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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgaaacttgaacttgcatcatagatcaaggatttcttgtctgaaataagctgatgggtctacttcggacttggcatttttcagGACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC

Basic information

species Zea mays
transcript GRMZM2G136803_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136803_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os07g46790.1 (Oryza sativa), 3'ss of exon 21
gtgcgaaacttgaacttgcatcatagatcaaggatttcttgtctgaaataagctgatgggtctacttcggacttggcatttttcagGACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC
||    |  |||   |   | | || || || |||   |   | |||  |||  |||   | ||||| ||   |   |||| ||||||||| |||||||| ||||||||||||||||||||||||||   ||||||||||||||||||||| |||||||| ||||| |||||||||||||
gtatataggttggcttgttaacttatataaaagatcaata--cagaataaagtagattaatgtacttggggtgttctatttgtcagGACCTGCTTGCACTTAAAGACAAGTACACCACAAGACCAGCAAAAGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC

upper sequence: GRMZM2G136803_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA19G30580.1 (Glycine max), 3'ss of exon 22
--------------------------------------------------------------------------------------------------gtgcgaaacttgaacttgcatcatagatcaaggatttcttgtctgaaataagctgatgggtctactt---cggacttggcatttttcagGACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC
                                                                                                  ||       |        || | |   |  ||   ||  | | |  |   | || |||   ||| |    ||||| | | |   | |||||| | || ||| | |||||  | || || ||| | || ||  ||||||| |||||||||||||| || || || |||||||||||||||||||
gtattctgactgacatgttattttaacagggtgaaataaacttattgtggttttccattttaatttcccaagacagccctttcagcttgcactagttggtttatggttgtcggggacaacttcattttagttatttctctgtacatggaactcatgctcctaatgtggcggacctcgaa---tgcagGACTTGCTAGCATTAAAAGAAGAATATACAACACGCCCTGCAACAGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCC
















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|6022364|gb|AW067292.1|AW067292
EST:     TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCNCTTCAG                         GCCCTCCTTGCACTGAAAGACAAGTCCACCACAAGACCAGCGCCAGAGGAA
genomic: TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAGgtgcgaaact ... catttttcagGACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAA
EST: gi|32932784|gb|CF037596.1|CF037596
EST:     TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAG                         GACCTCCTTGCACTGAAAGACAAGTA
genomic: TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAGgtgcgaaact ... catttttcagGACCTCCTTGCACTGAAAGACAAGTA
EST: gi|32930716|gb|CF035528.1|CF035528
EST:     TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAG                         GACCTCCTTACACTGAAAGACAAGT
genomic: TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAGgtgcgaaact ... catttttcagGACCTCCTTGCACTGAAAGACAAGT
EST: gi|32931864|gb|CF036676.1|CF036676
EST:     TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAG                         GACCTCCTTGCACTGAAAGACAAGTAC
genomic: TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAGgtgcgaaact ... catttttcagGACCTCCTTGCACTGAAAGACAAGTAC
EST: gi|16927586|gb|BM080655.1|BM080655
EST:     TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAG                         GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAA
genomic: TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAGgtgcgaaact ... catttttcagGACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAA
EST: gi|78120826|gb|DV539210.1|DV539210
EST:     TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAG                         GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAA
genomic: TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAGgtgcgaaact ... catttttcagGACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAA
EST: gi|32867796|gb|CF007478.1|CF007478
EST:     TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAG                         GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAA
genomic: TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAGgtgcgaaact ... catttttcagGACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAA
EST: gi|60394528|gb|DN227398.1|DN227398
EST:     TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAG                         GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAA
genomic: TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAGgtgcgaaact ... catttttcagGACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAA
EST: gi|32932809|gb|CF037621.1|CF037621
EST:     TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAG                         GACCTCCTTGCACTGAAAGACAAGTA
genomic: TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAGgtgcgaaact ... catttttcagGACCTCCTTGCACTGAAAGACAAGTA
EST: gi|76015306|gb|DT942476.1|DT942476
EST:     TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAG                         GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAA
genomic: TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAGgtgcgaaact ... catttttcagGACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAA
EST: gi|32837361|gb|CD977039.1|CD977039
EST:     TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAG                         GACCTCCTTGCACTGAAAGACAAGT
genomic: TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAGgtgcgaaact ... catttttcagGACCTCCTTGCACTGAAAGACAAGT
EST: gi|32932023|gb|CF036835.1|CF036835
EST:     TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAG                         GACCTCCTTGCACTGAAAGACAAGTAC
genomic: TTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAGgtgcgaaact ... catttttcagGACCTCCTTGCACTGAAAGACAAGTAC

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: 99

TGATGAGGAGCCCCCATCTCGTTGCACCCCGGAAGTAGTGCACTTCATTGTTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAGgtgcgaaact ... catttttcagGACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

TGATGAGGAGCCCCCATCTCGTTGCACCCCGGAAGTAGTGCACTTCATTGTTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAGgtgcgaaact ... catttttcagGACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

TGATGAGGAGCCCCCATCTCGTTGCACCCCGGAAGTAGTGCACTTCATTGTTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAGgtgcgaaact ... catttttcagGACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 241

TGATGAGGAGCCCCCATCTCGTTGCACCCCGGAAGTAGTGCACTTCATTGTTCAGCAGCATTTTGACGCTCCATCAATGTGGGCAATCTTTCCACTTCAGgtgcgaaact ... catttttcagGACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatttcttgtctgaaataagctgatgggtctacttcggacttggcatttttcagGACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC
                   agctgat  putative branch site (score: 241)
                                             catttttc  putative PPT
            tgaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgaaacttgaacttgcatcatagatcaaggatttcttgtctgaaataagctgatgggtctacttcggacttggcatttttcagGACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT