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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccatttgttttattgtaaagatgtttctgtttgactgttatataaaatgtttcttgccaatggacttccttcaggtatctcatagtttcatgagca...

Basic information

species Zea mays
transcript GRMZM2G115424_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115424_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT1G14510.1 (Arabidopsis thaliana), 5'ss of exon 3
AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccatttgttttattgtaaagatgtttctgtttgactgttatataaaatgtttcttgccaatggacttccttcaggtatctcatagtttcatgagca--
||||||| ||| | ||  | |||||||| || |||||||| ||||| || |||||||||||||| ||||| ||| | || ||||| | |||| |    |||||    ||| |||   ||   ||   | | ||||||    || |      |   |   ||         |  |  ||      |||| ||  |  | |   
AAAAAGACTGGATTTCTTTGGTTGCAGTTCACAGTGATTCATGGCTTATCTCTGTTGCATTTTACTTTGGTGCACGTTTCGGATTTGGCAAGAATGAGAGgtaa--gtttctttctctgctcagtgttctgtgtttgttaattttgcttgtttggtaaagcttcaatgactagtatagtagctgcataattctagcatccaa
















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|60396717|gb|DN229583.1|DN229583
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|60400143|gb|DN232950.1|DN232950
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|26457236|gb|CA828819.1|CA828819
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|60342995|gb|DN209968.1|DN209968
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|76018651|gb|DT945821.1|DT945821
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCGGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|17969981|gb|BM276750.1|BM276750
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCC
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCC
EST: gi|60343251|gb|DN210224.1|DN210224
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|17970075|gb|BM276842.1|BM276842
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGA
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGA
EST: gi|18964582|gb|BM661089.1|BM661089
EST:     TCTG-TGCATTTTA-TTTGGAGC-AGGTTTGGATTCGACATGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|19821822|gb|BQ047846.1|BQ047846
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTCCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|149088113|gb|EE287286.2|EE287286
EST:     ACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: ACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|32857894|gb|CD997575.1|CD997575
EST:     GCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAGACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|31353558|gb|CD437915.1|CD437915
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|78544653|gb|DV622151.1|DV622151
EST:     GGAGCAAGG-TTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: GGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT

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: 204

AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGTCCAAAGAAAAAACTCCTAAAAGCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 186

AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGTCCAAAGAAAAAACTCCTAAAAGCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGTCCAAAGAAAAAACTCCTAAAAGCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 58

AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGTCCAAAGAAAAAACTCCTAAAAGCAGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccatttgttttattgtaaagatgtttctgtttgactgttatataaaatgtttcttgccaatggacttccttcaggtatctcatagtttcatgagca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA