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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgtagcaactacattttttactattatctctgtatatggctacaaatcactcatattatttaatgtctaactacatttccaaaaaaatttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG

Basic information

species Zea mays
transcript GRMZM2G169773_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169773_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 9
-----gctgtagcaactacattttttactattatctctgtatatggctacaaatcactcatattatttaatgtctaactacatttccaaaaaaatttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
       |||||||| |  | ||        | ||  | |      || ||| | |   |||  | ||    ||||| | | | |||       |||    |||||||||||||||||||||||||| ||||||| |  | |||||||||||||
acaaacttgtagcaattcaacttgcag--gctgtccattttctctacttcaatttataaataccacttc---tctaattgcctctcccttttttttttgccacagTGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
















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|76293307|gb|DV032875.1|DV032875
EST:     GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGC                         TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
genomic: GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGCgtaagtgtta ... ttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
EST: gi|88749197|gb|DY533338.1|DY533338
EST:     GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGC                         TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
genomic: GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGCgtaagtgtta ... ttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
EST: gi|76293306|gb|DV032874.1|DV032874
EST:     GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGC                         TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
genomic: GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGCgtaagtgtta ... ttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
EST: gi|71449251|gb|DR830301.1|DR830301
EST:     GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGACAATCCTTGGC                         TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
genomic: GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGCgtaagtgtta ... ttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
EST: gi|8368017|gb|BE050962.1|BE050962
EST:     GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGC                         TGGGATTTTGCCGGCTATGGATATCATAGGCAGGAGTGCTATTGTGGGG
genomic: GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGCgtaagtgtta ... ttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
EST: gi|211151165|gb|FL467100.1|FL467100
EST:     GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGC                         TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
genomic: GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGCgtaagtgtta ... ttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
EST: gi|78115059|gb|DV533447.1|DV533447
EST:     TCTGGTCAGCTGTGGCTCCTCCATTTC-ATTTCAANG-AAA-TCCTTGGC                         TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGC
genomic: TCTGGTCAGCTGTGGCTCCTCCATTTCCATT-CAAAGGAAAATCCTTGGCgtaagtgtta ... ttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGC
EST: gi|78115058|gb|DV533446.1|DV533446
EST:     GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGC                         TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
genomic: GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGCgtaagtgtta ... ttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
EST: gi|78077114|gb|DV505548.1|DV505548
EST:     GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGGAAATCCTTGGC                         TGGGATTTTGCCGGCTATTGATATCATAGGCA
genomic: GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGCgtaagtgtta ... ttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCA
EST: gi|91049868|gb|EB160286.1|EB160286
EST:     GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGC                         TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
genomic: GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGCgtaagtgtta ... ttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
EST: gi|78077113|gb|DV505547.1|DV505547
EST:     GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGC                         TGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
genomic: GTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGCgtaagtgtta ... ttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG

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: 42 (upstream exon), 49 (downstream exon)
Score: 103

CTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGCgtaagtgtta ... ttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 280

CTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGCgtaagtgtta ... ttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 379

CTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGCgtaagtgtta ... ttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 188

CTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGCgtaagtgtta ... ttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatcactcatattatttaatgtctaactacatttccaaaaaaatttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
                     gtctaac  putative branch site (score: 188)
                                            tttctgt  putative PPT
         atattatttaatgtct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgtagcaactacattttttactattatctctgtatatggctacaaatcactcatattatttaatgtctaactacatttccaaaaaaatttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG

gctgtag
- - - - aactaca
- - - - - - - - - - - - - - - - - - - - -ctacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa