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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gactttgatatcaaatcatttgctagaagtttgcacagattgcttgtgatgacaaggtggctccagaaataatttaaattgtttgtgtatttctttttagGCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAAACAAAGGAGAAGCAAACCAATGAGGAAAATAAAAAAGAGGCAACATTGT

Basic information

species Zea mays
transcript GRMZM2G129554_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129554_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g51900.1 (Oryza sativa), 3'ss of exon 8
---gactttgatatcaaatcatttgctagaagtttgcacagattgcttgtgatgacaaggtg-gctccagaaataatttaaattgtttgtgtatttctttttagGCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAAAC---AAAGGAGAAGCAAACCAATGAGGAAAATAAAAAAGAGGCAACATTGT
   | ||     |     | |    ||||   | |  | |  |        ||  |    || | |     |   ||||||| | ||    | |||||||| |||||||||| || ||||||||||||||||| |||||||||||||||| |||  |   | |||||| |||| ||||| ||| ||| ||||| ||  | |      
gtgggctccaggaaatgtttaggctctagtgttctaaagaagtctgaaagaatatcttcttgcgttgtcctaccgatttaaactatt---atctttctttt-agGCATTCAATGCTAGGCTATTTGATTATCTGATAGCAACGGATGACAATAAGTCTAAAGAGGAGAGGCAAGCCAATAAGGGAAACAAAAAGGATTCTAGGG---
















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|31353721|gb|CD438078.1|CD438078
EST:     CAGTTTTGAATGCTGAGTTGCCACAAAATTCCCGACTACATATTATAGAG                         GCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAA
genomic: CAGTTTTGAATGCTGAGTTGCCACAAAATTCCCGACTACATATTATAGAGgtatcttttt ... ttctttttagGCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAA
EST: gi|211412133|gb|FL450831.1|FL450831
EST:     AGTTTTGAATGCTGAGTTGCCACAAAATTCCCGACTCACATATTATAGAG                         GCATTCAACGCAAGGCTATTTGATTATTTAATAGCAACGGATGACACTAAA
genomic: AGTTTTGAATGCTGAGTTGCCACAAAATTCCCGACT-ACATATTATAGAGgtatcttttt ... ttctttttagGCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAA
EST: gi|31349879|gb|CD434236.1|CD434236
EST:     CAGTTTTGAATGCTGAGTTGCCACAAAATTCCCGACTACATATTATAGAG                         GCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAA
genomic: CAGTTTTGAATGCTGAGTTGCCACAAAATTCCCGACTACATATTATAGAGgtatcttttt ... ttctttttagGCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAA
EST: gi|87155790|gb|DY400579.1|DY400579
EST:     CCACAAAATTCCCGACTACATATTATAGAG                         GCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAA
genomic: CCACAAAATTCCCGACTACATATTATAGAGgtatcttttt ... ttctttttagGCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAA
EST: gi|78122698|gb|DV541082.1|DV541082
EST:     CAGTTTTGAATGCTGAGTTGCCACAAAATTCCCGACTACATATTATAGAG                         GCATTCAACGCAGGGCTATTTGATTATCTAATAGCAACGGATGACACTAAA
genomic: CAGTTTTGAATGCTGAGTTGCCACAAAATTCCCGACTACATATTATAGAGgtatcttttt ... ttctttttagGCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAA
EST: gi|32933916|gb|CF038728.1|CF038728
EST:     CAGTTTTGAATGCTGAGTTGCCACAAAATTCCCGACTACATATTATAGAG                         GCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAA
genomic: CAGTTTTGAATGCTGAGTTGCCACAAAATTCCCGACTACATATTATAGAGgtatcttttt ... ttctttttagGCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAA
EST: gi|26560161|gb|CA832396.1|CA832396
EST:     ACAAAATTCCCGACTACATATTATAGAG                         GCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAA
genomic: ACAAAATTCCCGACTACATATTATAGAGgtatcttttt ... ttctttttagGCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAA
EST: gi|32935293|gb|CF040105.1|CF040105
EST:     CAGTTTTGAATGCTGAGTTGCCACAAAATTCCCGGCTACATATTATAGAG                         GCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAA
genomic: CAGTTTTGAATGCTGAGTTGCCACAAAATTCCCGACTACATATTATAGAGgtatcttttt ... ttctttttagGCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAA

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: 57

TTTGGGATAAGATCTGCAGTTTTGAATGCTGAGTTGCCACAAAATTCCCGACTACATATTATAGAGgtatcttttt ... ttctttttagGCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAAACAAAGGAGAAGCAAACCAATGAGGAAAATAAAAAAGAGGCAACATTGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 45

TTTGGGATAAGATCTGCAGTTTTGAATGCTGAGTTGCCACAAAATTCCCGACTACATATTATAGAGgtatcttttt ... ttctttttagGCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAAACAAAGGAGAAGCAAACCAATGAGGAAAATAAAAAAGAGGCAACATTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 63

TTTGGGATAAGATCTGCAGTTTTGAATGCTGAGTTGCCACAAAATTCCCGACTACATATTATAGAGgtatcttttt ... ttctttttagGCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAAACAAAGGAGAAGCAAACCAATGAGGAAAATAAAAAAGAGGCAACATTGT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 31

TTTGGGATAAGATCTGCAGTTTTGAATGCTGAGTTGCCACAAAATTCCCGACTACATATTATAGAGgtatcttttt ... ttctttttagGCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAAACAAAGGAGAAGCAAACCAATGAGGAAAATAAAAAAGAGGCAACATTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatgacaaggtggctccagaaataatttaaattgtttgtgtatttctttttagGCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAAACAAAGGAGAAGCAAACCAATGAGGAAAATAAAAAAGAGGCAACATTGT
                                          tatttcttttt  CT-rich tract
                   agaaataatttaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gactttgatatcaaatcatttgctagaagtttgcacagattgcttgtgatgacaaggtggctccagaaataatttaaattgtttgtgtatttctttttagGCATTCAACGCAAGGCTATTTGATTATCTAATAGCAACGGATGACACTAAAACAAAGGAGAAGCAAACCAATGAGGAAAATAAAAAAGAGGCAACATTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - catttgc
- - - - - - - - - - - - - - - -tgcacag
- - - - - - - - - - - - - - - - - - - - tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt