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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattttgataaattgtcttcataaaagatctattttttgtatgcccacaaaagaaaagaaaggaaaagttaagttaattgcatatttcccattggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAACATTAACTATAAGCCCGGCACTGGCATCTGGTGTGATCAGACAG

Basic information

species Zea mays
transcript GRMZM2G061938_T03
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|71447327|gb|DR828377.1|DR828377
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---G                         C--AGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|71434726|gb|DR815776.1|DR815776
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         CAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|38688396|gb|CK145427.1|CK145427
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         CAAAGGTAGTTGAATGGCTTCAAGTGCACGGGAC
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGAC
EST: gi|21843164|gb|BQ703760.1|BQ703760
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCC-GCAGCCGGCCTGCAG                         CAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCGTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|71449505|gb|DR830555.1|DR830555
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         CAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|78091421|gb|DV519795.1|DV519795
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---G                         C--AGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|74238569|gb|DT646483.1|DT646483
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         CAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|21843272|gb|BQ703853.1|BQ703853
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         CAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCGTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|76285208|gb|DV024776.1|DV024776
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         CAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|71306065|gb|DR789177.1|DR789177
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         CAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|149042496|gb|EE047179.2|EE047179
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---G                         C--AGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|50336832|gb|CO531958.1|CO531958
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---G                         C--AGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|71304895|gb|DR788568.1|DR788568
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---G                         C--AGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|148949635|gb|EC895107.2|EC895107
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         CAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|211307886|gb|FL435246.1|FL435246
EST:     CGGCCCCTCCTCCNATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---G                         C--AGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: CGGCCCCTCCTCC-ATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|71306093|gb|DR789196.1|DR789196
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         CAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|37418255|gb|CF646795.1|CF646795
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         CAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|74244554|gb|DT652468.1|DT652468
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---G                         C--AGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|148974627|gb|EE025424.2|EE025424
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---G                         C--AGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|148948567|gb|EC894092.2|EC894092
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         CAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|76280361|gb|DV019929.1|DV019929
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---G                         C--AGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|87153148|gb|DY397937.1|DY397937
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         CAAAGGTAGTTTAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCGTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|89761337|gb|DY689389.1|DY689389
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCT---G                         C--AGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|89755704|gb|DY686027.1|DY686027
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         CAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|91050990|gb|EB161408.1|EB161408
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         CAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
EST: gi|149009976|gb|EE041806.2|EE041806
EST:     TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAG                         CAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT
genomic: TCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCT

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: 45 (upstream exon), 49 (downstream exon)
Score: 120

ACTGTGCCGGTGACGGCGGCGCGCTACCGGTGACGGGGGATACGGCGGCATCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAACATTAACTATAAGCCCGGCACTGGCATCTGGTGTGATCAGACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 43

ACTGTGCCGGTGACGGCGGCGCGCTACCGGTGACGGGGGATACGGCGGCATCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAACATTAACTATAAGCCCGGCACTGGCATCTGGTGTGATCAGACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 31

ACTGTGCCGGTGACGGCGGCGCGCTACCGGTGACGGGGGATACGGCGGCATCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAACATTAACTATAAGCCCGGCACTGGCATCTGGTGTGATCAGACAG


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 55

ACTGTGCCGGTGACGGCGGCGCGCTACCGGTGACGGGGGATACGGCGGCATCGGCCCCTCCTCCATCCCCGGCGCGGCGGCGCCAGCAGCCGGCCTGCAGgtacggtctc ... attggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAACATTAACTATAAGCCCGGCACTGGCATCTGGTGTGATCAGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacaaaagaaaagaaaggaaaagttaagttaattgcatatttcccattggtgtagCAAAGGTAGTTGAATGGCTTCAAGTGCACGGGACATTATGTTTCGGCCTCTCAAAACATTAACTATAAGCCCGGCACTGGCATCTGGTGTGATCAGACAG
                          agttaat  putative branch site (score: 55)
                                       tttcccatt  putative PPT
                  aaaagttaagttaatt  TA-rich tract