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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgtcagttcaatagagttgaaagctgctgtctctgcataaattcttgtaccgtgaaattcttcaagtctctgaatactccatgtgcttgtctttcagGGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCGTTGTGGAAGGTTACCGTAATGCCCAGATACCGCTGGACGTGATCTGGAA

Basic information

species Zea mays
transcript GRMZM2G009282_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009282_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g03950.1 (Oryza sativa), 3'ss of exon 2
ttttgtcagtt-caatagagttgaaagctgctgtctctgcataaattcttgtaccgtgaaattcttcaagtctctga-atactcc--atgtgcttgtctttcagGGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCGTTGTGGAAGGTTACCGTAATGCCCAGATACCGCTGGACGTGATCTGGAA
|  | | | ||  | |  |    |||  |||     |   ||||    | ||  |    ||   | | | ||||| |  | || |  |  ||||||| | ||||||||||||||||| || ||||| ||||||||| | |||||||| |||||||| ||||| || ||||| || || || || || || ||||||||||||||
tgctctaaattgtactgcaaaacaaatatgcaaataccaaataa---ttcgtttcagataacgatgcgactctctaatgttcttctcacatgcttgt-tctcagGGTTCCACCAATGCAGATGGGGATACAAGAACTTGTCAGTGGTCGAGGGCGTCGTGGAGGGCTACCGGAACGCGCAAATCCCCCTCGACGTGATCTGGAA
















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|148973623|gb|EE024733.2|EE024733
EST:     GTATACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTACTGGGCATTCG                         GGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCG
genomic: GTACACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTACTGGGCATTCGgtaaggactg ... tgtctttcagGGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCG
EST: gi|149016438|gb|EE154237.2|EE154237
EST:     GTACACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTACTGGGCATTCG                         GGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCG
genomic: GTACACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTACTGGGCATTCGgtaaggactg ... tgtctttcagGGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCG
EST: gi|5555560|gb|AI881511.1|AI881511
EST:     GTACACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTATTGGGCATTCG                         GGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGAGCG
genomic: GTACACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTACTGGGCATTCGgtaaggactg ... tgtctttcagGGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCG
EST: gi|89252471|gb|DY624257.1|DY624257
EST:     GTACACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTACTGGGCATTCG                         GGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCG
genomic: GTACACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTACTGGGCATTCGgtaaggactg ... tgtctttcagGGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCG
EST: gi|148971102|gb|EE021947.2|EE021947
EST:     GTACACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTACTGGGCATTCG                         GGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCG
genomic: GTACACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTACTGGGCATTCGgtaaggactg ... tgtctttcagGGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCG
EST: gi|91874962|gb|EB404919.1|EB404919
EST:     GTACACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTACTGGGCATTCG                         GGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCG
genomic: GTACACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTACTGGGCATTCGgtaaggactg ... tgtctttcagGGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCG
EST: gi|50330692|gb|CO525818.1|CO525818
EST:     GTACACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTACTGGGCATTCG                         GGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCG
genomic: GTACACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTACTGGGCATTCGgtaaggactg ... tgtctttcagGGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCG

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: 393

CTCGACTTCTACTTCTTCTCGGGCCCGACGCCGTTGGCCATAGTGGATCAGTACACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTACTGGGCATTCGgtaaggactg ... tgtctttcagGGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCGTTGTGGAAGGTTACCGTAATGCCCAGATACCGCTGGACGTGATCTGGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

CTCGACTTCTACTTCTTCTCGGGCCCGACGCCGTTGGCCATAGTGGATCAGTACACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTACTGGGCATTCGgtaaggactg ... tgtctttcagGGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCGTTGTGGAAGGTTACCGTAATGCCCAGATACCGCTGGACGTGATCTGGAA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 18

CTCGACTTCTACTTCTTCTCGGGCCCGACGCCGTTGGCCATAGTGGATCAGTACACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTACTGGGCATTCGgtaaggactg ... tgtctttcagGGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCGTTGTGGAAGGTTACCGTAATGCCCAGATACCGCTGGACGTGATCTGGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

CTCGACTTCTACTTCTTCTCGGGCCCGACGCCGTTGGCCATAGTGGATCAGTACACGTCGATGATCGGCCGTCCCGCGCCCATGCCTTACTGGGCATTCGgtaaggactg ... tgtctttcagGGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCGTTGTGGAAGGTTACCGTAATGCCCAGATACCGCTGGACGTGATCTGGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgtaccgtgaaattcttcaagtctctgaatactccatgtgcttgtctttcagGGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCGTTGTGGAAGGTTACCGTAATGCCCAGATACCGCTGGACGTGATCTGGAA
                                           cttgtctttc  CT-rich tract
            aaattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgtcagttcaatagagttgaaagctgctgtctctgcataaattcttgtaccgtgaaattcttcaagtctctgaatactccatgtgcttgtctttcagGGTTCCACCAATGTAGGTGGGGGTACAAGAACCTTTCAGTGGTAGAGGGCGTTGTGGAAGGTTACCGTAATGCCCAGATACCGCTGGACGTGATCTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - -gctgctg
- - - - - - - - - - - - - - - - - -ctgcata
- - - - - - - - - - - - - - - - - - - - - -attcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccatg