF.GLLIGP.GN.L.NI.KECN.KI.I.RGK..V..GK.G.KDGQMLP.E.EP.HAL..ANTMENVKKA | |
| Retrocopy | INFLGLLIGPSGNILRNIKKECNVKIVI<RGKW-VCQGKAGSKDGQMLPREGEPRHALASANTMENVKKA |
| Parental | VEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLREDDNRILRPWQSSETRSITNTTVCTKCGGAGHI |
| .EQIR.I.KQ.IETP.DQ.DL.KMQLR.LA.LN.TL.E.DNRILRPWQSSET..I.NTTV.TKCG...H. | |
| Retrocopy | LEQIRSIQKQAIETPADQDDLWKMQLR*LACLNRTLQEYDNRILRPWQSSETHNIANTTVHTKCG---HK |
| Parental | ASDCKFQRPGDPQSAQDKARMDKEYLSLMAELGEAPVPASVGSTSGPATTPLASAPRPAAPANNPPPPSL |
| A.DCKFQRP.D.QSAQDKA.MDKE.LSL.AELGEAP......STSGP.TTPL.SAP.PAAP.NNPPPPSL | |
| Retrocopy | AFDCKFQRPDDTQSAQDKAWMDKESLSLRAELGEAP----MDSTSGPTTTPLDSAPWPAAPTNNPPPPSL |
| Parental | MSTTQSRPP-WMNSGPSESRPYHGMHGGGPGGPGGGPHSFPHPLPSLTGGHGGHPMQHNPNGPPPPWMQP |
| M.TTQS.P...MN.G.SES.PYHGMH.GG.GGPGGGPHS.PHPLPSLTG.H.GHPMQHN.NGPP.P.MQP | |
| Retrocopy | MATTQSCPL*MMNFGTSESWPYHGMHRGGLGGPGGGPHSLPHPLPSLTGRHAGHPMQHNLNGPPLP*MQP |
| Parental | PPPPMNQ-GPHPPGHHGPPPMDQYLGSTPVGSGVYRLHQGKGMMPPPPMGMMPPPPPPPSGQ-PPPPPSG |
| .PP.M.Q.GPHPPG.H.P.P.DQ.LGS.PVGSGV..L.QGK.MM..P.MG.M..P.P..S......PPS. | |
| Retrocopy | LPPQMDQ<GPHPPGYHCPLPVDQ*LGSMPVGSGVSCLLQGKDMM--PSMGVMLAPCPLSSPM>QQQPPSP |
| Parental | PLPPWQQQQQQPPP |
| .LP........P.P | |
| Retrocopy | CLPNSSMASRSPLP |
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 |
|---|---|---|
| SRP012049_cerebellum | 0 .00 RPM | 201 .13 RPM |
| SRP017611_brain | 0 .00 RPM | 102 .26 RPM |
| SRP017611_kidney | 0 .00 RPM | 69 .34 RPM |
| SRP017611_liver | 0 .00 RPM | 86 .58 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_2148 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_2148 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_2148 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000017828 | 1 retrocopy | |
| Canis familiaris | ENSCAFG00000014239 | 1 retrocopy |
retro_cfam_2148 ,
|
| Callithrix jacchus | ENSCJAG00000002780 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000009790 | 1 retrocopy |