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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtagatttttcaccaaacttttttattgttcttcataaatttgttgccagtatacttatcgctgtcatccttcattctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGTTCACTGCCACAGTACTAGATGTAGAGAAATGCAAAGAACTAAAGATGGG

Basic information

species Zea mays
transcript GRMZM2G178958_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178958_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g55140.1 (Oryza sativa), 3'ss of exon 3
gtcagtagatttttcaccaaactttt-----ttattgttcttcataaatttgttgccagtatact----tatcgctg-tcatcc--ttcattctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGTTCACTGCCACAGTACTAGATGTAGAGAAATGCAAAGAACTAAAGATGGG
     ||  | |||    ||||         |   | | || |||| ||    | |   | |  |    | || ||  |||  |   || ||  | ||||||||||||| |||||||| ||||| || |||||||| ||||||||||| |||||||| ||| || ||||||| |||||||| |||||  ||||||||||
--gtatatttcttttgttaaacgccaaacagtggatctcctccatagatgccattctgatgttttcttatttcactactcactcatctcctttatccagCTGTGCTTGCCGAGGAGGCATCAAACATTGCTTCTACATACAGTGATGTATTCACTGCGACAATATTAGATGTGGAGAAATGTAAAGAGTTAAAGATGGG
















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|211130401|gb|FL313022.1|FL313022
EST:     GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTG                         CTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
genomic: GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
EST: gi|148936677|gb|EC880805.2|EC880805
EST:     GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTG                         CTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
genomic: GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
EST: gi|93012171|gb|EB637691.1|EB637691
EST:     GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTG                         CTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
genomic: GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
EST: gi|67022782|gb|CO451531.1|CO451531
EST:     GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTG                         CTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
genomic: GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
EST: gi|67042042|gb|CO468297.1|CO468297
EST:     GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTG                         CTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
genomic: GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
EST: gi|149111708|gb|EE190853.2|EE190853
EST:     GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTG                         CTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
genomic: GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
EST: gi|211473206|gb|FL353033.1|FL353033
EST:     GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTG                         CTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
genomic: GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
EST: gi|148972721|gb|EE023682.2|EE023682
EST:     GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTG                         CTGTGCCTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
genomic: GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
EST: gi|149026812|gb|EE046172.2|EE046172
EST:     GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTG                         CTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
genomic: GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
EST: gi|76291680|gb|DV031248.1|DV031248
EST:     GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTG                         CTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
genomic: GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
EST: gi|211018803|gb|FL351168.1|FL351168
EST:     GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTG                         CTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
genomic: GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
EST: gi|76013429|gb|DT940599.1|DT940599
EST:     GATATTCGGGAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTG                         CTGTGCTTGCGGA
genomic: GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGA
EST: gi|71323796|gb|DR798569.1|DR798569
EST:     GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTG                         CTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
genomic: GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
EST: gi|211347363|gb|FL343425.1|FL343425
EST:     GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTG                         CTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
genomic: GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
EST: gi|67023272|gb|CO452021.1|CO452021
EST:     GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTG                         CTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
genomic: GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
EST: gi|71448100|gb|DR829150.1|DR829150
EST:     GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTG                         CTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
genomic: GATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGT
EST: gi|110519120|gb|EE023707.1|EE023707
EST:     ATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCCTG                         CTGTGCTTGCGGAGG
genomic: ATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCC-TGgtcagtagat ... attctttcagCTGTGCTTGCGGAGG

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: 371

GCAGAGGTGGATCAGAAACTTAAGTATGCTAATGATCTTTCGTCGGGTGTGATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGTTCACTGCCACAGTACTAGATGTAGAGAAATGCAAAGAACTAAAGATGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1119

GCAGAGGTGGATCAGAAACTTAAGTATGCTAATGATCTTTCGTCGGGTGTGATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGTTCACTGCCACAGTACTAGATGTAGAGAAATGCAAAGAACTAAAGATGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 778

GCAGAGGTGGATCAGAAACTTAAGTATGCTAATGATCTTTCGTCGGGTGTGATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGTTCACTGCCACAGTACTAGATGTAGAGAAATGCAAAGAACTAAAGATGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 582

GCAGAGGTGGATCAGAAACTTAAGTATGCTAATGATCTTTCGTCGGGTGTGATATTCGGAAGAGAGCTTGTGAACTCTCCTGCAAATGTCCTTACCCCTGgtcagtagat ... attctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGTTCACTGCCACAGTACTAGATGTAGAGAAATGCAAAGAACTAAAGATGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttcataaatttgttgccagtatacttatcgctgtcatccttcattctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGTTCACTGCCACAGTACTAGATGTAGAGAAATGCAAAGAACTAAAGATGGG
                                    tcatccttcattcttt  CT-rich tract
      ataaatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtagatttttcaccaaacttttttattgttcttcataaatttgttgccagtatacttatcgctgtcatccttcattctttcagCTGTGCTTGCGGAGGAGGCGTCAAAGATCGCTTCTACTTACAGTGATGTGTTCACTGCCACAGTACTAGATGTAGAGAAATGCAAAGAACTAAAGATGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG