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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATCGACTGCCCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtggggccgttttttgattaatcacgcctccatcataataatgtattgcttttttattttggccgagaacaccatgtcatgggatgcatcatgcatgcgcctttaatttgcag

Basic information

species Zea mays
transcript GRMZM2G151268_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151268_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os12g01170.1 (Oryza sativa), 5'ss of exon 7
ATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATCGACTGCCCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtggggccgttttttgattaatcacgcctccatcataataatgtattgcttttttattttggccg-agaacaccatgtcatgggatgcatcatgcatgcgcctttaatttgcag
||    | |||||||| |||||||| ||| |||| ||||| | ||| |||||||  || ||||||||||| ||| |||| |||||| |||| |||||||||| ||       |  |||   ||  |  | ||| |    |     ||  | ||  |||  || ||  |  |||| | | |||     |                              
ATGATGCTGATGATATCTCTGAAGAAGTGTTGCGAGCATCAAGTGCTCTAGAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaactattgcctttc--ttctttgcaccttccctttt----tgcctggccatttgtttctgatcatagaatatc-tgtttccag------------------------------
















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|12971760|gb|BG267644.1|BG267644
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|4647161|gb|AI622236.1|AI622236
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|32833706|gb|CD973384.1|CD973384
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|32834914|gb|CD974592.1|CD974592
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|91049337|gb|EB159755.1|EB159755
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|32909956|gb|CF014768.1|CF014768
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|60348471|gb|DN215444.1|DN215444
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|74239381|gb|DT647295.1|DT647295
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|21809549|gb|BQ667867.1|BQ667867
EST:     GAAAGTGTTCAAATAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|47961828|gb|CN844537.1|CN844537
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGNGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGCGTTGCT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTG-GTTGCT
EST: gi|94478768|gb|EB707726.1|EB707726
EST:     GAAAGTGTTCCGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|60399998|gb|DN232805.1|DN232805
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|15323531|gb|BI478753.1|BI478753
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|211191649|gb|FL029190.1|FL029190
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|32938881|gb|CF043700.1|CF043700
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|60400202|gb|DN233009.1|DN233009
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
EST: gi|45847355|gb|CN071298.1|CN071298
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTT

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: 722

ATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATCGACTGCCCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTTGACTTGACCGACCCTGTATCATGTAATTTGTATGCCACTCATTTGTGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 299

ATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATCGACTGCCCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTTGACTTGACCGACCCTGTATCATGTAATTTGTATGCCACTCATTTGTGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

ATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATCGACTGCCCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTTGACTTGACCGACCCTGTATCATGTAATTTGTATGCCACTCATTTGTGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 290

ATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATCGACTGCCCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtgggg ... taatttgcagGCATTCAGGGGATGGCGCCGAGTAACAAGAAGGCTTTGGAGCTGGTTGCTTGACTTGACCGACCCTGTATCATGTAATTTGTATGCCACTCATTTGTGGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATCGACTGCCCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCGACATCTTGGAGgtaggtggggccgttttttgattaatcacgcctccatcataataatgtattgcttttttattttggccgagaacaccatgtcatgggatgcatcatgcatgcgcctttaatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG