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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtaatccaagttgaattcgacgtaagtgcattctagtcacctcatcctgcatccttatatttgggactaaacttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCAAGTGCTCCTCGAGGAGGCGAGGGAGAGCTACAGAGAGGACATCGTGATG

Basic information

species Zea mays
transcript GRMZM2G032699_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032699_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g22950.1 (Oryza sativa), 3'ss of exon 2
gtaggtaatccaagttgaattcgacg--taagtgcattctagtcacctcatcctgca-tccttatatttgggactaaact---tgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCAAGTGCTCCTCGAGGAGGCGAGGGAGAGCTACAGAGAGGACATCGTGATG
    ||||| || |  ||| |  ||    |    | |  | |      |||  || | | ||||| | ||      |  |   |  |||||||||| |||||| |||| ||| | ||||||||||| || ||||| |||||  ||||||| |||||||| ||||||||||||| |||||| || ||||||
----gtaattcatgcagaactgcacaatcacccacctgttggaatagccattatgaaatgcttatttctgactaagagttctattcacagAGGTTATATGGGTGCCAAGCTCACAAACAACATAGAATGTGAAATTTTCCAGATGCTCCTGGAGGAGGCAAGGGAGAGCTACAAAGAGGAGATAGTGATG

upper sequence: GRMZM2G032699_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g22950.3 (Oryza sativa), 3'ss of exon 2
gtaggtaatccaagttgaattcgacg--taagtgcattctagtcacctcatcctgca-tccttatatttgggactaaact---tgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCAAGTGCTCCTCGAGGAGGCGAGGGAGAGCTACAGAGAGGACATCGTGATG----------------------------------------------------
    ||||| || |  ||| |  ||    |    | |  | |      |||  || | | ||||| | ||      |  |   |  |||||||||| |||||| |||| ||| | ||||||||||| || ||||| |||||  ||||||| |||||||| ||||||||||||| |||||| || ||||||                                                    
----gtaattcatgcagaactgcacaatcacccacctgttggaatagccattatgaaatgcttatttctgactaagagttctattcacagaggttatatgggtgccaagctcacaaacaacatagaatgtgaaattttccagATGCTCCTGGAGGAGGCAAGGGAGAGCTACAAAGAGGAGATAGTGATGCCCTTGCGAAGTGACAATGTGGAGGATATCAGTAGGAATGTGGGCACACTGA
















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|9733393|gb|BE512250.1|BE512250
EST:     GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTCG                         AGGTTACATGGGTTCCAAGCTCGCCAACAATATAGAGTGCGAAATCTTCCA
genomic: GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAGgtaggtaatc ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
EST: gi|5525640|gb|AI861533.1|AI861533
EST:     GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGCAG                         AGGTTACATGGGTTCCAAGCTCGCCAACAACATAGAGTGCGAAATCTTCCA
genomic: GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAGgtaggtaatc ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
EST: gi|37387580|gb|CF630987.1|CF630987
EST:     GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTCG                         AGGTTACATGGGTTCCAAGCTCGCCAACAATATAGAGTGCGAAATCTTCCA
genomic: GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAGgtaggtaatc ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
EST: gi|211226976|gb|FL456590.1|FL456590
EST:     GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGAC--G--G                         AGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
genomic: GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAGgtaggtaatc ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
EST: gi|6194875|gb|AW146979.1|AW146979
EST:     GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGCAG                         AGGTTACATGGGTTCCAAGCTCGCCAACAACATAGAGTGCGAAATCTTCCA
genomic: GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAGgtaggtaatc ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
EST: gi|211450962|gb|FK989163.1|FK989163
EST:     GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAG                         AGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
genomic: GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAGgtaggtaatc ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
EST: gi|113615722|gb|DW781078.1|DW781078
EST:     GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAG                         AGGTTACATGGGTTCCAAACTCGCCAACAACA
genomic: GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAGgtaggtaatc ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACA
EST: gi|6695878|gb|AW288986.1|AW288986
EST:     GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGCAG                         AGGTTACATGGGTTCCAAGCTCGCCAACAACATAGAGTGCGAAATCTTCCA
genomic: GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAGgtaggtaatc ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
EST: gi|60341109|gb|DN208082.1|DN208082
EST:     GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAG                         AGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
genomic: GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAGgtaggtaatc ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
EST: gi|40335831|gb|CK369901.1|CK369901
EST:     GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTCG                         AGGTTACATGGGTTCCAAGCTCGCCAACAATATAGAGTGCGAAATCTTCCA
genomic: GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAGgtaggtaatc ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
EST: gi|60359354|gb|DN226327.1|DN226327
EST:     GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTCG                         AGGTTACATGGGTTCCAAGCTCGCCAACAATATAGAGTGCGAAATCTTCCA
genomic: GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAGgtaggtaatc ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
EST: gi|6056726|gb|AW091131.1|AW091131
EST:     GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGCAG                         AGGTTNCATGGGTTCCAAGCTCGCCAACAACATAGAGTGCGAAATCTTCCA
genomic: GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAGgtaggtaatc ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
EST: gi|60358371|gb|DN225344.1|DN225344
EST:     GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGG--AG                         -G-TTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA
genomic: GTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAGgtaggtaatc ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCA

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), 46 (downstream exon)
Score: 117

TAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAGgtaggtaatc ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCAAGTGCTCCTCGAGGAGGCGAGGGAGAGCTACAGAGAGGACATCGTGATG


Block sizes: 48 (upstream exon), 28 (downstream exon)
Score: 39

TAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAGgtaggtaatc ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCAAGTGCTCCTCGAGGAGGCGAGGGAGAGCTACAGAGAGGACATCGTGATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 71

TAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAGgtaggtaatc ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCAAGTGCTCCTCGAGGAGGCGAGGGAGAGCTACAGAGAGGACATCGTGATG


Block sizes: 48 (upstream exon), 28 (downstream exon)
Score: 38

TAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTGTGCTCCAGACTGACAACTCAATTCTGCATGATCGCCTGACGGGTAGgtaggtaatc ... acttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCAAGTGCTCCTCGAGGAGGCGAGGGAGAGCTACAGAGAGGACATCGTGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcattctagtcacctcatcctgcatccttatatttgggactaaacttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCAAGTGCTCCTCGAGGAGGCGAGGGAGAGCTACAGAGAGGACATCGTGATG
                                       gactaaa  putative branch site (score: 38)
                             ttatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtaatccaagttgaattcgacgtaagtgcattctagtcacctcatcctgcatccttatatttgggactaaacttgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCAAGTGCTCCTCGAGGAGGCGAGGGAGAGCTACAGAGAGGACATCGTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA