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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGCCACCGTCGTTGCTCTCCCGCCTTCACCGTGCCAACTCCCCTCCTTGCCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCTGGTCAGgtatagtcgccacctttcttttctttcccttaccattttctttcatgcgctcaagagccaacacggctcgatccagaattccag

Basic information

species Zea mays
transcript GRMZM2G137479_T02
intron # 1
splice site 5'
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|50325214|gb|CO520340.1|CO520340
EST:     CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCTGGTCAGAATTCCAG                  
genomic: CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCT-G---G---T-CAGgtatagtcgc ... aga
EST: gi|50326187|gb|CO521313.1|CO521313
EST:     CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCTGGTCAGAATTCCAG                  
genomic: CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCT-G---G---T-CAGgtatagtcgc ... aga
EST: gi|149083392|gb|EE172703.2|EE172703
EST:     CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCTGGTCAGAATTCCAG                  
genomic: CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCT-G---G---T-CAGgtatagtcgc ... aga
EST: gi|31406080|gb|CD484812.1|CD484812
EST:     CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCTGGTCAGAATTCCAG                  
genomic: CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCT-G---G---T-CAGgtatagtcgc ... aga
EST: gi|149084036|gb|EE173431.2|EE173431
EST:     CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCTGGTCAGAATTCCAG                  
genomic: CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCT-G---G---T-CAGgtatagtcgc ... aga
EST: gi|211140433|gb|FL390022.1|FL390022
EST:     CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCTGGTCAG                         ATCCAGGTGTCCTTTGACCCAGACCGCGCCTGCCTTTCCCTCCGCTCGGAT
genomic: CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCTGGTCAGgtatagtcgc ... agaattccagATCCAGGTGTCCTTTGACCCAGACCGCGCCTGCCTTTCCCTCCGCTCGGAT
EST: gi|211307824|gb|FK975925.1|FK975925
EST:     CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCTGGTCAGAATTCCAG                  
genomic: CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCT-G---G---T-CAGgtatagtcgc ... aga
EST: gi|148965556|gb|EE016384.2|EE016384
EST:     CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCTGGTCAGAATTCCAG                  
genomic: CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCT-G---G---T-CAGgtatagtcgc ... aga
EST: gi|31406440|gb|CD485172.1|CD485172
EST:     CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCTGGTCAGAATTCCAG                  
genomic: CCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCT-G---G---T-CAGgtatagtcgc ... aga

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: 21

TCGCCACCGTCGTTGCTCTCCCGCCTTCACCGTGCCAACTCCCCTCCTTGCCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCTGGTCAGgtatagtcgc ... agaattccagATCCAGGTGTCCTTTGACCCAGACCGCGCCTGCCTTTCCCTCCGCTCGGATTCTTCGCCGTCTTCGTTCCTACTGGGCGCCGCCGGGGTGGAGCGGAGAT


Block sizes: 23 (upstream exon), 48 (downstream exon)
Score: 6

TCGCCACCGTCGTTGCTCTCCCGCCTTCACCGTGCCAACTCCCCTCCTTGCCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCTGGTCAGgtatagtcgc ... agaattccagATCCAGGTGTCCTTTGACCCAGACCGCGCCTGCCTTTCCCTCCGCTCGGATTCTTCGCCGTCTTCGTTCCTACTGGGCGCCGCCGGGGTGGAGCGGAGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 10

TCGCCACCGTCGTTGCTCTCCCGCCTTCACCGTGCCAACTCCCCTCCTTGCCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCTGGTCAGgtatagtcgc ... agaattccagATCCAGGTGTCCTTTGACCCAGACCGCGCCTGCCTTTCCCTCCGCTCGGATTCTTCGCCGTCTTCGTTCCTACTGGGCGCCGCCGGGGTGGAGCGGAGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 16

TCGCCACCGTCGTTGCTCTCCCGCCTTCACCGTGCCAACTCCCCTCCTTGCCTCCCCCGCGCTTCAGTCGCTCCACTCCCCATCGCTTTCGCCTGGTCAGgtatagtcgc ... agaattccagATCCAGGTGTCCTTTGACCCAGACCGCGCCTGCCTTTCCCTCCGCTCGGATTCTTCGCCGTCTTCGTTCCTACTGGGCGCCGCCGGGGTGGAGCGGAGAT