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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatatatcttttgacttgtttttttttttttgctaaaacatttttttagtttgttgggaggatttatatatgtttagttccagaagaacacacact...

Basic information

species Zea mays
transcript GRMZM2G135132_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 7
GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatatatcttttgacttgtttttttttttttgcta--aaacatttttttagtttgttgggaggatttatatatgt-ttagttccag-aagaacacacact--
 ||| || |||||||  | || || |||||||| ||||||||||||||||| |||| ||| |||||||||||||||||||      || | ||||  | || |    ||||||| |  | | ||||  | | ||  || || |||||| | |   | | || | ||  ||     || |||  
ATCACTGGTTGCAAACTTATCAGCAGCAAACTGCTACAAATCTGAGCATCTGAAGAAACCGGAGAACTGGGCACTAGgta------atttattgagatattctgagctttttgccaccacatatttcatcacttaatttgggggatttctgtgcatatcagctgcattaattgtgcaaactct

upper sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA03G33910.3 (Glycine max), 5'ss of exon 4
GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatat-----atcttttgacttgtttttttttttttgctaaaacattttt-ttagtttgttgggaggatttatatatgtt-tagttccagaagaacacacact-
|||  |  | || ||  |  | || ||||| || ||||||||||| ||| | ||||||||||| || |||||||||||||   | |      ||| |  |     | |||| ||| ||     || |  |   |   |  ||  | ||| | | || | || | || | |      | ||| |  
GTCTCTTGTGGCGAACTTAGCAGCTGCAAATTGCTACAAATCTGATCATTTGAAGAGACCAGAAAATTGGGCACTAGgtaccctgtcattggtctatgcaggctctcttttatttctgtctccacttcatagctgactaattcagtggactgacattttttattgtgcaattttttctcacgcag
















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|211433554|gb|FL254730.1|FL254730
EST:     AAACTGGTACAAATCTGAGCATCTCNAGAGACCAGAGAACTGGGCACTAG                         TTGAGAAGGCAAA-TACATCTACATTGCTGGATTTTCCCTCACG-TGTCAC
genomic: AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCAC
EST: gi|211433558|gb|FL254734.1|FL254734
EST:     AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAG                         TTGAGAAGGCAAAATACATC
genomic: AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATC
EST: gi|211535004|gb|FL000873.1|FL000873
EST:     AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAG                         TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCAC
genomic: AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCAC
EST: gi|87155643|gb|DY400432.1|DY400432
EST:     AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAG                         TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCAC
genomic: AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCAC
EST: gi|60355835|gb|DN222808.1|DN222808
EST:     GCATCTCAAGAGACCAGAGAACTGGGCACTAG                         TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCAC
genomic: GCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCAC
EST: gi|211433550|gb|FL254726.1|FL254726
EST:     AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAG                         TTGAGAAGGCAAAATACATCTACA
genomic: AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACA
EST: gi|211430955|gb|FL254717.1|FL254717
EST:     AACTGTTACAAATCTGAGCATCTNCA-GAGACCAGAGAACTGGGCACTAG                         TTGAGAAGGCAAAATACATCTACATTGCTG
genomic: AACTGTTACAAATCTGAGCATCT-CAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTG
EST: gi|32916313|gb|CF021125.1|CF021125
EST:     AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAG                         TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACGGTGTCAC
genomic: AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCAC
EST: gi|211430957|gb|FL254719.1|FL254719
EST:     AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAG                         TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCAC
genomic: AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCAC
EST: gi|22546548|gb|BU098859.1|BU098859
EST:     AACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGGCACTAG                         TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGG
genomic: AACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGG-CACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGG
EST: gi|211430954|gb|FL254716.1|FL254716
EST:     AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAG                         TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCAC
genomic: AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCAC
EST: gi|211433557|gb|FL254733.1|FL254733
EST:     ACTGTTACAAATCTGAGCTTCCTCA-GAGACCAGAGAACTGCGCACTTAG                         TTGAGAAGGCAAAATACATCTACCTTGGCTG-ATTTTTCCTCACGG
genomic: ACTGTTACAAATCTGAGCATC-TCAAGAGACCAGAGAACTGGGCACT-AGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACATTG-CTGGATTTTTCCTCACGG
EST: gi|31353988|gb|CD438345.1|CD438345
EST:     AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAG                         TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCAC
genomic: AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCAC
EST: gi|60395531|gb|DN228401.1|DN228401
EST:     AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAG                         TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCAC
genomic: AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCAC
EST: gi|211538002|gb|FL000876.1|FL000876
EST:     AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAG                         TTGAGAAGGCAAA-TACATCTACATTGCTGGAT
genomic: AAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGAT

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: 48 (upstream exon), 46 (downstream exon)
Score: 85

GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAG


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 99

GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 163

GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 196

GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatata ... ttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATTGATTGCAAATCTGTCGGCGGCAAACTGTTACAAATCTGAGCATCTCAAGAGACCAGAGAACTGGGCACTAGgtataatatatcttttgacttgtttttttttttttgctaaaacatttttttagtttgttgggaggatttatatatgtttagttccagaagaacacacact

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaaca