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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggggatgtacatgaacagagtaggatttatgctttgtctcatttattttttggaccagtaagattagaggtagtattgattcttttccccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGCAGTCGGAGAAAGTAACTGTAGAATCTGATGCAGATCTCTTGTGGACAAT

Basic information

species Zea mays
transcript GRMZM2G055458_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055458_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g25440.1 (Oryza sativa), 3'ss of exon 6
-taggggatgtacatgaacagagtaggatttatgctttgtctcatttattttttggaccagtaagattagaggtagtattgattcttttcccca-cttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGCAGTCGGAGAAAGTAACTGTAGAATCTGATGCAGATCTCTTGTGGACAAT
 |  |  |  || | |||||       ||  |      ||   ||  |  | ||   ||| |   ||| || |    |    || ||| |   | |||||||||||| | ||||||||||||||||| ||||||||||||||||||||||| ||  | || || || |||||| |||| |||||||||||  | ||||||||
atttgaaac-tataagaacattactt-ataaaattacagtgatatggaggtgtttctccatttctattggaagcctgaggcgttgtttacattatcttccagGTGAAGCGAAGATGAGATTTGGGAGTATGATAAGCACATCCAACATTGTTCACGCAGAAAAGGTTACTGTACAATCCGATGCAGATCTTCTCTGGACAAT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|32925838|gb|CF030650.1|CF030650
EST:     TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAA                         GTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
genomic: TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
EST: gi|93014428|gb|EB639948.1|EB639948
EST:     TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAA                         GTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
genomic: TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
EST: gi|6095651|gb|AW120318.1|AW120318
EST:     GGAGCACCATCANACAAGCACAACAACTACTGGCCTGAAATGGAATCTAA                         GTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACCATTGTG
genomic: GGAGCACCATCA-ACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAA-CATTGTG
EST: gi|32926190|gb|CF031002.1|CF031002
EST:     TGGGGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAA                         GTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
genomic: TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
EST: gi|78022577|gb|DV490964.1|DV490964
EST:     TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAA                         GTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
genomic: TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
EST: gi|32925170|gb|CF029982.1|CF029982
EST:     TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAA                         GTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
genomic: TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
EST: gi|101387488|gb|EB815759.1|EB815759
EST:     TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAA                         GTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
genomic: TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
EST: gi|74243578|gb|DT651492.1|DT651492
EST:     AACAACTACTGGCCTGAAATGGAATTTAA                         GTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
genomic: AACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
EST: gi|6020450|gb|AW065378.1|AW065378
EST:     TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAA                         GTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
genomic: TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
EST: gi|32925551|gb|CF030363.1|CF030363
EST:     TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAA                         GTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
genomic: TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
EST: gi|5762179|gb|AI967227.1|AI967227
EST:     TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAA                         GTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
genomic: TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
EST: gi|32926935|gb|CF031747.1|CF031747
EST:     TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAA                         GTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
genomic: TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
EST: gi|211148272|gb|FL467064.1|FL467064
EST:     TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAA                         GTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
genomic: TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
EST: gi|50337458|gb|CO532584.1|CO532584
EST:     TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAA                         GTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
genomic: TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
EST: gi|32926208|gb|CF031020.1|CF031020
EST:     TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAA                         GTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
genomic: TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
EST: gi|16926658|gb|BM079726.1|BM079726
EST:     TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAA                         GTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
genomic: TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
EST: gi|32926302|gb|CF031114.1|CF031114
EST:     TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAA                         GTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC
genomic: TGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 7

CTTTATATTGAGTCGTCTGTTGAAGGACCCCATTGTGGGCTTTTCCCTGTTGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGCAGTCGGAGAAAGTAACTGTAGAATCTGATGCAGATCTCTTGTGGACAAT


Block sizes: 47 (upstream exon), 11 (downstream exon)
Score: 7

CTTTATATTGAGTCGTCTGTTGAAGGACCCCATTGTGGGCTTTTCCCTGTTGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGCAGTCGGAGAAAGTAACTGTAGAATCTGATGCAGATCTCTTGTGGACAAT


Block sizes: 49 (upstream exon), 19 (downstream exon)
Score: 6

CTTTATATTGAGTCGTCTGTTGAAGGACCCCATTGTGGGCTTTTCCCTGTTGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGCAGTCGGAGAAAGTAACTGTAGAATCTGATGCAGATCTCTTGTGGACAAT


Block sizes: 39 (upstream exon), 28 (downstream exon)
Score: 4

CTTTATATTGAGTCGTCTGTTGAAGGACCCCATTGTGGGCTTTTCCCTGTTGGAGCACCATCAACAAGCACAACAACTACTGGCCTGAAATGGAATCTAAgtaaatttct ... ccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGCAGTCGGAGAAAGTAACTGTAGAATCTGATGCAGATCTCTTGTGGACAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttttggaccagtaagattagaggtagtattgattcttttccccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGCAGTCGGAGAAAGTAACTGTAGAATCTGATGCAGATCTCTTGTGGACAAT
                              tattgat  putative branch site (score: 4)
                                ttgattcttttcccca  CT-rich tract
               taagatta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggggatgtacatgaacagagtaggatttatgctttgtctcatttattttttggaccagtaagattagaggtagtattgattcttttccccacttccagGTGAATCAAAGATGAGATTTGGGAGCATGATAAGCACATCCAACATTGTGCAGTCGGAGAAAGTAACTGTAGAATCTGATGCAGATCTCTTGTGGACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT