Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattttctgctattagttatcagattaaattataaattgcaccagaatgtttgcaagtaccctgtttttcatgcaaattacggaaacctatgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGATGGCTGCACACCGGGGACATTGGTTATGTGGACGATGACGACGAGATCTT

Basic information

species Zea mays
transcript GRMZM2G055320_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055320_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g44620.1 (Oryza sativa), 3'ss of exon 3
tattttctgctattagttatcagattaaattataaattgcaccagaatgtttgcaa----gtaccctgtt-tttcatgcaaattacggaaacctatgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGATGGCTGCACACCGGGGACATTGGTTATGTGGACGATGACGACGAGATCTT
|  | | |||| |   ||||  || | ||     || |||||  |||||| || ||    | |  | |   |||||||| | | |  |   ||| ||||  ||||||||||||||||| || ||| | || ||||||||||| || |||| ||| ||||||||||| || |||||||||||||| ||||| ||||||||||| ||
tggtatatgctctggcttatacgagtgaac----aagtgcacatgaatgtctgaaactctgaatgcagccatttcatgccagtgatcgtg-cctgtgatttgcagGTTATCTGAATGACCCGGAGTCCACGAAGAACACCATCGACAAGGGCGGTTGGCTGCACACAGGAGACATTGGTTATGTTGACGACGACGACGAGATTTT

upper sequence: GRMZM2G055320_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv11s0052g01090.t01 (Vitis vinifera), 3'ss of exon 2
----tattttctgctatta-gttatcagattaaattataaattgcaccagaatgtttgcaagtaccctgtttttcatgcaaattacggaaacctatgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGATGGCTGCACACCGGGGACATTGGTTATGTGGACGATGACGACGAGATCTT
    | ||   |  | | |  |||| |  ||   ||  |||||  |  | | |         |    |  ||||  |     |||  |     | |  ||   |||||||||||||||||||||||| ||| | |  ||||| ||||| || |||||||||||||| || ||||| || ||| | || ||||| || ||| | ||
ttaattttcctttttctcatattattaagttcggttgaaaattttaataaattaagctttttttaattaatttttttattgtttattg-----tttattgtttagGTTATCTGAATGATCCAGAGGCCACAGAAAGAACCATAGATAAAGAAGGATGGCTGCACACAGGTGACATCGGATATATTGATGATGATGATGAGCTTTT
















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|211363276|gb|FL274312.1|FL274312
EST:     ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAG                         GTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
genomic: ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
EST: gi|211365918|gb|FL274316.1|FL274316
EST:     ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAG                         GTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
genomic: ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
EST: gi|211365921|gb|FL274319.1|FL274319
EST:     ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAG                         GTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
genomic: ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
EST: gi|213188246|gb|FM188404.1|FM188404
EST:     ACGGAA-CAGCCAGGCGAGATACGCATCCGCGGCGAACAAATCATGAAAG                         GTTATCTGAATGATCCAGAGGCGACAAAGAACACC
genomic: ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACC
EST: gi|211365916|gb|FL274314.1|FL274314
EST:     ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAG                         GTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
genomic: ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
EST: gi|211365917|gb|FL274315.1|FL274315
EST:     ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAG                         GTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
genomic: ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
EST: gi|211082093|gb|FL165107.1|FL165107
EST:     ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAG                         GTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
genomic: ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
EST: gi|211365919|gb|FL274317.1|FL274317
EST:     NCGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAG                         GTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
genomic: -CGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
EST: gi|211082090|gb|FL165104.1|FL165104
EST:     ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAG                         GTTATCTGAATGATCCAGANGCGACAAAGAACACCATTGATAAGGACGGAT
genomic: ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
EST: gi|211211872|gb|FL151947.1|FL151947
EST:     ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAG                         GTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
genomic: ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
EST: gi|211365923|gb|FL274321.1|FL274321
EST:     ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAG                         GTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
genomic: ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
EST: gi|67019027|gb|CO447776.1|CO447776
EST:     ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAG                         GTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
genomic: ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
EST: gi|148978851|gb|EE026338.2|EE026338
EST:     ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAG                         GTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
genomic: ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
EST: gi|211365920|gb|FL274318.1|FL274318
EST:     ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAG                         GTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
genomic: ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
EST: gi|211365915|gb|FL274313.1|FL274313
EST:     ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAG                         GTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
genomic: ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
EST: gi|211082094|gb|FL165108.1|FL165108
EST:     ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAG                         GTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
genomic: ACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
EST: gi|149000216|gb|EE037361.2|EE037361
EST:     GGAACCAGCCAGGGGAGATATGCATCCGCGGCGAACAAATCATGAAAG                         GTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT
genomic: GGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGAT

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: 34 (upstream exon), 49 (downstream exon)
Score: 45

AGGAACGCGGAGCTGAAGATCGTCGACCCAGACACCAGCGCGTCGCTGGGACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGATGGCTGCACACCGGGGACATTGGTTATGTGGACGATGACGACGAGATCTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 90

AGGAACGCGGAGCTGAAGATCGTCGACCCAGACACCAGCGCGTCGCTGGGACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGATGGCTGCACACCGGGGACATTGGTTATGTGGACGATGACGACGAGATCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 75

AGGAACGCGGAGCTGAAGATCGTCGACCCAGACACCAGCGCGTCGCTGGGACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGATGGCTGCACACCGGGGACATTGGTTATGTGGACGATGACGACGAGATCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 733

AGGAACGCGGAGCTGAAGATCGTCGACCCAGACACCAGCGCGTCGCTGGGACGGAACCAGCCAGGCGAGATATGCATCCGCGGCGAACAAATCATGAAAGgtaccgtcca ... tgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGATGGCTGCACACCGGGGACATTGGTTATGTGGACGATGACGACGAGATCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtttgcaagtaccctgtttttcatgcaaattacggaaacctatgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGATGGCTGCACACCGGGGACATTGGTTATGTGGACGATGACGACGAGATCTT
                   tttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattttctgctattagttatcagattaaattataaattgcaccagaatgtttgcaagtaccctgtttttcatgcaaattacggaaacctatgatgcgcagGTTATCTGAATGATCCAGAGGCGACAAAGAACACCATTGATAAGGACGGATGGCTGCACACCGGGGACATTGGTTATGTGGACGATGACGACGAGATCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC