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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGGGCGAGATCTGCTTGAGGGGCCACACCATGTTCTCCGGGTACTACAAGCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaataaaaaaaatcatttctcacttcttttaatttgcacctaactgaaggatcagtcagtgaagcagctggtcgattcgtggaacttgtcatcaccctatgtgtgcag

Basic information

species Zea mays
transcript GRMZM2G104847_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104847_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os11g35400.2 (Oryza sativa), 5'ss of exon 15
CGGGGCGAGATCTGCTTGAGGGGCCACACCATGTTCTCCGGGTACTACAAGCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaataaaaaaaatcatttctcacttcttttaatttgcacctaactgaaggatcagtcagtgaagcagctggtcgattcgtggaacttgtcatcaccctatgtgtgcag
 |||| ||||||||||||||||| |||||| ||||||||||||||||||||||||||  |||||| || ||||| ||||||||||| |||||||||||||||            ||| ||||||  |     ||| |     | ||| |||||| |||| | ||||| ||       | |  ||    || | |  |||| | ||||| || ||
AGGGGTGAGATCTGCTTGAGGGGTCACACCTTGTTCTCCGGGTACTACAAGCGCCCTGACCTCACCGAGGAAGTATTCTCAGATGGTTGGTTCCATACAGgt------------aaagtcatttaccctcagtttca-----cgccttactgaatgatctgacagtggag--ataaattgtctca---aattagcaatcatcttatgtatgaag
















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|67024206|gb|CO452955.1|CO452955
EST:     GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAG                         GTGATATCGGGGAGTGGCAATCCA-TGGCACGATGAAGATCATCGACAGAA
genomic: GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
EST: gi|7162313|gb|AW519920.1|AW519920
EST:     GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAG                         GTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
genomic: GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
EST: gi|148958442|gb|EC904676.2|EC904676
EST:     GATGGCTGGTTCCATACAG                         GTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
genomic: GATGGCTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
EST: gi|32838972|gb|CD978653.1|CD978653
EST:     GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAG                         GTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
genomic: GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
EST: gi|26456355|gb|CA827938.1|CA827938
EST:     GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAG                         GTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
genomic: GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
EST: gi|83279443|gb|DV943451.1|DV943451
EST:     GAAGAAGTGTTCTCAGATGGCTGGTTCCATACAG                         GTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
genomic: GAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
EST: gi|32837781|gb|CD977459.1|CD977459
EST:     GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAG                         GTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
genomic: GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
EST: gi|4628405|gb|AI619279.1|AI619279
EST:     GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAG                         GTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
genomic: GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
EST: gi|13150470|gb|BG320792.1|BG320792
EST:     GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAG                         GTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
genomic: GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
EST: gi|74243995|gb|DT651909.1|DT651909
EST:     GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAG                         GTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
genomic: GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
EST: gi|32837912|gb|CD977590.1|CD977590
EST:     GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAG                         GTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
genomic: GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
EST: gi|78544549|gb|DV622047.1|DV622047
EST:     GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAG                         GTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
genomic: GCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
EST: gi|149076510|gb|EE165136.2|EE165136
EST:     GATGGCTGGTTCCATACAG                         GTGATATCGGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGA
genomic: GATGGCTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATC-GGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGA
EST: gi|149085815|gb|EE175337.2|EE175337
EST:     CTGGTTCCATACAG                         GTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA
genomic: CTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAA

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: 186

CGGGGCGAGATCTGCTTGAGGGGCCACACCATGTTCTCCGGGTACTACAAGCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAAAGAAGAACATCTTCAAGCTGTCCCAGGGGGAGTATGTGGCAGTTGAGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

CGGGGCGAGATCTGCTTGAGGGGCCACACCATGTTCTCCGGGTACTACAAGCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAAAGAAGAACATCTTCAAGCTGTCCCAGGGGGAGTATGTGGCAGTTGAGGT


Block sizes: 34 (upstream exon), 40 (downstream exon)
Score: 2

CGGGGCGAGATCTGCTTGAGGGGCCACACCATGTTCTCCGGGTACTACAAGCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAAAGAAGAACATCTTCAAGCTGTCCCAGGGGGAGTATGTGGCAGTTGAGGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 350

CGGGGCGAGATCTGCTTGAGGGGCCACACCATGTTCTCCGGGTACTACAAGCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaat ... atgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAAAGAAGAACATCTTCAAGCTGTCCCAGGGGGAGTATGTGGCAGTTGAGGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGGGCGAGATCTGCTTGAGGGGCCACACCATGTTCTCCGGGTACTACAAGCGCCCTAGCCTCACTGAAGAAGTGTTCTCAGATGGCTGGTTCCATACAGgtgaaagaataaaaaaaatcatttctcacttcttttaatttgcacctaactgaaggatcagtcagtgaagcagctggtcgattcgtggaacttgtcatcaccctatgtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG