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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccctagtcccctcgaagttgtccaccagactctcttgcaccactatttccttagcaatttttagtagcatgcttattctgattgcgcatatactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTTCTAAAG

Basic information

species Zea mays
transcript GRMZM2G153068_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153068_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os06g02620.1 (Oryza sativa), 3'ss of exon 13
ccctagtc----ccctcgaagttgtccaccagac-tctcttgcaccactatttccttagcaatttttagtag-catgcttattctgattgcgcatatactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTTCTAAAG
  |||  |    |     | |||||| |  || | |||| |   ||||  ||  | ||    |  | ||||  ||   | |   | | |||  | || ||||||||||||||||||| ||||||||||| || |||||||||  |||||| || |||||||||
tactaaacaaaacttgtaatgttgtcgagtaggcatctcct---ccacagttctcatatt--tcatcagtattcagattaagattaactgcaaacat-ctttgtagGCAATTTTGGGCGGGACAGTTCAGGTTCCAACTCTCTCTGGAGATGTAGTTCTAAAG

upper sequence: GRMZM2G153068_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA15G42640.1 (Glycine max), 3'ss of exon 14
ccctagtcccctcgaagttgtccaccagactctcttgcaccactatttcctta--gcaatttttagtagcatgcttattctgattgcgcatatactttgt-agGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTTCTAAAG
   |   |   |  | | | |  | ||   |       |    | || | |||  |   |  | | |         |   |  ||   |   | |||| | ||||||||||||| || ||  |||| ||||||||||| | |||||| ||||||||||||
---tgtgcatgtttaggatcttaaacatcttgctagttatttgtgttgcattatgggggtgctaaatgtttcttgaaaattatttaaacgcttgctttttcagGCAATTTTGGGTGGAACCATTCAGGTCCCAACTCTTACTGGAGATGTTGTTCTAAAG
















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|149037745|gb|EE155407.2|EE155407
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|148995724|gb|EE034952.2|EE034952
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|76285611|gb|DV025179.1|DV025179
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|8930050|gb|BE224888.1|BE224888
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|4730359|gb|AI649525.1|AI649525
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGNCGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|71323237|gb|DR798274.1|DR798274
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|14700982|gb|BI233400.1|BI233400
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|149075297|gb|EE163803.2|EE163803
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|87157555|gb|DY402344.1|DY402344
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|91874623|gb|EB404580.1|EB404580
EST:     TGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTAGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGT
genomic: TGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTT-GGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGT
EST: gi|67021949|gb|CO450698.1|CO450698
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAN                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|67022581|gb|CO451330.1|CO451330
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAN                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|61117818|gb|DN558779.1|DN558779
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|61117821|gb|DN558782.1|DN558782
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|8930051|gb|BE224889.1|BE224889
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|4730351|gb|AI649517.1|AI649517
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|113700982|gb|EE678486.1|EE678486
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|87151654|gb|DY396443.1|DY396443
EST:     TGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: TGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|37381164|gb|CF627442.1|CF627442
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|61117820|gb|DN558781.1|DN558781
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|86467336|gb|DY233706.1|DY233706
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|148929595|gb|EC875960.2|EC875960
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCACCTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
EST: gi|21828586|gb|BQ703270.1|BQ703270
EST:     GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAG                         GCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT
genomic: GAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTT

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: 542

GTTCGTGAGGATCCTGTTTTCCGAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTTCTAAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 258

GTTCGTGAGGATCCTGTTTTCCGAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTTCTAAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 247

GTTCGTGAGGATCCTGTTTTCCGAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTTCTAAAG


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

GTTCGTGAGGATCCTGTTTTCCGAAGAGAGAAAGGTGATATTCATGTTGATGCTGTCCTGAATGTGACTCAGgtaatttggt ... tactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTTCTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccttagcaatttttagtagcatgcttattctgattgcgcatatactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTTCTAAAG
                              ttctgat  putative branch site (score: 315)
          aatttttagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccctagtcccctcgaagttgtccaccagactctcttgcaccactatttccttagcaatttttagtagcatgcttattctgattgcgcatatactttgtagGCAATTTTGGGAGGGACAGTTCAAGTCCCAACTCTCAGTGGAGACGTTGTTCTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - -ccaccag
- - - - - - - - - - - - - - - - -cttgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattgc