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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgggtcttcaaattagttgactttgtaaataaataaataggatggatggttttagcactttctatttagacctggtaatgttgatacttgtattaacagGATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTAAAGATAAGGCACAACCACAGGATGACTCCAAAGCTACACTGGCACCAAA

Basic information

species Zea mays
transcript GRMZM2G019437_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019437_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g49330.1 (Oryza sativa), 3'ss of exon 6
-----ccgggtcttcaaattagttgactttgtaaataaataaataggatggatggttttagcactttctatttagacctggtaatgttgatacttgtattaa-cagGATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTAAAGATAAGGCACAACCACAGGATGACTCCAAAGCTACACTGGCACCAAA
     ||   | ||||||||  ||||   | |   |   |||||| | |     | | ||  | |||    ||     | ||||| | ||| ||||| ||||  |||||||||||||||| || ||||||| || || |||||||||||  |||||||||| |||||| ||||||| ||||||||||||  |||||  ||||| ||
acagaccttat-ttcaaattt-ttgatactatctttttctaaatatggttctgagctatatgattttgagatt----tttgtaatttggattcttgtgttaaatagGATCCAAGCTATTGCTTCATGAACTACCCTCTATTCTTGATGGAACGGCTAAAGAAAAGGCAAAACCACAAGATGACTCCAAAATTACACATGCACCGAA
















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|31360881|gb|CD445238.1|CD445238
EST:     GCACCAGAGCTACTTTCTATGCTGTTTCATTTAG                         GATCCCAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTA
genomic: GCACCAGAGCTACTTTCTATGCTGTTTCATTTAGgtaaagacca ... gtattaacagGATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTA
EST: gi|67022687|gb|CO451436.1|CO451436
EST:     GCACCAGAGCTACTTTCTATGCTGTTTCATTTAG                         GATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTA
genomic: GCACCAGAGCTACTTTCTATGCTGTTTCATTTAGgtaaagacca ... gtattaacagGATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTA
EST: gi|71420934|gb|DR805240.1|DR805240
EST:     GCACCAGAGCTACTTTCTATGCTGTTTCATTTAG                         GATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTA
genomic: GCACCAGAGCTACTTTCTATGCTGTTTCATTTAGgtaaagacca ... gtattaacagGATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTA
EST: gi|149076153|gb|EE164742.2|EE164742
EST:     GCACCAGAGCTACTTTCTATGCTGTTTCATTTAG                         GATCCAAGCTATTGATTAATGAACTTCCCTCCATTCTTGATGGTTCGGCTA
genomic: GCACCAGAGCTACTTTCTATGCTGTTTCATTTAGgtaaagacca ... gtattaacagGATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTA
EST: gi|67023553|gb|CO452302.1|CO452302
EST:     GCACCAGAGCTACTTTCTATGCTGTTTCATTTAG                         GATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTA
genomic: GCACCAGAGCTACTTTCTATGCTGTTTCATTTAGgtaaagacca ... gtattaacagGATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTA
EST: gi|50332369|gb|CO527495.1|CO527495
EST:     GCACCAGAGCTACTTTCTATGCTGTTTCATTTAG                         GATCCAAGCTATTGATT
genomic: GCACCAGAGCTACTTTCTATGCTGTTTCATTTAGgtaaagacca ... gtattaacagGATCCAAGCTATTGATT
EST: gi|76289469|gb|DV029037.1|DV029037
EST:     GCACCAGAGCTACTTTCTATGCTGTTTCATTTAG                         GATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTA
genomic: GCACCAGAGCTACTTTCTATGCTGTTTCATTTAGgtaaagacca ... gtattaacagGATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTA
EST: gi|148952757|gb|EC898739.2|EC898739
EST:     GCACCAGAGCTACTTTCTATGCTGTTTCATTTAG                         GATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTA
genomic: GCACCAGAGCTACTTTCTATGCTGTTTCATTTAGgtaaagacca ... gtattaacagGATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTA
EST: gi|71420929|gb|DR805239.1|DR805239
EST:     ACACCAGAGCTACTTTCTATGCTGTTTCATTTAG                         GATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTA
genomic: GCACCAGAGCTACTTTCTATGCTGTTTCATTTAGgtaaagacca ... gtattaacagGATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTA

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), 49 (downstream exon)
Score: 52

GCACCAGAGCTACTTTCTATGCTGTTTCATTTAGgtaaagacca ... gtattaacagGATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTAAAGATAAGGCACAACCACAGGATGACTCCAAAGCTACACTGGCACCAAA


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 35

GCACCAGAGCTACTTTCTATGCTGTTTCATTTAGgtaaagacca ... gtattaacagGATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTAAAGATAAGGCACAACCACAGGATGACTCCAAAGCTACACTGGCACCAAA


Block sizes: 34 (upstream exon), 48 (downstream exon)
Score: 9

GCACCAGAGCTACTTTCTATGCTGTTTCATTTAGgtaaagacca ... gtattaacagGATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTAAAGATAAGGCACAACCACAGGATGACTCCAAAGCTACACTGGCACCAAA


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 12

GCACCAGAGCTACTTTCTATGCTGTTTCATTTAGgtaaagacca ... gtattaacagGATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTAAAGATAAGGCACAACCACAGGATGACTCCAAAGCTACACTGGCACCAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatggttttagcactttctatttagacctggtaatgttgatacttgtattaacagGATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTAAAGATAAGGCACAACCACAGGATGACTCCAAAGCTACACTGGCACCAAA
                                  tgttgat  putative branch site (score: 12)
              tttctattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccgggtcttcaaattagttgactttgtaaataaataaataggatggatggttttagcactttctatttagacctggtaatgttgatacttgtattaacagGATCCAAGCTATTGATTAATGAACTTCCATCCATTCTTGATGGTTCGGCTAAAGATAAGGCACAACCACAGGATGACTCCAAAGCTACACTGGCACCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - atggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat