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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCCCTGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCAGATGGGTAGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagcgctcgtagtgagcttgtatatgcatgtatatcgtttctctggtgacgcttttgctttgcttccactcctactcgtag

Basic information

species Zea mays
transcript GRMZM2G044629_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044629_T03 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 14
ACCCCTGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCAGATGGGTAGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagcgctcgt--agtgagcttgtatatgcatgtatatcgtttctctggtgacgcttttgctttgcttccactcctactcgtag------------------
|||||||||||||| ||||| |||||||| || ||||| || ||||||||||| |||||||| ||||||||||| || ||||| || ||||| ||||||||||| |   | |  ||  | |    |   | |       | | |      |  |  |   |  |  ||| |||  |||  || |   |                   
ACCCCTGATAGCGCAAAGCTGATGCTGCTTCGTCTCCATAGTAGATGGGTAGTTGCTGCTGGTGGCTTCTTGACCCATTCTGTCCCATTGTACATGACAGgtaaattttctcctgtccaatacattcagaaacttgccaagaacaaaaaacaaggaaaaatgatatttt-cttttactaatattgtcatgattgattttgcttgtag
















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|149100895|gb|EE186990.2|EE186990
EST:     AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTTTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
genomic: AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
EST: gi|71429564|gb|DR810614.1|DR810614
EST:     AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
genomic: AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
EST: gi|211094109|gb|FL460556.1|FL460556
EST:     AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
genomic: AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
EST: gi|37378055|gb|CF625683.1|CF625683
EST:     AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
genomic: AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
EST: gi|211406602|gb|FL094198.1|FL094198
EST:     AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAG                         GCCGTCGAAGTTTCTCCGGCTCTCCTCCTACGCCGGGAGAGAACCCTGGAA
genomic: AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGC-GTCGAAGTTTCTCCG-CTCTCCTCCTACGCCGG-AGAGAACC-TGGAA
EST: gi|78115802|gb|DV534190.1|DV534190
EST:     AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
genomic: AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
EST: gi|37376092|gb|CF624546.1|CF624546
EST:     AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
genomic: AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
EST: gi|149014876|gb|EE044587.2|EE044587
EST:     AGTCGTTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAG                         GCGTGGAAGTTTCTCCGCTCTCCTCTTACGCCGGAGAGAACCTGGAAGCCA
genomic: AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
EST: gi|94477176|gb|EB706134.1|EB706134
EST:     AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAG                         GCGTGGAAGTTTTTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
genomic: AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
EST: gi|37397991|gb|CF636304.1|CF636304
EST:     AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
genomic: AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
EST: gi|211119106|gb|FL479441.1|FL479441
EST:     CTCTGTCCCCTTGTATATGACAG                         GCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
genomic: CTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
EST: gi|211119105|gb|FL479440.1|FL479440
EST:     AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
genomic: AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
EST: gi|16926727|gb|BM079795.1|BM079795
EST:     AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
genomic: AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
EST: gi|91052248|gb|EB162666.1|EB162666
EST:     AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTTTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
genomic: AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
EST: gi|24769018|gb|CA404147.1|CA404147
EST:     AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
genomic: AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
EST: gi|16926697|gb|BM079765.1|BM079765
EST:     AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
genomic: AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
EST: gi|14244148|gb|BG841843.2|BG841843
EST:     AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
genomic: AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
EST: gi|4225561|gb|AI396014.1|AI396014
EST:     AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA
genomic: AGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCA

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), 48 (downstream exon)
Score: 78

ACCCCTGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCAGATGGGTAGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCATCTGCCGTGGGCGAACGTTCCATGCGCCGAGCGAGATCTCGTTTTAGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 166

ACCCCTGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCAGATGGGTAGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCATCTGCCGTGGGCGAACGTTCCATGCGCCGAGCGAGATCTCGTTTTAGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 173

ACCCCTGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCAGATGGGTAGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCATCTGCCGTGGGCGAACGTTCCATGCGCCGAGCGAGATCTCGTTTTAGGA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 223

ACCCCTGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCAGATGGGTAGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagc ... ctactcgtagGCGTCGAAGTTTCTCCGCTCTCCTCCTACGCCGGAGAGAACCTGGAAGCCATCTGCCGTGGGCGAACGTTCCATGCGCCGAGCGAGATCTCGTTTTAGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCCCTGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCAGATGGGTAGTCGCTGCTGGCGGCTTCTTGACGCACTCTGTGCCCTTGTATATGACAGgtaattaagcgctcgtagtgagcttgtatatgcatgtatatcgtttctctggtgacgcttttgctttgcttccactcctactcgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT