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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttgtaccttttgccacctcattgtgaatgtggatacatgttgaatgactggttaatatttgatctaatgttgagggtgtgttcttctatccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA

Basic information

species Zea mays
transcript GRMZM2G108829_T01
intron # 12
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|60349468|gb|DN216441.1|DN216441
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|32871065|gb|CF010747.1|CF010747
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGC-ATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|32932540|gb|CF037352.1|CF037352
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|71304777|gb|DR788504.1|DR788504
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|211496287|gb|FL041699.1|FL041699
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|31350422|gb|CD434779.1|CD434779
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACCACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|32870331|gb|CF010013.1|CF010013
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|32869779|gb|CF009461.1|CF009461
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|67011156|gb|CO439905.1|CO439905
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
EST: gi|5932684|gb|AW057045.1|AW057045
EST:     GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAG                         ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA
genomic: GGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCA

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), 49 (downstream exon)
Score: 242

TGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

TGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 194

TGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 149

TGAGATTCACAAGATATGCAATGTCATCGGTAGTCCAGATGAGCAATCTTGGCCTCAAGGATTGTCACTTGCAGAAGCAATGAAGTATCAGTTCCCACAGgtcaatattc ... atccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgactggttaatatttgatctaatgttgagggtgtgttcttctatccatgcagATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA
                   atctaat  putative branch site (score: 149)
                                      ttcttctatcc  putative PPT
         ttaatatttgatctaa  TA-rich tract