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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaaaattgtatagttagcagatagttagtacttcatcttacaaaattctaagcgaaaatccagattaactgacctcattttatttgaaacataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAATTGCGTTGGCGCTGTAAGAGTTGCTCAAGATTTGGGTCCAGGGCATACA

Basic information

species Zea mays
transcript GRMZM2G128744_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128744_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g11660.1 (Oryza sativa), 3'ss of exon 5
ggaaaattgtatagttagcagatagttagtacttcatcttacaaaattctaagcgaaaatccagattaactgacctcattttatttg-aaacat-aacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAATTGCGTTGGCGCTGTAAGAGTTGCTCAAGATTTGGGTCCAGGGCATACA
 |   || || |  |||     |  |    |  | ||   |  |||  ||||      ||    |||| || |||||| | || ||| ||| || |||||||||||||| ||||||| ||||| || || ||||| |||||||||||||||||||| ||||| ||||||||||||||||||||||| |||||||| ||||||
-gctcatagt-tgtttattctcttatcttaagataattcaaagaaaagctaaaaatgtatttcaattatctaacctcaatctacttgtaaatattaacttagGTTCTTGTTGAAAAATGATGGGCTGTTCGTTGGGAGTTCTTCAGCCATGAATTGTGTTGGTGCTGTAAGAGTTGCTCAAGATTTAGGTCCAGGACATACA

upper sequence: GRMZM2G128744_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv19s0015g00380.t01 (Vitis vinifera), 3'ss of exon 6
----ggaaaattgtatagttagcagatagttagtacttcatc-ttacaaaattct-aagcgaaaatccagattaactgacctcattttatttgaaacataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAATTGCGTTGGCGCTGTAAGAGTTGCTCAAGATTTGGGTCCAGGGCATACA
      ||||||   | |  | |    ||    |  || ||  ||  |   ||||  |||       |  |||   ||  | |||||      |||| |   | ||||   | || || || ||||| |||||||| || ||||||||||||||||| |||||||| ||||| ||||| || ||     | || || || || |||
aattctaaaatttcttggccaccctgaagaacatctttaatagttgtatttttcttgagcattggctcttattctatgttcccattt------aaactttcatcagGTATCTTCTCAAGAATGATGGGCTATTTGTCGGGAGTTCTTCAGCCATGAACTGCGTTGGAGCTGTCAGAGTGGCACAGTCGATCGGCCCTGGTCACACA
















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|211158859|gb|FL446927.1|FL446927
EST:     CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAG                         GTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
genomic: CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
EST: gi|76290986|gb|DV030554.1|DV030554
EST:     CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAG                         GTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
genomic: CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
EST: gi|71426658|gb|DR807708.1|DR807708
EST:     CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAG                         GTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
genomic: CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
EST: gi|89754881|gb|DY685507.1|DY685507
EST:     CGGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAG                         GTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
genomic: CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
EST: gi|50339752|gb|CO534878.1|CO534878
EST:     AAGCTGTTGAGATGTCAAG                         GTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
genomic: AAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
EST: gi|149100998|gb|EE187095.2|EE187095
EST:     CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAG                         GTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
genomic: CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
EST: gi|71313253|gb|DR793151.1|DR793151
EST:     CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAG                         GTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
genomic: CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
EST: gi|149001294|gb|EE038578.2|EE038578
EST:     CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAG                         GTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
genomic: CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
EST: gi|60352237|gb|DN219210.1|DN219210
EST:     CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAG                         GTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
genomic: CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
EST: gi|89248920|gb|DY620706.1|DY620706
EST:     CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAG                         GTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
genomic: CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
EST: gi|60358324|gb|DN225297.1|DN225297
EST:     CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAG                         GTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
genomic: CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
EST: gi|71758983|gb|DR956920.1|DR956920
EST:     CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAG                         GTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
genomic: CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
EST: gi|78082010|gb|DV510422.1|DV510422
EST:     CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAG                         GTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
genomic: CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
EST: gi|76286344|gb|DV025912.1|DV025912
EST:     CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAG                         GTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA
genomic: CTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAA

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: 54

CTGAAGGAATAGGAATCAATAGGGTCACTAAAAATTTCATGATGGCGGAACTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAATTGCGTTGGCGCTGTAAGAGTTGCTCAAGATTTGGGTCCAGGGCATACA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 25

CTGAAGGAATAGGAATCAATAGGGTCACTAAAAATTTCATGATGGCGGAACTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAATTGCGTTGGCGCTGTAAGAGTTGCTCAAGATTTGGGTCCAGGGCATACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84

CTGAAGGAATAGGAATCAATAGGGTCACTAAAAATTTCATGATGGCGGAACTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAATTGCGTTGGCGCTGTAAGAGTTGCTCAAGATTTGGGTCCAGGGCATACA


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 30

CTGAAGGAATAGGAATCAATAGGGTCACTAAAAATTTCATGATGGCGGAACTGGATGGAGCCTATCGAGGATCAGATAGGGAAGCTGTTGAGATGTCAAGgtacatggtt ... cataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAATTGCGTTGGCGCTGTAAGAGTTGCTCAAGATTTGGGTCCAGGGCATACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctaagcgaaaatccagattaactgacctcattttatttgaaacataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAATTGCGTTGGCGCTGTAAGAGTTGCTCAAGATTTGGGTCCAGGGCATACA
                                attttatttgaaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaaaattgtatagttagcagatagttagtacttcatcttacaaaattctaagcgaaaatccagattaactgacctcattttatttgaaacataacttagGTTCTTGCTGAAAAACGATGGACTATTTGTTGGCAGTTCTTCAGCCATGAATTGCGTTGGCGCTGTAAGAGTTGCTCAAGATTTGGGTCCAGGGCATACA

- - - - - - - - - - - - - - - -cttcatc
- - - - - - - - - - - - - - - - - - - -tacaaaa