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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcccgtgttccgtactggaggatttggattgatgattatggtgactttcgctcaggtttcactcaccattccccgttgggaattttcttgatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCAGGACCAAAGGAGGCGCCAGCGAATAACCCTGGGCTCCAGACCGAGGTCG

Basic information

species Zea mays
transcript GRMZM2G125310_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G125310_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g22970.1 (Oryza sativa), 3'ss of exon 1
------------------------------------gtcccgtgttccgtactggaggatttggattgatgattatggtgactttcgctcaggtttcactcaccattccccgttgggaattttcttga-----------tttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCC---CGCCGCCATGGCGACTTCCTCAGGACCAAAGGAGGCGCCAGCGAATAACCCTGGGCTCCAGACCGAGGTCG
                                    |   | | | ||   |            |  |  |||| | | |  | |||| |  ||||| ||||||||  |  | | ||  || |||              ||  |||||||||||| |||| |||||||||||||||   |||||||||| |||| || || || || ||||||||||| || || ||||| || |||||| | |  ||  
gtaaccccggttgaaactcaacgaaattcgtcaccgggatcctttccccccccccccccccctcaccg--gattcttgagtttctcgcgcttgtttcgctcaccatgtcttggttggggttctctgatctctctccctcttctgtagAGATTCGACCGGGCTCGCCGGTTCGCGCCGGCCGCCGCCATGTCGACGTCGTCGGGGCCGAAGGAGGCGCCGGCAAACAACCCGGGCCTCCAGGC-GCCGT--
















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|13178259|gb|BG349517.1|BG349517
EST:     TGCACGCTCCTCCG-CTGATTCCCAGCGCGTCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: TGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|78113103|gb|DV531497.1|DV531497
EST:     CCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: CCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|149071547|gb|EE159940.2|EE159940
EST:     GCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: GCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|13198653|gb|BG354455.1|BG354455
EST:     -CCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: CCCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|211376698|gb|FL282321.1|FL282321
EST:     CCCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: CCCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|211376699|gb|FL282322.1|FL282322
EST:     CCCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: CCCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|211376692|gb|FL282315.1|FL282315
EST:     CCCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: CCCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|113701200|gb|EE678704.1|EE678704
EST:     CGTCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: CGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|213174962|gb|FM184828.1|FM184828
EST:     GCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: GCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|211376696|gb|FL282319.1|FL282319
EST:     CCCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: CCCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|211280531|gb|FL042849.1|FL042849
EST:     CGTCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: CGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|67022929|gb|CO451678.1|CO451678
EST:     GCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: GCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|113703344|gb|EE680848.1|EE680848
EST:     CGCATTTCAAG                         AGATTCGATCGGGTTCGCC-GTTCGCGCCCGCCGCCATGGCGACTTCTTCA
genomic: CGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|30087092|gb|CB885300.1|CB885300
EST:     TCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: TCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|67031599|gb|CO460348.1|CO460348
EST:     CGTCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: CGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|40334690|gb|CK368760.1|CK368760
EST:     CGTCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: CGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|211376693|gb|FL282316.1|FL282316
EST:     CCCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: CCCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|211376697|gb|FL282320.1|FL282320
EST:     CCCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: CCCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
EST: gi|149069536|gb|EE157909.2|EE157909
EST:     GCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAG                         AGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA
genomic: GCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCA

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), 48 (downstream exon)
Score: 261

TAGGTTTATATATCCTGGTGCTCTTGCCATGGCTGGTGCATCGCTCCTCTCCCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCAGGACCAAAGGAGGCGCCAGCGAATAACCCTGGGCTCCAGACCGAGGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 438

TAGGTTTATATATCCTGGTGCTCTTGCCATGGCTGGTGCATCGCTCCTCTCCCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCAGGACCAAAGGAGGCGCCAGCGAATAACCCTGGGCTCCAGACCGAGGTCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 198

TAGGTTTATATATCCTGGTGCTCTTGCCATGGCTGGTGCATCGCTCCTCTCCCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCAGGACCAAAGGAGGCGCCAGCGAATAACCCTGGGCTCCAGACCGAGGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 250

TAGGTTTATATATCCTGGTGCTCTTGCCATGGCTGGTGCATCGCTCCTCTCCCCATCCTGCACGCTCCTCCGCCTGATTCCCAGCGCGTCGCACTTCAAGgtcccgtgtt ... gatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCAGGACCAAAGGAGGCGCCAGCGAATAACCCTGGGCTCCAGACCGAGGTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcgctcaggtttcactcaccattccccgttgggaattttcttgatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCAGGACCAAAGGAGGCGCCAGCGAATAACCCTGGGCTCCAGACCGAGGTCG
                                      ttttcttg  CT-rich tract
                                    aattttcttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcccgtgttccgtactggaggatttggattgatgattatggtgactttcgctcaggtttcactcaccattccccgttgggaattttcttgatttcgtagAGATTCGATCGGGTTCGCCGGTTCGCGCCCGCCGCCATGGCGACTTCCTCAGGACCAAAGGAGGCGCCAGCGAATAACCCTGGGCTCCAGACCGAGGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -CGCCGCCA