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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctattgtataaaccggctgcggcatgatgctttggtgatttggttgcttaataactcagttcattggaaaatttattggtttgtctctccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTGGGCCTATCTTCAGGTTGTGTTTCTTCTCAAGTCAACCAAGAGCAGCCTC

Basic information

species Zea mays
transcript GRMZM2G063792_T04
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|211184127|gb|FL126415.1|FL126415
EST:     TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAT                         TTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
genomic: TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
EST: gi|6020972|gb|AW065900.1|AW065900
EST:     TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAG                         TTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
genomic: TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
EST: gi|211188926|gb|FL126432.1|FL126432
EST:     TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAG                         TTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
genomic: TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
EST: gi|211186524|gb|FL126419.1|FL126419
EST:     TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAG                         TTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
genomic: TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
EST: gi|211186528|gb|FL126423.1|FL126423
EST:     TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAG                         TTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
genomic: TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
EST: gi|211186529|gb|FL126424.1|FL126424
EST:     TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAG                         TTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
genomic: TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
EST: gi|18650268|gb|BM499087.1|BM499087
EST:     TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAG                         TTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
genomic: TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
EST: gi|211186533|gb|FL126428.1|FL126428
EST:     TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAG                         TTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
genomic: TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
EST: gi|211184126|gb|FL126414.1|FL126414
EST:     TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAG                         TTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
genomic: TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
EST: gi|211186527|gb|FL126422.1|FL126422
EST:     TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAG                         TTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
genomic: TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
EST: gi|13249793|gb|BG360698.1|BG360698
EST:     TACGCGGCCGCGGTCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAG                         TTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
genomic: TACGCGGCCGCGG-CTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
EST: gi|211186523|gb|FL126418.1|FL126418
EST:     TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAG                         TTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
genomic: TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
EST: gi|211186534|gb|FL126429.1|FL126429
EST:     TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAG                         TTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
genomic: TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
EST: gi|211186530|gb|FL126425.1|FL126425
EST:     TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAG                         TTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG
genomic: TTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTG

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: 321

CAAGCGGCAGCGGCTCGGGTGGGACGTCGTTCCCGCCGAGATGTATCAGGTTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTGGGCCTATCTTCAGGTTGTGTTTCTTCTCAAGTCAACCAAGAGCAGCCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 515

CAAGCGGCAGCGGCTCGGGTGGGACGTCGTTCCCGCCGAGATGTATCAGGTTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTGGGCCTATCTTCAGGTTGTGTTTCTTCTCAAGTCAACCAAGAGCAGCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 617

CAAGCGGCAGCGGCTCGGGTGGGACGTCGTTCCCGCCGAGATGTATCAGGTTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTGGGCCTATCTTCAGGTTGTGTTTCTTCTCAAGTCAACCAAGAGCAGCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 354

CAAGCGGCAGCGGCTCGGGTGGGACGTCGTTCCCGCCGAGATGTATCAGGTTACGCGGCCGCGGCTTGGTTGGGACGTCGGCCCCGCCGAGATGAATCAGgtataatctc ... ccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTGGGCCTATCTTCAGGTTGTGTTTCTTCTCAAGTCAACCAAGAGCAGCCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttaataactcagttcattggaaaatttattggtttgtctctccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTGGGCCTATCTTCAGGTTGTGTTTCTTCTCAAGTCAACCAAGAGCAGCCTC
     taataac  putative branch site (score: 354)
                                    tttgtctctcc  putative PPT
                   attggaaaatttatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctattgtataaaccggctgcggcatgatgctttggtgatttggttgcttaataactcagttcattggaaaatttattggtttgtctctccatgttcagTTTGCACTTTGTGGACAAGAAGTTGTGAATGCCTTCAGTGCTGCAGTGTTGGGCCTATCTTCAGGTTGTGTTTCTTCTCAAGTCAACCAAGAGCAGCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG