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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtttttagattttcatgtttgatcactatagttgcggcgacatcgtttttatacacactactgaaaaatgaaatgtccttctctgtacttactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGCTTTGCTGATGGAGAAATTTATGTGCAACTGCAAGAGAGCGTGAGAGGAT

Basic information

species Zea mays
transcript GRMZM2G180863_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180863_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g41360.1 (Oryza sativa), 3'ss of exon 2
ggtttttagattttcatgt---ttgatcactatagttgcggcgacatcgtttttatacac-actactgaaaaatgaaatgtccttctctgtacttactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGCTTTGCTGATGGAGAAATTTATGTGCAACTGCAAGAGAGCGTGAGAGGAT
    | | ||||   ||||   ||   ||| || | |  |  | |  | |||||  ||   | | ||||||| |    | |  || | |    |   |||  ||||||||||| ||||| ||||| |||| || || ||| |||| |||||||| ||||| ||||| ||||| || ||||| ||||| ||||| ||||| || |
----tatggattggtatgtgtgttatccacgatggatatgaaggcgacctttttggaccttagttctgaaaattttgtttttgtttttttgtttcgttttgcagGAAATTGCTTCTTACTTGGGTGTAGACCTGGGTAAGGTCCTCATCAAGCGTTTTGCCGATGGGGAAATCTACGTGCAGCTGCAGGAGAGTGTGAGGGGTT

upper sequence: GRMZM2G180863_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S152_123V6.1 (Physcomitrella patens), 3'ss of exon 2
ggtttttagattttcatgtttgat-cactatagttgcggcgacatcgtttttatacacactactgaaaaatgaaatgtccttctctgtacttactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGCTTTGCTGATGGAGAAATTTATGTGCAACTGCAAGAGAGCGTGAGAGGAT
   || ||| |  | ||     |  || ||| ||  |     || | ||||   |  ||    |  |       || |  ||  |  |  |   | |  ||||||| |||  |||  ||||| | ||  | |||||||||  ||||||||| ||||| ||||||||||| ||||||||||| |||||||||||  | || |
ctgttctaggtcatgattgcaaacacattatggtcccatgtgcagcattttccgatgcatagttctattgctgtatatttttgacc-tcttggatctgcagGAAATCGCTTGTTATATGGGTCTTGATTTGGGCAAGATCAAGATCAAGCGGTTTGCGGATGGAGAAATATATGTGCAACTCCAAGAGAGCGTCCGTGGTT
















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|8367462|gb|BE050407.1|BE050407
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|149088668|gb|EE177786.2|EE177786
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|78088529|gb|DV516922.1|DV516922
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|149112871|gb|EE191452.2|EE191452
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|74240297|gb|DT648211.1|DT648211
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|50339735|gb|CO534861.1|CO534861
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|149006976|gb|EE040195.2|EE040195
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|50325135|gb|CO520261.1|CO520261
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|71770134|gb|DR968071.1|DR968071
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|74243332|gb|DT651246.1|DT651246
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|31354391|gb|CD438748.1|CD438748
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|149000114|gb|EE037239.2|EE037239
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|71766416|gb|DR964353.1|DR964353
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|149079724|gb|EE168725.2|EE168725
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|91053049|gb|EB163467.1|EB163467
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|148973790|gb|EE024926.2|EE024926
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|148947744|gb|EC893227.2|EC893227
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|211172960|gb|FL281672.1|FL281672
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
EST: gi|91874828|gb|EB404785.1|EB404785
EST:     ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAG                         GAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC
genomic: ACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGC

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: 48 (upstream exon), 49 (downstream exon)
Score: 92

GGTGCCCGCACCGGAGTCCAGGCTTGCCGCACTGCCAAGGGAGCTGCGGGACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGCTTTGCTGATGGAGAAATTTATGTGCAACTGCAAGAGAGCGTGAGAGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

GGTGCCCGCACCGGAGTCCAGGCTTGCCGCACTGCCAAGGGAGCTGCGGGACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGCTTTGCTGATGGAGAAATTTATGTGCAACTGCAAGAGAGCGTGAGAGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 89

GGTGCCCGCACCGGAGTCCAGGCTTGCCGCACTGCCAAGGGAGCTGCGGGACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGCTTTGCTGATGGAGAAATTTATGTGCAACTGCAAGAGAGCGTGAGAGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

GGTGCCCGCACCGGAGTCCAGGCTTGCCGCACTGCCAAGGGAGCTGCGGGACTCCAGGATGAAGATCTTCTCCGGCACGGCTAACCGTCCGCTCGCTCAGgtgtttaccg ... tactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGCTTTGCTGATGGAGAAATTTATGTGCAACTGCAAGAGAGCGTGAGAGGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttatacacactactgaaaaatgaaatgtccttctctgtacttactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGCTTTGCTGATGGAGAAATTTATGTGCAACTGCAAGAGAGCGTGAGAGGAT
                                         tacttac  putative branch site (score: 81)
                               tccttctctgtactta  CT-rich tract
                   aaaaatgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtttttagattttcatgtttgatcactatagttgcggcgacatcgtttttatacacactactgaaaaatgaaatgtccttctctgtacttactttctagGAAATTGCTGCTTACCTGGGTATAGAACTCGGCAAGATCCTGATCAAGCGCTTTGCTGATGGAGAAATTTATGTGCAACTGCAAGAGAGCGTGAGAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT