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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCAAATTTGGAAGGAAGAATTGTCAACGTGTCATCAGAGGGGCACAGACTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaattgctgtgctgtgattatgttctacggtctaatttactttgttttgaagaaaacctagccacttgttcaatcttgtgttgtgcag

Basic information

species Zea mays
transcript GRMZM2G009940_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009940_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os09g39670.1 (Oryza sativa), 5'ss of exon 3
AATCAAATTTGGAAGGAAGAATTGTCAACGTGTCATCAGAGGGGCACAGACTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaattgctgtgc--tgtgattatgttctacggtctaatttacttt----gttttgaagaaaacctagccacttgttcaatcttgtgttgtgcag
|||||||| ||||||||||||| || || || |||||||||||||||||  |||||||||||||||| ||||| |||| |||||| || || || || | ||||| || |  | |||  | || || | || | |    ||| || |||     |  ||| |    ||  |   | | ||||||||||||||||| |||
AATCAAATGTGGAAGGAAGAATCGTTAATGTTTCATCAGAGGGGCACAGGTTTGCATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGAgtatgcaacttttatgcactttgtttttcttttccttgttaacttccttcaaaggaattgtactgtactaatata-tggttcaatcttgtgttgtacag

upper sequence: GRMZM2G009940_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G37750.2 (Glycine max), 5'ss of exon 4
AATCAAATTTGGAAGGAAGAATTGTCAACGTGTCATCAGAGGGGCACAGACTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgta-tgta--------attgctgtgctgtgattatgttct-acggtctaatttactt-tgttttgaagaaaacctagccacttgttcaatcttgtgttgtgcag
|| | ||    |||||||||||||| || || || || ||||  ||| || || |||||   |||||||||||||||||||| || ||||||||||||  ||| ||||        |||  | |   |  |  || | || ||  | |  | |  || | |||| | | ||  | ||    |||   |     ||||       
AAACTAAGAAAGAAGGAAGAATTGTTAATGTCTCCTCTGAGGCTCACCGATTTACATATTCTGAAGGAATCCGTTTTGACAAAATTAACGATGAATCAAGgtaatgtataacctaaattcttattacgaaaagatatgctgacaattttttctttttattttttaatggaagacgagtttattgag-aggaacgtgtaaaa---

upper sequence: GRMZM2G009940_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G37760.1 (Glycine max), 5'ss of exon 4
AATCAAATTTGGAAGGAAGAATTGTCAACGTGTCATCAGAGGGGCACAGACTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgta---tgtaattgctgtgc------tgtgattatgttcta-cggtctaatttactttg----ttttgaagaaaacctagccacttgttcaatcttgtgttgtgcag
|||||||    |||||||||||||| || || || |||||||  ||| || ||||||||   ||||||||||||||| |||| || || |||||||||  |||   |||||      | |      ||  |  || | ||  | || |  ||||  ||     |||| ||   ||  |   |        |  ||||||        
AATCAAAGAAAGAAGGAAGAATTGTTAATGTTTCCTCAGAGGCTCACCGATTTGCATATTCTGAAGGAATCCGTTTTAACAAAATTAATGATGAATCAAGgtaatatgtaacctaaattcaatttatggcaagatatgctggcagttttttttatctttctattttttaatgtaagatgaactggaaggaaggcttgtgc-------

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|76280839|gb|DV020407.1|DV020407
EST:     CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
EST: gi|32165056|gb|CD670374.1|CD670374
EST:     CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
EST: gi|60347345|gb|DN214318.1|DN214318
EST:     CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
EST: gi|78078135|gb|DV506550.1|DV506550
EST:     GGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: GGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
EST: gi|78106300|gb|DV524718.1|DV524718
EST:     CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
EST: gi|211543309|gb|FL433009.1|FL433009
EST:     TGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: TGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
EST: gi|91875958|gb|EB405915.1|EB405915
EST:     CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
EST: gi|78106299|gb|DV524717.1|DV524717
EST:     CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
EST: gi|76280838|gb|DV020406.1|DV020406
EST:     CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
EST: gi|76021078|gb|DT948248.1|DT948248
EST:     CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCCACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGG
genomic: CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGG
EST: gi|17931680|gb|BM268640.1|BM268640
EST:     CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
EST: gi|78084860|gb|DV513253.1|DV513253
EST:     CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGC
genomic: CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGC
EST: gi|149082933|gb|EE172168.2|EE172168
EST:     CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
EST: gi|71438305|gb|DR819355.1|DR819355
EST:     CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
EST: gi|74244969|gb|DT652883.1|DT652883
EST:     CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
EST: gi|71317601|gb|DR795544.1|DR795544
EST:     CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
EST: gi|18650256|gb|BM499075.1|BM499075
EST:     ACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: ACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
EST: gi|13249759|gb|BG360664.1|BG360664
EST:     CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
EST: gi|60343084|gb|DN210057.1|DN210057
EST:     CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
EST: gi|78105169|gb|DV523587.1|DV523587
EST:     CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGT                         GTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA
genomic: CTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCA

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), 47 (downstream exon)
Score: 171

AATCAAATTTGGAAGGAAGAATTGTCAACGTGTCATCAGAGGGGCACAGACTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 315

AATCAAATTTGGAAGGAAGAATTGTCAACGTGTCATCAGAGGGGCACAGACTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 362

AATCAAATTTGGAAGGAAGAATTGTCAACGTGTCATCAGAGGGGCACAGACTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 85

AATCAAATTTGGAAGGAAGAATTGTCAACGTGTCATCAGAGGGGCACAGACTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaatt ... tgttgtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCAAATTTGGAAGGAAGAATTGTCAACGTGTCATCAGAGGGGCACAGACTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaattgctgtgctgtgattatgttctacggtctaatttactttgttttgaagaaaacctagccacttgttcaatcttgtgttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA