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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgccctccggagccctagtttccaacctccgcttctcgctccgtgtgctctgagatcctagctttgtcaactcatggtcacgccccgcctcgctcggctgctcgtttcttggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATCGCCAGCGACCGCCGCCTCGGCGTGCAGCTGCAGACGATCG

Basic information

species Zea mays
transcript GRMZM2G117544_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117544_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g08520.1 (Oryza sativa), 3'ss of exon 1
gtgagtgccctccggagccctagtttccaacctccgcttctcgctccgtgtgctctgagatcctagctttgtcaactcatggtcacgccccgcctcgctcggctgctcgtttcttggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATCGCCAGCGACCGCCGCCTCGGCGTGCAGCTGCAGACGATCG
|||||||||| |||    ||   |  ||   ||||||| |                 | | |||||| |     |  |  ||  | | |  |    | |  |  | |||| ||   |    |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||||||||||||| |||
gtgagtgccccccgcgatccccctcccccttctccgctccca-------------caaaaccctagcgtc--tgatccgcggcgatggcgggg---gatttggggttcgtgtcgctg----cagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATCGCCAGCGACCGGCGCCTCGGGGTGCAGCTGCAGACGGTCG

upper sequence: GRMZM2G117544_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT1G77440.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgagtgccctccg--gagccctagtttccaacctccgcttctcgctccgtgtgctctgagatcctagctttgtcaactcatggtcacgccccgcctcgctcggctgctcgtttcttggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATCGCCAGCGACCGCCGCCTCGGCGTGCAGCTGCAGACGATCG
|| ||||  |   |  ||   ||  ||| |||  ||    | | | |   | ||| |  ||||  |     | | || | |  |  |         ||| | | |       || | |    |||||||||||||||||| || || ||||| || || ||||| |||||||| |||||||| || || || || ||  | || || |||||  | || || || |
gtaagtgttccttgccgaattctttttttcaatttctaacttttgtttgttctgcgcaaagat--tgatagtatgaattgaacgata------aaatcggtggaca------ttgtggtgattcagATCTTCGAGTACAATGGAAGTGCCGTCGTAGCTATGGTAGGGAAGAATTGCTTCGCTATAGCTAGTGATCGGAGGCTTGGTGTGCAATTACAAACCATTG

upper sequence: GRMZM2G117544_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT1G77440.2 (Arabidopsis thaliana), 3'ss of exon 1
gtgagtgccctccggagccctagtttccaacctccgcttctcgctccgtgtgctctgagatcctagctttgtcaactcatggtcacgccccgcctcgctcggctgctcgtttcttggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATCGCCAGCGACCGCCGCCTCGGCGTGCAGCTGCAGACGATCG
          | | ||   ||  ||| |||  ||    | | | |   | ||| |  ||||  |     | | || | |  |  |         ||| | | |       || | |    |||||||||||||||||| || || ||||| || || ||||| |||||||| |||||||| || || || || ||  | || || |||||  | || || || |
----------tgccgaattctttttttcaatttctaacttttgtttgttctgcgcaaagat--tgatagtatgaattgaacgata------aaatcggtggaca------ttgtggtgattcagATCTTCGAGTACAATGGAAGTGCCGTCGTAGCTATGGTAGGGAAGAATTGCTTCGCTATAGCTAGTGATCGGAGGCTTGGTGTGCAATTACAAACCATTG

upper sequence: GRMZM2G117544_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv18s0001g02260.t01 (Vitis vinifera), 3'ss of exon 1
gtgagtgccctccggagccctagtttccaacctccgcttctcgctccgtgtgctctgagatcctagctttgtcaactcatggtcacgccccgcctcgctcggctgctcgtttcttggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATCGCCAGCGACCGCCGCCTCGGCGTGCAGCTGCAGACGATCG
                         |      ||    |||  | |  | |  |||   ||   | ||||    | | |     |  |||    | |  ||         |||    |   ||||||||||||||||| || || ||  |  | || ||||| || ||||||||||| || ||||||||||| |||||  ||||||| ||||| |||||  |||
------------------------gtatggtttctctctctaaccctttctcttct---atttcaccttttctcattgactcagaaaccctaatttgtccg---------ttccaaatcaacagATCTTCGAGTACAATGGCAGTGCGCTAATCGCCATGGTTGGCAAGAACTGCTTTGCAATCGCCAGCGATCGCCGATTCGGCGTTCAGCTCCAGACCGTCG

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|211032111|gb|FL157495.1|FL157495
EST:     TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAAGTCAGGGTCATGTCG                         ATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCGgtgagtgccc ... tggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|211034564|gb|FL157510.1|FL157510
EST:     TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCG                         ATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCGgtgagtgccc ... tggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|211034557|gb|FL157503.1|FL157503
EST:     TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCG                         ATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCGgtgagtgccc ... tggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|211034563|gb|FL157509.1|FL157509
EST:     TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCG                         ATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCGgtgagtgccc ... tggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|116825073|gb|EC868771.1|EC868771
EST:     TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGG-CATGTCG                         ATCTTCGAGTAC-ACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCGgtgagtgccc ... tggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|211037015|gb|FL157528.1|FL157528
EST:     TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCG                         ATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCGgtgagtgccc ... tggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|211037014|gb|FL157527.1|FL157527
EST:     TCGCCGTCGCCTCCGCCTCCGCTGCCGYCGCGCAGGTCAGGGTCATGTCG                         ATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCGgtgagtgccc ... tggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|76014624|gb|DT941794.1|DT941794
EST:     TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCG                         ATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCGgtgagtgccc ... tggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|211039456|gb|FL157536.1|FL157536
EST:     TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCG                         ATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCGgtgagtgccc ... tggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|211037013|gb|FL157526.1|FL157526
EST:     TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCG                         ATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCGgtgagtgccc ... tggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|211034556|gb|FL157502.1|FL157502
EST:     TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCG                         ATCTTCGASTACAACRGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCGgtgagtgccc ... tggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
EST: gi|211037008|gb|FL157521.1|FL157521
EST:     TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCG                         ATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC
genomic: TCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCGgtgagtgccc ... tggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGC

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: 48 (upstream exon), 49 (downstream exon)
Score: 131

GTTTTTTTTACGCCGGCGGAAATCAACCTGCGCCGCTGCCTTCTCCGTTCTCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCGgtgagtgccc ... tggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATCGCCAGCGACCGCCGCCTCGGCGTGCAGCTGCAGACGATCG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 99

GTTTTTTTTACGCCGGCGGAAATCAACCTGCGCCGCTGCCTTCTCCGTTCTCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCGgtgagtgccc ... tggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATCGCCAGCGACCGCCGCCTCGGCGTGCAGCTGCAGACGATCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 128

GTTTTTTTTACGCCGGCGGAAATCAACCTGCGCCGCTGCCTTCTCCGTTCTCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCGgtgagtgccc ... tggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATCGCCAGCGACCGCCGCCTCGGCGTGCAGCTGCAGACGATCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 94

GTTTTTTTTACGCCGGCGGAAATCAACCTGCGCCGCTGCCTTCTCCGTTCTCGCCGTCGCCTCCGCCTCCGCTGCCGCCGCGCAGGTCAGGGTCATGTCGgtgagtgccc ... tggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATCGCCAGCGACCGCCGCCTCGGCGTGCAGCTGCAGACGATCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcaactcatggtcacgccccgcctcgctcggctgctcgtttcttggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATCGCCAGCGACCGCCGCCTCGGCGTGCAGCTGCAGACGATCG
                                    ctcgtttctt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgccctccggagccctagtttccaacctccgcttctcgctccgtgtgctctgagatcctagctttgtcaactcatggtcacgccccgcctcgctcggctgctcgtttcttggtgctcagATCTTCGAGTACAACGGGAGCGCCGTGGTGGCGATGGTGGGGAAGAACTGCTTCGCGATCGCCAGCGACCGCCGCCTCGGCGTGCAGCTGCAGACGATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG