Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttgtggttttgtaataaccaaatacgacgatcaaatcaattactgcagccacttcaaggatatttttagtgcttgctgtttttttaatttggg...

Basic information

species Zea mays
transcript GRMZM2G357972_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G357972_T02 (Zea mays), 5'ss of exon 6
lower sequence: 13113.m00156 (Oryza sativa), 5'ss of exon 6
TTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttgtggttttgtaataaccaaatacgacgatcaaat-caattactgcagccacttcaa---ggatatttttagtgcttgctgtttttttaatttggg
 |||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||    | || |   |  ||||  ||      ||  | ||  ||||      | ||      | ||| |         ||||  |  |  |    
CTTGCATTTTTCACAACCAAGAAGGTGGAGGCATTTGAGGAGCTCACATGGgtaagtcttgt---ctagttacttctgaatattactgcagcatatactttgtgcaaatgtctgaacatatgtgtttctctaagaaagtgttcctgcagatgct-
















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|78544370|gb|DV621868.1|DV621868
EST:     TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG                         GATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
genomic: TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttg ... ttggtttcagGATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
EST: gi|78125802|gb|DV544186.1|DV544186
EST:     TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG                         GATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
genomic: TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttg ... ttggtttcagGATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
EST: gi|76926465|gb|DV170878.1|DV170878
EST:     TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG                         GATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
genomic: TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttg ... ttggtttcagGATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
EST: gi|24767854|gb|CA402990.1|CA402990
EST:     TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG                         GATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
genomic: TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttg ... ttggtttcagGATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
EST: gi|5296185|gb|AI782865.1|AI782865
EST:     TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG                         GATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
genomic: TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttg ... ttggtttcagGATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
EST: gi|32931110|gb|CF035922.1|CF035922
EST:     TAGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG                         GATTATGGTATTGATTTTGATGATGATAAGCATCCTGTCAAATCATTTGAA
genomic: TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttg ... ttggtttcagGATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
EST: gi|32796222|gb|CD948458.1|CD948458
EST:     TAGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG                         GATTATGGTATTGATTTTGATGATGATAAGCATCCTGTCAAATCATTTGAA
genomic: TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttg ... ttggtttcagGATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
EST: gi|22541936|gb|BU092374.1|BU092374
EST:     TGCATTTTTCACAACCCAGAAGGTGGAAGCCTTTGAGGAGCTCACACTGG                         GATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGA
genomic: TGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACA-TGGgtaagccttg ... ttggtttcagGATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGA
EST: gi|5915516|gb|AW053157.1|AW053157
EST:     TTGCATTTTTCNCAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG                         GATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
genomic: TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttg ... ttggtttcagGATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
EST: gi|50338839|gb|CO533965.1|CO533965
EST:     TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG                         GATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
genomic: TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttg ... ttggtttcagGATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
EST: gi|12968346|gb|BG265292.1|BG265292
EST:     TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG                         GATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
genomic: TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttg ... ttggtttcagGATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
EST: gi|76926464|gb|DV170877.1|DV170877
EST:     TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG                         GATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
genomic: TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttg ... ttggtttcagGATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
EST: gi|78091874|gb|DV520248.1|DV520248
EST:     TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG                         GATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA
genomic: TTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttg ... ttggtttcagGATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAA

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: 91

TTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttg ... ttggtttcagGATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 29

TTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttg ... ttggtttcagGATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 41

TTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttg ... ttggtttcagGATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 70

TTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttg ... ttggtttcagGATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGGgtaagccttgtggttttgtaataaccaaatacgacgatcaaatcaattactgcagccacttcaaggatatttttagtgcttgctgtttttttaatttggg

- - - - - - - - - AAGAAG
- - - - - - - - - - -  GGTGGA
- - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - AGCTCA