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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgataaattgtcttcataaaagatctattttttgtatgcccacaaaagaaaagaaaggaaaagttaagttaattgcatatttcccattggtgtagcaaagGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAACATTAACTATAAGCCCGGCACTGGCATCTGGTGTGATCAGACAGCGTTA

Basic information

species Zea mays
transcript GRMZM2G061938_T01
intron # 1
splice site 3'
intron type U2

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|74244554|gb|DT652468.1|DT652468
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         GTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... tgtagcaaagGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
EST: gi|71449505|gb|DR830555.1|DR830555
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGCAAAG                     
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---GC--AGgtacggtctc ... tgtagc
EST: gi|37418255|gb|CF646795.1|CF646795
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGCAAAG                     
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---GC--AGgtacggtctc ... tgtagc
EST: gi|89755704|gb|DY686027.1|DY686027
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGCAAAG                     
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---GC--AGgtacggtctc ... tgtagc
EST: gi|71304895|gb|DR788568.1|DR788568
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         GTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... tgtagcaaagGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
EST: gi|76285208|gb|DV024776.1|DV024776
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGCAAAG                     
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---GC--AGgtacggtctc ... tgtagc
EST: gi|148949635|gb|EC895107.2|EC895107
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGCAAAG                     
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---GC--AGgtacggtctc ... tgtagc
EST: gi|74238569|gb|DT646483.1|DT646483
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGCAAAG                     
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---GC--AGgtacggtctc ... tgtagc
EST: gi|71306065|gb|DR789177.1|DR789177
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGCAAAG                     
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---GC--AGgtacggtctc ... tgtagc
EST: gi|89761337|gb|DY689389.1|DY689389
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         GTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... tgtagcaaagGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
EST: gi|76280361|gb|DV019929.1|DV019929
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         GTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... tgtagcaaagGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
EST: gi|71306093|gb|DR789196.1|DR789196
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGCAAAG                     
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---GC--AGgtacggtctc ... tgtagc
EST: gi|71434726|gb|DR815776.1|DR815776
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGCAAAG                     
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---GC--AGgtacggtctc ... tgtagc
EST: gi|78091421|gb|DV519795.1|DV519795
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         GTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... tgtagcaaagGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
EST: gi|50336832|gb|CO531958.1|CO531958
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         GTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... tgtagcaaagGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
EST: gi|71447327|gb|DR828377.1|DR828377
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         GTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... tgtagcaaagGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
EST: gi|149009976|gb|EE041806.2|EE041806
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGCAAAG                     
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---GC--AGgtacggtctc ... tgtagc
EST: gi|211307886|gb|FL435246.1|FL435246
EST:     CGGCCCCTCCTCCNATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         GTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
genomic: CGGCCCCTCCTCC-ATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... tgtagcaaagGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
EST: gi|91050990|gb|EB161408.1|EB161408
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGCAAAG                     
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---GC--AGgtacggtctc ... tgtagc
EST: gi|148974627|gb|EE025424.2|EE025424
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         GTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... tgtagcaaagGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
EST: gi|149042496|gb|EE047179.2|EE047179
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         GTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... tgtagcaaagGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAA
EST: gi|21843164|gb|BQ703760.1|BQ703760
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCC-GCAGCCGGCCTGCAGCAAAG                     
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---GC--AGgtacggtctc ... tgtagc
EST: gi|148948567|gb|EC894092.2|EC894092
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGCAAAG                     
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---GC--AGgtacggtctc ... tgtagc

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: 59

ACTGTGCCGGTGACGGCGGCGCGCTACCGGTGACGGGGGATACGGCGGCATCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... tgtagcaaagGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAACATTAACTATAAGCCCGGCACTGGCATCTGGTGTGATCAGACAGCGTTA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 14

ACTGTGCCGGTGACGGCGGCGCGCTACCGGTGACGGGGGATACGGCGGCATCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... tgtagcaaagGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAACATTAACTATAAGCCCGGCACTGGCATCTGGTGTGATCAGACAGCGTTA


Block sizes: 45 (upstream exon), 42 (downstream exon)
Score: 10

ACTGTGCCGGTGACGGCGGCGCGCTACCGGTGACGGGGGATACGGCGGCATCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... tgtagcaaagGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAACATTAACTATAAGCCCGGCACTGGCATCTGGTGTGATCAGACAGCGTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

ACTGTGCCGGTGACGGCGGCGCGCTACCGGTGACGGGGGATACGGCGGCATCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... tgtagcaaagGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAACATTAACTATAAGCCCGGCACTGGCATCTGGTGTGATCAGACAGCGTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaaaagaaaggaaaagttaagttaattgcatatttcccattggtgtagcaaagGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAACATTAACTATAAGCCCGGCACTGGCATCTGGTGTGATCAGACAGCGTTA
                     agttaat  putative branch site (score: 55)
             aaaagttaagttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgataaattgtcttcataaaagatctattttttgtatgcccacaaaagaaaagaaaggaaaagttaagttaattgcatatttcccattggtgtagcaaagGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAACATTAACTATAAGCCCGGCACTGGCATCTGGTGTGATCAGACAGCGTTA

- - - - - - - cataaaag
- - - - - - - - - - - - - - - - tgtatgc
- - - - - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - aaggaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aattgca