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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcgctcttgattccgagcgcggtgtgcagctgtgtctggctgttcgctgcttcgcgtccttggtcctgatccgacggccgtgttcgattccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGTACAGCCTCGCCGAGCTCCGGGTGGCCACCGACGGCTTCGCCACCGACCG

Basic information

species Zea mays
transcript GRMZM2G121826_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121826_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g61010.1 (Oryza sativa), 3'ss of exon 1
ttcgctcttgattccgagcgcgg-tgtgcagctgtgtctggctgttcgctgcttcgcgtccttggtcctgatccgacggccgtgttcgattccct----gtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGTACAGCCTCGCCGAGCTCCGGGTGGCCACCGACGGCTTCGCCACCGACCG
     |      ||   ||| |  |  |  | ||  || | | |  ||| |    || |  ||||| |||||||||      |||  | ||   |    |||||||||||||||||||||  || |||||||||||||||||||||||||||||||||||||||| |||||| |||||||| |||||||| ||| |  |||| ||
---attgcgacctcttcgcgagaatccgtggttgattccgac-gcgcgc-gtcgtgcttttttggtgctgatccgagctatctgtgtggttttgttgacgtgcagAGAATGGCGCCGCCGCGGACGACGGCAGCGGCGTGCCGGTGTTCGCCGAGTACAGCCTCGACGAGCTACGGGTGGCGACCGACGGGTTCTCTCCCGAGCG
















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|211419062|gb|FL425552.1|FL425552
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|148945740|gb|EC891020.2|EC891020
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|50338612|gb|CO533738.1|CO533738
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|91055451|gb|EB165869.1|EB165869
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|211284190|gb|FL390123.1|FL390123
EST:     CAAGCTCTCCGCCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|71436499|gb|DR817549.1|DR817549
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|211493009|gb|FL369794.1|FL369794
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|71299876|gb|DR785964.1|DR785964
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|71772711|gb|DR970638.1|DR970638
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|148982427|gb|EE028311.2|EE028311
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|211317028|gb|FL376020.1|FL376020
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|149102733|gb|EE188271.2|EE188271
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|149103589|gb|EE288989.2|EE288989
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|149036971|gb|EE155209.2|EE155209
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|71302365|gb|DR787300.1|DR787300
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|211227820|gb|FL399533.1|FL399533
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|149012049|gb|EE042465.2|EE042465
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCCCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|9255138|gb|BE345606.1|BE345606
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|211332705|gb|FL418379.1|FL418379
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|71327655|gb|DR800438.1|DR800438
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|211443081|gb|FL371156.1|FL371156
EST:     CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCG                         AGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT

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: 47 (upstream exon), 49 (downstream exon)
Score: 112

GAGATCTAGGCAAGCGAGCGAGCGAGCGCGGCCATGGGTGCTCGCTGCTCCAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGTACAGCCTCGCCGAGCTCCGGGTGGCCACCGACGGCTTCGCCACCGACCG


Block sizes: 36 (upstream exon), 43 (downstream exon)
Score: 24

GAGATCTAGGCAAGCGAGCGAGCGAGCGCGGCCATGGGTGCTCGCTGCTCCAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGTACAGCCTCGCCGAGCTCCGGGTGGCCACCGACGGCTTCGCCACCGACCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 50

GAGATCTAGGCAAGCGAGCGAGCGAGCGCGGCCATGGGTGCTCGCTGCTCCAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGTACAGCCTCGCCGAGCTCCGGGTGGCCACCGACGGCTTCGCCACCGACCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 92

GAGATCTAGGCAAGCGAGCGAGCGAGCGCGGCCATGGGTGCTCGCTGCTCCAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcct ... ccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGTACAGCCTCGCCGAGCTCCGGGTGGCCACCGACGGCTTCGCCACCGACCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctgcttcgcgtccttggtcctgatccgacggccgtgttcgattccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGTACAGCCTCGCCGAGCTCCGGGTGGCCACCGACGGCTTCGCCACCGACCG
                   tcctgat  putative branch site (score: 92)
                                           ttccctgt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcgctcttgattccgagcgcggtgtgcagctgtgtctggctgttcgctgcttcgcgtccttggtcctgatccgacggccgtgttcgattccctgtgcagAGAATGGCGCCGCCGAAGATGACGGCAGCGGCGTGCCGGTGTTCGCCGAGTACAGCCTCGCCGAGCTCCGGGTGGCCACCGACGGCTTCGCCACCGACCG

- -gctcttg
- - - - - - - - - - - - - gcagctg
- - - - - - - - - - - - - - - - - - - -gctgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtcctg