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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtacaatatccttttcgccaacaccttctgtttaatgcattcactttattgagctatgaagtctagtttatggctgtcaagatcagtagcaatcgacccatctgagttgcatcgtggctattgatttgcaacttatatatgttaaatctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAAGCGGTGGACCTATATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGT

Basic information

species Zea mays
transcript GRMZM2G313649_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G313649_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g28640.1 (Oryza sativa), 3'ss of exon 4
gtgggtacaatatccttttcgccaacaccttctgtttaatgcattcactttattgagctatgaagtctagtttatggctgtcaa--gatcagtagcaatcgacccatctgag--ttgcatcgtggctattgatttgcaacttatatatgttaaatctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAAGCGGTGGACCTATATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGT
                                                          | |  |   |  ||| || | ||  |   ||       | ||     ||   ||  || ||||   |||||| || ||| ||| | || |||| |    || |||||||||||||||||||| ||||||||||  || || ||||| ||||||||||| |||||| |||||||||| |||||||| |||||||| |||||||| |
-------------------------------------------------------gtgtgtagaacttcctttctgtcagttcatgcattttcttgagtcatttaattcaagacttacatccgagctattaatgtgccactca-atgtgttca--tattccagGTTCTTATTGATTTTGGTCTGAGTTTCATATCAACTATTCCTGAGGACAAAGCAGTGGACTTATATGTGCTTGAGAGAGCATTGATTTCTATGCATTCAT
















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|71427980|gb|DR809030.1|DR809030
EST:     TGA-TTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG                         GTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
genomic: TGATTTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
EST: gi|88748628|gb|DY532769.1|DY532769
EST:     TGA-TTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG                         GTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
genomic: TGATTTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
EST: gi|71442372|gb|DR823422.1|DR823422
EST:     TGA-TTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG                         GTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
genomic: TGATTTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
EST: gi|76294398|gb|DV033966.1|DV033966
EST:     TGA-TTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG                         GTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
genomic: TGATTTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
EST: gi|213182702|gb|FM195363.1|FM195363
EST:     TGATTT-GACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG                         GTTCTTATTGATTTTGGNCNGAGTTTCACTTCGACAATTCCCGAGGACAAA
genomic: TGATTTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
EST: gi|60343573|gb|DN210546.1|DN210546
EST:     TGA-TTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG                         GTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
genomic: TGATTTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
EST: gi|32836689|gb|CD976367.1|CD976367
EST:     TGATTT-GACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG                         GTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
genomic: TGATTTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
EST: gi|71762245|gb|DR960182.1|DR960182
EST:     TGA-TTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG                         GTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
genomic: TGATTTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
EST: gi|88748493|gb|DY532634.1|DY532634
EST:     TGA-TTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG                         GTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
genomic: TGATTTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
EST: gi|32942234|gb|CF047053.1|CF047053
EST:     TGATTT-GACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG                         GTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA
genomic: TGATTTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAA

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: 45 (upstream exon), 49 (downstream exon)
Score: 109

CAAATAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATTTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAAGCGGTGGACCTATATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGT


Block sizes: 45 (upstream exon), 44 (downstream exon)
Score: 64

CAAATAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATTTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAAGCGGTGGACCTATATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGT


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 88

CAAATAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATTTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAAGCGGTGGACCTATATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 69

CAAATAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATTTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAAGCGGTGGACCTATATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgagttgcatcgtggctattgatttgcaacttatatatgttaaatctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAAGCGGTGGACCTATATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGT
                  tattgat  putative branch site (score: 69)
                                              tctttgc  putative PPT
                             aacttatatatgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtacaatatccttttcgccaacaccttctgtttaatgcattcactttattgagctatgaagtctagtttatggctgtcaagatcagtagcaatcgacccatctgagttgcatcgtggctattgatttgcaacttatatatgttaaatctttgcagGTTCTTATTGATTTTGGGCTGAGTTTCACTTCGACAATTCCCGAGGACAAAGCGGTGGACCTATATGTGCTAGAGAGAGCTTTGATTTCCATGCATTCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT