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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctccttactcttctcatattatggtcatttagcttcttagtgtcgtaaaagggcctctatctgagttggttaggtggtctgagtagcactcctc...

Basic information

species Zea mays
transcript GRMZM2G094978_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094978_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g36750.1 (Oryza sativa), 5'ss of exon 2
AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctccttactcttct-catattatggtcatttagcttcttagtgtcgtaaaagggcctctatctgagttggttaggtggtctgagtagcactcctc-----
|||||||||||||| |||||||||||||| || |||||||||||||||| ||||||||| ||||||||||||| | || | ||| | || | | | | | || || | | || || | | | || || || | | | | |
AGGGAATTAGGTGTGAGCTGGGATGTTGAGCTATATGGAGAATTGCTCAAGATAGGTGGCGGAAAGGAAAGgttaatcaac--actttgctgctttctttcatttgttggcctgccaaaatccta----gccattcatttgcattcttcaatacaaacaggcgtttcctcgaaacat
















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|211136606|gb|FL156037.1|FL156037
EST:     GAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCGAAGAC
genomic: GAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|148972975|gb|EE024010.2|EE024010
EST:     ATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGGAAAG                         GATGACAGCTTTACTTCAACCAGAACAGGATGGCCGGCTAAAGCCCCAAA
genomic: ATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGG-AAAGgtcagtctcc ... tttttttcagGATGACAGCTT-ACTTCAACCAGA-CAGGATGGCCGGCTAAAGCACCAAA
EST: gi|91056651|gb|EB167069.1|EB167069
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|211135672|gb|FL156035.1|FL156035
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCA
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCA
EST: gi|211136605|gb|FL156036.1|FL156036
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|149014075|gb|EE043602.2|EE043602
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|13490397|gb|BG517161.1|BG517161
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|149112364|gb|EE295251.2|EE295251
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|211136608|gb|FL156039.1|FL156039
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|50333792|gb|CO528918.1|CO528918
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|71764323|gb|DR962260.1|DR962260
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|71300514|gb|DR786312.1|DR786312
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|211136613|gb|FL156044.1|FL156044
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|101382873|gb|EB813490.1|EB813490
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|211136615|gb|FL156046.1|FL156046
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|13558960|gb|BG550315.1|BG550315
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|71448345|gb|DR829395.1|DR829395
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAT
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|86467369|gb|DY233739.1|DY233739
EST:     GATGTTGAACTGTATGGAAAATTGCTCAAGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|71300530|gb|DR786320.1|DR786320
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|50327117|gb|CO522243.1|CO522243
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|101388003|gb|EB816016.1|EB816016
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
EST: gi|71766392|gb|DR964329.1|DR964329
EST:     GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAG                         GATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC
genomic: GATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGAC

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), 47 (downstream exon)
Score: 46

AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGACAGATGACAAAAGAAAGGAGTTCATAGCTTCTCTTCACAAGAGGAAAACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 283

AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGACAGATGACAAAAGAAAGGAGTTCATAGCTTCTCTTCACAAGAGGAAAACA


Block sizes: 32 (upstream exon), 47 (downstream exon)
Score: 9

AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGACAGATGACAAAAGAAAGGAGTTCATAGCTTCTCTTCACAAGAGGAAAACA


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 71

AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctcc ... tttttttcagGATGACAGCTTACTTCAACCAGACAGGATGGCCGGCTAAAGCACCAAAGACAGATGACAAAAGAAAGGAGTTCATAGCTTCTCTTCACAAGAGGAAAACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGGATAGGTGGTGGAAAGGAAAGgtcagtctccttactcttctcatattatggtcatttagcttcttagtgtcgtaaaagggcctctatctgagttggttaggtggtctgagtagcactcctc

- - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA