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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaaaaacctgtcctctcgctacaaacacagaagaattttacagttgatagctttttccttccctaattcgtaaattgctgttcactgttttcagcttgcctgctcattattggttatgtttgatattgtacttagATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACCTGCTTTTGACTATGATCATGAAGGTGACATTCTCAGTTGATCTTCTCTTCCTAACGCTGTGGTC

Basic information

species Zea mays
transcript GRMZM2G146472_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146472_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g06760.1 (Oryza sativa), 3'ss of exon 5
gtaagtcaaaaacctgtcctctcgctacaaacacagaagaattttacagttgatagctttttcctt--ccctaattcgtaaattgctgttcactgttttcagcttgcctgctcattattggttatgtttgatattgtacttagATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACCTGCTTTTGACTATGATCATGAAGGTGACATTCTCAGTTGATCTTCTCTTCCTAACGCTGTGGTC
||||||  ||  |||||||          | |  | | |  || | || ||  ||     ||  ||    ||   |  ||| |||    | |  ||    |   || ||| ||||| |  |||      |||    | ||||| |||||||||||||||||||||||||| |||| ||| |||||||||||||| || ||||                                         
gtaagttgaac-cctgtcca--------gagctaatatgttttatccacttattattcacttatttggtgctgtatattaatttgaaactgatagtg---aatatgtctgatcattgtctgtt------gattaaatccttagGTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAG-----------------------------------------
















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|89248294|gb|DY620080.1|DY620080
EST:     ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG                         ATACCAGCCACCTATCCCAGCTG
genomic: ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGGgtaagtcaaa ... ttgtacttagATACCAGCCACCTATCCCAGCTG
EST: gi|211062365|gb|FL252795.1|FL252795
EST:     ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG                         ATACCAGCCACCT
genomic: ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGGgtaagtcaaa ... ttgtacttagATACCAGCCACCT
EST: gi|211059403|gb|FL252784.1|FL252784
EST:     ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG                         ATACCAGCCACCTATC
genomic: ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGGgtaagtcaaa ... ttgtacttagATACCAGCCACCTATC
EST: gi|211062364|gb|FL252794.1|FL252794
EST:     ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG                         ATACCAGCCACCTATCCCAGCTG
genomic: ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGGgtaagtcaaa ... ttgtacttagATACCAGCCACCTATCCCAGCTG
EST: gi|211062361|gb|FL252791.1|FL252791
EST:     ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG                         ATAC-AGCCACCTATCCCAGCTG
genomic: ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGGgtaagtcaaa ... ttgtacttagATACCAGCCACCTATCCCAGCTG
EST: gi|149078577|gb|EE167361.2|EE167361
EST:     ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG                         ATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACCTGCTTTTGACTATGA
genomic: ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGGgtaagtcaaa ... ttgtacttagATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACCTGCTTTTGACTATGA
EST: gi|149109057|gb|EE189984.2|EE189984
EST:     ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG                         ATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACCTGCTTTTGACTATGA
genomic: ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGGgtaagtcaaa ... ttgtacttagATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACCTGCTTTTGACTATGA
EST: gi|211062360|gb|FL252790.1|FL252790
EST:     ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG                         ATACCAGCCACCTATCCCAGCTGAAGANGTGAAACCTGCTTTTGACTATGA
genomic: ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGGgtaagtcaaa ... ttgtacttagATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACCTGCTTTTGACTATGA
EST: gi|211062359|gb|FL252789.1|FL252789
EST:     ATGATCAMTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG                         ATACCAGCCACCTATCCCAGCTGAAGA
genomic: ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGGgtaagtcaaa ... ttgtacttagATACCAGCCACCTATCCCAGCTGAAGA
EST: gi|211059404|gb|FL252785.1|FL252785
EST:     ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG                         ATACCAGCCACCTATCCCAGCTGAAAGAGGTGAAACCTGCTTTTGACTATG
genomic: ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGGgtaagtcaaa ... ttgtacttagATACCAGCCACCTATCCCAGCTGAA-GAGGTGAAACCTGCTTTTGACTATG
EST: gi|29945425|gb|CB815632.1|CB815632
EST:     ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG                         ATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACCTGCTTTTGACTATGA
genomic: ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGGgtaagtcaaa ... ttgtacttagATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACCTGCTTTTGACTATGA
EST: gi|211062366|gb|FL252796.1|FL252796
EST:     ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG                         ATACCAGCCACCTATCCCAGCTGAAGAAGTGGAACCCTGCTTTT
genomic: ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGGgtaagtcaaa ... ttgtacttagATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACC-TGCTTTT
EST: gi|211059402|gb|FL252783.1|FL252783
EST:     ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGG                         ATACCAGCCACCTATCCCAGC
genomic: ATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGGgtaagtcaaa ... ttgtacttagATACCAGCCACCTATCCCAGC

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: 1754

ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGGgtaagtcaaa ... ttgtacttagATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACCTGCTTTTGACTATGATCATGAAGGTGACATTCTCAGTTGATCTTCTCTTCCTAACGCTGTGGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1765

ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGGgtaagtcaaa ... ttgtacttagATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACCTGCTTTTGACTATGATCATGAAGGTGACATTCTCAGTTGATCTTCTCTTCCTAACGCTGTGGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1382

ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGGgtaagtcaaa ... ttgtacttagATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACCTGCTTTTGACTATGATCATGAAGGTGACATTCTCAGTTGATCTTCTCTTCCTAACGCTGTGGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1067

ACTAGAGACAACTCGCCATGTGTCGATGATCACTGTGACACTGTCAAAGAACCCTCTGGATACATCATCTCCAGGgtaagtcaaa ... ttgtacttagATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACCTGCTTTTGACTATGATCATGAAGGTGACATTCTCAGTTGATCTTCTCTTCCTAACGCTGTGGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcactgttttcagcttgcctgctcattattggttatgtttgatattgtacttagATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACCTGCTTTTGACTATGATCATGAAGGTGACATTCTCAGTTGATCTTCTCTTCCTAACGCTGTGGTC
                                     gtttgat  putative branch site (score: 1067)
                                 ttatgtttgatatt  TA-rich tract