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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggtccatgaaacatttcaacatactgttttcattttattattctatgttggagaaaggaaatacaaatactcaagaatttgcattatgatgaataattttctgtgaacatgggttaaccattaattttgtcttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAATGAAGGCAAAATCCAAAGTTATTAAGAAAGTCGCCGCTGAAGACCTTGGC

Basic information

species Zea mays
transcript GRMZM2G173040_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173040_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g10400.1 (Oryza sativa), 3'ss of exon 3
gtagggtccatgaaacatttcaacatactgttttcattttattattctatgttggag------------aaaggaaatacaaatactcaagaat--------------------------ttgcattatgatgaataattttctgtgaacatgggttaaccattaattttgtcttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAATGAAGGCAAAATCCAAAGTTATTAAGAAAGTCGCCGCTGAAGACCTTGGC
||| | ||||||||||||||        | ||||  ||| |||   | | | | |              | | | | | | |  | | |   ||                          ||||||| || |    |      |    | || |  ||| |  |  |||  | || |   |||||||||||| ||||| ||||| ||||| |||||||| ||||| |||||||||||||||||||| ||||| || ||||||||| || | ||||| || |  
gtatgttccatgaaacatttattttctttcttttagtttaatttaacaaggctagtacttcgattcttcataagcattgcgatcatttagtgatctctgtcacatagctggatctttgtattgcattgtggttttgagccaatttcagaaattgcctaaactattgtttgatttttgtgacagCACGGATTTGAGACTGAACCAACCAAGGTATGCAACATTGCCAAACATAATGAAGGCAAAATCAAAAGTCATCAAGAAAGTCACCCCCGAAGATCTGGAT
















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|5398729|gb|AI812194.1|AI812194
EST:     GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCAC                         CACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
genomic: GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
EST: gi|5915581|gb|AW053222.1|AW053222
EST:     GTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCAC                         CACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
genomic: GTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
EST: gi|60359023|gb|DN225996.1|DN225996
EST:     GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCAC                         CACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
genomic: GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
EST: gi|6056684|gb|AW091089.1|AW091089
EST:     GTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCGC                         CTCGGATTTAAGACTTAACCAGCCAAGATATGCAGCTTNTGCCCAACATAA
genomic: GTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTT-TGCCCAACATAA
EST: gi|113701878|gb|EE679382.1|EE679382
EST:     GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCAC                         CACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
genomic: GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
EST: gi|74034853|gb|DT535344.1|DT535344
EST:     GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCAC                         CACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
genomic: GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
EST: gi|211328554|gb|FL083184.1|FL083184
EST:     GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCAC                         CACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
genomic: GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
EST: gi|149073678|gb|EE161983.2|EE161983
EST:     GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCAC                         CACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
genomic: GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
EST: gi|211328555|gb|FL083185.1|FL083185
EST:     GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCAC                         CACGGATTTAAGACTTNACCAGCCAAGATATGCAACTTTGCCCAACATAAT
genomic: GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
EST: gi|148991147|gb|EE032604.2|EE032604
EST:     GTTGATGGGGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCAC                         CACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
genomic: GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
EST: gi|32910828|gb|CF015640.1|CF015640
EST:     GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCAC                         CACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
genomic: GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
EST: gi|14202867|gb|BG836544.1|BG836544
EST:     TTGATGGCTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCAC                         YACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
genomic: TTGATGG-TGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
EST: gi|78026288|gb|DV494675.1|DV494675
EST:     GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCAC                         CACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
genomic: GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
EST: gi|60343553|gb|DN210526.1|DN210526
EST:     GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCAC                         CACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
genomic: GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
EST: gi|5740268|gb|AI947958.1|AI947958
EST:     GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCAC                         CACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
genomic: GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
EST: gi|5439238|gb|AI820159.1|AI820159
EST:     GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCAC                         CACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
genomic: GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
EST: gi|148991148|gb|EE032605.2|EE032605
EST:     GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCAC                         CACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT
genomic: GTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAAT

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: 46 (upstream exon), 26 (downstream exon)
Score: 18

GTTACATTGGACACAGAAAAACAAAAAGCTACTGTTGAGCGAGAAGTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAATGAAGGCAAAATCCAAAGTTATTAAGAAAGTCGCCGCTGAAGACCTTGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 102

GTTACATTGGACACAGAAAAACAAAAAGCTACTGTTGAGCGAGAAGTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAATGAAGGCAAAATCCAAAGTTATTAAGAAAGTCGCCGCTGAAGACCTTGGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 104

GTTACATTGGACACAGAAAAACAAAAAGCTACTGTTGAGCGAGAAGTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAATGAAGGCAAAATCCAAAGTTATTAAGAAAGTCGCCGCTGAAGACCTTGGC


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 20

GTTACATTGGACACAGAAAAACAAAAAGCTACTGTTGAGCGAGAAGTTGATGGTGGAATTGAAACCATCTGCCTTGATCTGCCAGCAGTGATCACgtagggtcca ... ttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAATGAAGGCAAAATCCAAAGTTATTAAGAAAGTCGCCGCTGAAGACCTTGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgaataattttctgtgaacatgggttaaccattaattttgtcttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAATGAAGGCAAAATCCAAAGTTATTAAGAAAGTCGCCGCTGAAGACCTTGGC
                                cattaat  putative branch site (score: 20)
                                      ttttgtcttc  CT-rich tract
                           ttaaccattaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagggtccatgaaacatttcaacatactgttttcattttattattctatgttggagaaaggaaatacaaatactcaagaatttgcattatgatgaataattttctgtgaacatgggttaaccattaattttgtcttcgctgcagCACGGATTTAAGACTTAACCAGCCAAGATATGCAACTTTGCCCAACATAATGAAGGCAAAATCCAAAGTTATTAAGAAAGTCGCCGCTGAAGACCTTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA