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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttgtcaatccagtaatgtttgtggactgtacttatctaattagcttattgaatcctttcttatgtgtgaataaatgtttttatattgttggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATACGCCTTGCAAAAGCTGAGCAGGTGACATGGACAACCCTGGATTATAGTG

Basic information

species Zea mays
transcript GRMZM2G105019_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105019_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g43540.1 (Oryza sativa), 3'ss of exon 6
---gcttgtcaatccagtaat----gtttgtggactgtacttatctaattagcttattgaatcctttcttatgtgtgaataaatgtttttatattgttggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATACGCCTTGCAAAAGCTGAGCAGGTGACATGGACAACCCTGGATTATAGTG
     ||   || ||| || |     | |||  | | |  || ||||   |   ||   |||| | ||   | |     ||| | ||  ||   | |||   ||||||| |||||||||||| ||| ||| |||||  ||||||| ||||| |||||| | || || |||||||| ||| | ||||||||  | || ||||||  | 
ttctttttgaaaaccaatactcagcatctgtttattatgatt-tctatgcacagtacc-aatcatctcacctct-----taacttttgctaatctcttgactatcagATCATCCCTGAGAAAAGCAGATACCAAGTGCTATCCACGAAGGTTGAAATAAGACTGGCTAAAGCTGAACAGATTACATGGACCTCACTTGATTATGATA
















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|67041846|gb|CO468101.1|CO468101
EST:     AAGTTCCTGGTGAAGA-CCATACCATTTTCAGCCCCGTCTGTTTTCTAAG                         ATTATCCCTGAGGAATGCNNAATATCA-GTCTTATCCACCAAGGTCGAAAT
genomic: AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactc ... tggaaatcagATTATCCCTGAGAAATGCA-AATATCAAGTCTTATCCACCAAGGTCGAAAT
EST: gi|67031272|gb|CO460021.1|CO460021
EST:     AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG                         ATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATA
genomic: AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactc ... tggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATA
EST: gi|5901292|gb|AW042392.1|AW042392
EST:     AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG                         ATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATA
genomic: AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactc ... tggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATA
EST: gi|149000611|gb|EE037809.2|EE037809
EST:     AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG                         ATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATA
genomic: AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactc ... tggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATA
EST: gi|60354886|gb|DN221859.1|DN221859
EST:     AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG                         ATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATA
genomic: AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactc ... tggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATA
EST: gi|148952074|gb|EC897865.2|EC897865
EST:     AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG                         ATTATCCCTGAGAAATGCAAATATNCA-GTCTTATCCACCAAGGTCGAAAT
genomic: AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactc ... tggaaatcagATTATCCCTGAGAAATGCAAATAT-CAAGTCTTATCCACCAAGGTCGAAAT
EST: gi|149095998|gb|EE181667.2|EE181667
EST:     AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG                         ATTATCCCTGAGAAATGCAAATATNCA-GTCTTATCCACCAAGGTCGAAAT
genomic: AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactc ... tggaaatcagATTATCCCTGAGAAATGCAAATAT-CAAGTCTTATCCACCAAGGTCGAAAT
EST: gi|22545963|gb|BU098322.1|BU098322
EST:     AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG                         ATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGGT-GAAAT
genomic: AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactc ... tggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGG-TCGAAAT
EST: gi|6056546|gb|AW090936.1|AW090936
EST:     AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG                         ATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATA
genomic: AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactc ... tggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATA
EST: gi|149014157|gb|EE043702.2|EE043702
EST:     AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG                         ATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATA
genomic: AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactc ... tggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATA
EST: gi|71429578|gb|DR810628.1|DR810628
EST:     AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG                         ATTATCCCTGAGNAATGCAAATATCAAGTCTTATCCACAAAGGTCGAAATA
genomic: AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactc ... tggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATA
EST: gi|148995931|gb|EE035174.2|EE035174
EST:     AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG                         ATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACTCA-GGTCGAAAT
genomic: AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactc ... tggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCAC-CAAGGTCGAAAT
EST: gi|5917336|gb|AW054127.1|AW054127
EST:     AAGTTCCTGG-GAAGAACC-T--CATTTTCAGCCCCGTCTGTTTTCTAAG                         ATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATA
genomic: AAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactc ... tggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATA

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: 335

TTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactc ... tggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATACGCCTTGCAAAAGCTGAGCAGGTGACATGGACAACCCTGGATTATAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 425

TTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactc ... tggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATACGCCTTGCAAAAGCTGAGCAGGTGACATGGACAACCCTGGATTATAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 556

TTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactc ... tggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATACGCCTTGCAAAAGCTGAGCAGGTGACATGGACAACCCTGGATTATAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 255

TTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAGgtaatcactc ... tggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATACGCCTTGCAAAAGCTGAGCAGGTGACATGGACAACCCTGGATTATAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttattgaatcctttcttatgtgtgaataaatgtttttatattgttggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATACGCCTTGCAAAAGCTGAGCAGGTGACATGGACAACCCTGGATTATAGTG
                ttatgtgtgaataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttgtcaatccagtaatgtttgtggactgtacttatctaattagcttattgaatcctttcttatgtgtgaataaatgtttttatattgttggaaatcagATTATCCCTGAGAAATGCAAATATCAAGTCTTATCCACCAAGGTCGAAATACGCCTTGCAAAAGCTGAGCAGGTGACATGGACAACCCTGGATTATAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttt