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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcctgagaatcatatggacaacctcagctgtacaacagtgtttatcagtgataattgcctatggggaaactttctaaagctttctcctcaatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCGGGGAGCGTGCATTGTTGCATGTTGGTTGGGAGCTAGGCTATGGCAAAGA

Basic information

species Zea mays
transcript GRMZM2G133624_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133624_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g05090.1 (Oryza sativa), 3'ss of exon 3
tagcctgagaatcatatggacaacctcagctgtacaacagtgtttatcagtgataattgcctatggggaaactttctaaagctttctcctca------atcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCGGGGAGCGTGCATTGTTGCATGTTGGTTGGGAGCTAGGCTATGGCAAAGA
      || ||  |   |   |   |     | |||   |||   |||| | | | |||||| | |   || | | | ||||||| |  |        |||||||||||||||  ||||| ||||||||||||| |||||  | | ||||| ||| ||||||||||||||||| ||||||   |||||||| |||||||| |||||
------gataactaaccgagtagtattgtacgaacagacgtgagcatcaattacacttgcctttagtataaatctttgaagcttttttttttcttctcatcaacagAGAAAAAGGAAATGACTGGTTTAGGCATTGGTGTCAGTAACATGAGAAGTGGGGAGCGTGCATTGTTACATGTTAACTGGGAGCTTGGCTATGGGAAAGA
















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|211436147|gb|FL367592.1|FL367592
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGGCATGAAAAGC
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAG-CATGAAAAGC
EST: gi|76918516|gb|DV167329.1|DV167329
EST:     GAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGC
genomic: GAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAA-Ggtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGC
EST: gi|71765927|gb|DR963864.1|DR963864
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|71438300|gb|DR819350.1|DR819350
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|71435151|gb|DR816201.1|DR816201
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|32864226|gb|CF003908.1|CF003908
EST:     GAGGATACCTGGCAAGGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
genomic: GAGGATACCTGGCAAG-AGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|211189090|gb|FL366153.1|FL366153
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|211270715|gb|FL364943.1|FL364943
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|78089641|gb|DV518015.1|DV518015
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|211133426|gb|FL346177.1|FL346177
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|211320437|gb|FL345942.1|FL345942
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAWATGTCTGGTTTAGGCATCGGTGTTGGCWGCATGAAAAGCG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|33104053|gb|CF064013.1|CF064013
EST:     ACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGTAGCATGAAAAGCG
genomic: ACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|71306393|gb|DR789338.1|DR789338
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|211078378|gb|FL344979.1|FL344979
EST:     TGAGGATACCTGGCAAAAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTG
EST: gi|149015212|gb|EE044997.2|EE044997
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|71299221|gb|DR785609.1|DR785609
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|78108738|gb|DV527155.1|DV527155
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|149076434|gb|EE165057.2|EE165057
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|211257634|gb|FL327800.1|FL327800
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGGTTTAGGCATCGGTGTTGGCAGCATG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGG-TTTAGGCATCGGTGTTGGCAGCATG
EST: gi|76021436|gb|DT948606.1|DT948606
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|211257312|gb|FL311217.1|FL311217
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGG
EST: gi|211465020|gb|FL331108.1|FL331108
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCT
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCT
EST: gi|71435313|gb|DR816363.1|DR816363
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|9794264|gb|BE552572.1|BE552572
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
EST: gi|71321226|gb|DR797322.1|DR797322
EST:     TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG                         AGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG
genomic: TGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCG

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: 213

TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCGGGGAGCGTGCATTGTTGCATGTTGGTTGGGAGCTAGGCTATGGCAAAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 106

TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCGGGGAGCGTGCATTGTTGCATGTTGGTTGGGAGCTAGGCTATGGCAAAGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 61

TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCGGGGAGCGTGCATTGTTGCATGTTGGTTGGGAGCTAGGCTATGGCAAAGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 106

TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAGgtgccacaac ... caatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCGGGGAGCGTGCATTGTTGCATGTTGGTTGGGAGCTAGGCTATGGCAAAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcagtgataattgcctatggggaaactttctaaagctttctcctcaatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCGGGGAGCGTGCATTGTTGCATGTTGGTTGGGAGCTAGGCTATGGCAAAGA
                            ttctaaa  putative branch site (score: 106)
                                    ctttctcctcaatc  CT-rich tract
     tgataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcctgagaatcatatggacaacctcagctgtacaacagtgtttatcagtgataattgcctatggggaaactttctaaagctttctcctcaatcaacagAGAAAAAACAAATGTCTGGTTTAGGCATCGGTGTTGGCAGCATGAAAAGCGGGGAGCGTGCATTGTTGCATGTTGGTTGGGAGCTAGGCTATGGCAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - -tcagctg
- - - - - - - - - - - - - - - - tacaaca