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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtttggtattcatatgttctgtgcatatttccattgaaagtgtatcatctactgagcattcttttctgtttctaatctgaattgccatcattatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAG

Basic information

species Zea mays
transcript GRMZM2G009849_T03
intron # 31
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 32
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 49
--ggtttggtattcatatgttctgtgcatatttccattgaaagtgtatcatctactgagcattcttttctgtttctaatc-tgaattgccatcattatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAG
    || | |||   | ||||   | ||       |||  || |||||  ||   | |||   ||||||| |||  | || ||||     | |  | | ||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||
gttattggttatgagtttgtttatttcagccagttattataa-tgtat-gtcgcataagctaccttttctattttaattcctgaaacaagaactat-tttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAG

upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 32
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 51
-----ggtttggtattcatatgttctgtgcatatttccattgaaagtgtatcatctactgagcattcttttctgtttctaatctgaattgccat-cattatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAG
        ||  |||| | ||    |||    ||||  ||  ||  |  | | | ||     |||| ||     |||   ||     ||    | | |||||| ||||||| ||||||||||||||||| ||||||||||| |||||| | ||||| || || ||||| || ||||||
gtttcatgttaatatttagataagatgtaaggattttaataaaaccttaagcctgtat----catttttgctcattt--gattaaggttctggtgctttatcttagGTTGACATATTTGCTCAGCTTCAAAATGCTAGTGAGGCATTTCGCACCTACATTAGAGATGGTCTTGCTCAG

upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 32
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 52
ggtttggtattcatatgttctgtgcatatttccattgaaagtgtatcatctactgagcat-tcttttctgttt--ctaatctgaattgccat-cattatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAG
   ||  | || |||| ||   |      |    ||   | | ||  | ||   |   || || ||| || |    | |||    ||    | | |||||| ||||||| ||||||||||||||||| ||||||||||| |||||| | ||||| || || ||||| || ||||||
---ttcatgttaatat-ttggataagatgtaatgttatgattttaaaaccttaagcctatatcatttttgctcaattgatcaaggttctagtgctttatcttagGTTGACATATTTGCTCAGCTTCAAAATGCTAGTGAGGCATTTCGCACCTACATTAGAGATGGTCTTGCTCAG

upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 32
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 21
----------------------------------------------------------ggtttggtattcatatgttctgtgc---atatttccattgaaagtgtatc--------atctactgagcattcttttctgtttct----aatctgaattgccatcattatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAG
                                                          |||||| ||||  |       | ||   | ||| | |    ||   | ||        |||||     |  |||  |   |||      ||  | | |||  ||   ||| |||||||||||||||||| ||||| || ||||||||||| || ||| | || ||||||||||||||| |||| |||
gtaaactataaattgcatggtatatgtttaaaagaagtttaagtagtgaatagcatgaggtttgttattggttgagctcgggccaaagattgctaacacaatgatctcttaattagatctatcttcctgtctactgcatttgccagaaagttaatttgtgatttctatttcagGTTGATATATTTGCGCAGCTCCAAAATGCTAGTGAGGCGTTTCGGACTTATATCAGGGATGGGTTAGCCCAG

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|12045716|gb|BF727855.1|BF727855
EST:     GTACTATTGGCTTCTACGAACTGTATCGGATAACTCAGCTCTACCCAAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTAT
genomic: GTACTATTGGCTTCTACGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattca ... attatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTAT
EST: gi|67019308|gb|CO448057.1|CO448057
EST:     GTACTATTGGCTTCTACGAACTGTATCGGATAACTCAGCTCTACCCAAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTAT
genomic: GTACTATTGGCTTCTACGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattca ... attatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTAT
EST: gi|67011174|gb|CO439923.1|CO439923
EST:     GTACTATTGGCTTCTACGAACTGTATCGGATAACTCAGCTCTACCCAAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTAT
genomic: GTACTATTGGCTTCTACGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattca ... attatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTAT

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: 172

CAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACTATTGGCTTCTACGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattca ... attatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 55

CAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACTATTGGCTTCTACGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattca ... attatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAG


Block sizes: 40 (upstream exon), 46 (downstream exon)
Score: 62

CAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACTATTGGCTTCTACGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattca ... attatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 92

CAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACTATTGGCTTCTACGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattca ... attatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatctactgagcattcttttctgtttctaatctgaattgccatcattatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAG
                         ttctaat  putative branch site (score: 92)
                                              ttatctc  putative PPT
             attctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtttggtattcatatgttctgtgcatatttccattgaaagtgtatcatctactgagcattcttttctgtttctaatctgaattgccatcattatctcagGTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - -ttcatat
- - - - - - - - - - -gtgcata
- - - - - - - - - - - - - - - - - - - - gtgtatc
- - - - - - - - - - - - - - - - - - - - - - - - tctactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaattg