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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caacttatattattagtttttctgatatatatatgtttcagattgtgatatgttatgtgtcggtatgtagccatctgaccaaaccttctgcactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCCGCGGATTACAGCGGCATCAAGGTTGAGTTGGTAAAAGACTTTCAAATGG

Basic information

species Zea mays
transcript GRMZM2G029559_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029559_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g12794.3 (Oryza sativa), 3'ss of exon 2
caacttata-ttattagttttt---ctgatatatatatgtttcagattgtgatatgttatgtgtcggtatgtagccatctgaccaaaccttctgcactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCCGCGGATTACAGCGGCATCAAGGTTGAGTTGGTAAAAGACTTTCAAATGG
     |||  || ||  | | |    || |   | |   | |    || |  | | | |||  |  || |  | || | ||  ||    |||  |  ||  |||||| |||||||||||||| | ||||| |||||||||||  |||| ||||| || || |||   ||  |||||||||||||||| ||  ||||||| ||||
---tatatgcttcttgatctgtgaattggttcctctgcttgtatcgtttttgtttatcatgcttgtgtctccaaccttatgtacat-tattcgtctgtgattagGTATTGCATGCTGGCAGTGGAAACAAGAATGCATTCAAGGCACTCATTGCTGCCGAGTACTCTGGTGTCAAGGTTGAGTTGGTGAAGAACTTTCAGATGG
















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|211045449|gb|FL056742.1|FL056742
EST:     ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTT                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|15426721|gb|BI542543.1|BI542543
EST:     TGAAAATATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTT                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: TGAAAATATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|17921811|gb|BM259462.1|BM259462
EST:     ATCGATATGGCGC-T                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|56382464|gb|CV985133.1|CV985133
EST:     ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTT                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|211221752|gb|FL290081.1|FL290081
EST:     ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTT                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|211045448|gb|FL056741.1|FL056741
EST:     ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTT                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|21987889|gb|BQ779417.1|BQ779417
EST:     CTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTT                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: CTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|32942861|gb|CF047680.1|CF047680
EST:     ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTT                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCANAACACTAATTGCC
genomic: ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|211045450|gb|FL056743.1|FL056743
EST:     ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTT                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|32908341|gb|CF013154.1|CF013154
EST:     ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTT                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|211045447|gb|FL056740.1|FL056740
EST:     ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTT                         GTACTGCGATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGC
genomic: ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGC-ATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGC
EST: gi|26456546|gb|CA828129.1|CA828129
EST:     ATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTT                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|211045445|gb|FL056738.1|FL056738
EST:     ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTT                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|211045441|gb|FL056734.1|FL056734
EST:     ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTT                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|31406016|gb|CD484748.1|CD484748
EST:     ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTT                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|74237946|gb|DT645860.1|DT645860
EST:     ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTT                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|31359821|gb|CD444178.1|CD444178
EST:     ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTT                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|21331579|gb|BQ486960.1|BQ486960
EST:     AAGCTAGCTTTTCATCGATATGGCGC-T                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: AAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|211045444|gb|FL056737.1|FL056737
EST:     ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTT                         GTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCC

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: 49 (upstream exon), 49 (downstream exon)
Score: 365

ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCCGCGGATTACAGCGGCATCAAGGTTGAGTTGGTAAAAGACTTTCAAATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 247

ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCCGCGGATTACAGCGGCATCAAGGTTGAGTTGGTAAAAGACTTTCAAATGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 220

ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCCGCGGATTACAGCGGCATCAAGGTTGAGTTGGTAAAAGACTTTCAAATGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 149

ATCTGAGATCGAGTGAAGCTAGCTTTTCATCGATATGGCGCTTgtaagtgttt ... cactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCCGCGGATTACAGCGGCATCAAGGTTGAGTTGGTAAAAGACTTTCAAATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatatgttatgtgtcggtatgtagccatctgaccaaaccttctgcactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCCGCGGATTACAGCGGCATCAAGGTTGAGTTGGTAAAAGACTTTCAAATGG
                           atctgac  putative branch site (score: 149)
                                      ccttctgc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caacttatattattagtttttctgatatatatatgtttcagattgtgatatgttatgtgtcggtatgtagccatctgaccaaaccttctgcactgtgtagGTACTGCATGCTGGCAGTAGTAACAAAAATGCATTCAAAACACTAATTGCCGCGGATTACAGCGGCATCAAGGTTGAGTTGGTAAAAGACTTTCAAATGG

- - - - - - - - -ttttctg
- - - - - - - - - - - - - - - - -tgtttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatctg