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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatattttctggcccttcaatagataacattttaatacctgtaaattgtaatgataaaggactagtatataggtttgaggatacttcattccttt...

Basic information

species Zea mays
transcript GRMZM2G045331_T01
intron # 3
splice site 5'
intron type U2

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|78123053|gb|DV541437.1|DV541437
EST:     TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAG                         GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
genomic: TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
EST: gi|76281973|gb|DV021541.1|DV021541
EST:     TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAG                         GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
genomic: TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
EST: gi|78088708|gb|DV517101.1|DV517101
EST:     TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAG                         GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
genomic: TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
EST: gi|60350887|gb|DN217860.1|DN217860
EST:     TTGCTCCGCTGCTTTGGCATTCATTTGGCACAATTGCTGCGTTACTCCAG                         GAGATTATATCCATTTACCCGTCACTATCTCCCCCCACACTGTCACCTGGA
genomic: TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
EST: gi|149048884|gb|EE048384.2|EE048384
EST:     TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAG                         GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
genomic: TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
EST: gi|31351237|gb|CD435594.1|CD435594
EST:     TTGCTCCGCTGCTTTGGCATTCATTTGGCACAATTGCTGCGTTACTCCAG                         GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
genomic: TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
EST: gi|78091209|gb|DV519583.1|DV519583
EST:     TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAG                         GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
genomic: TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
EST: gi|211374626|gb|FK958606.1|FK958606
EST:     TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAG                         GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
genomic: TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
EST: gi|9731640|gb|BE510392.1|BE510392
EST:     TTGCTCCGCTGCTTTGGCATTCATTTGGCACAATTGCTGCGTTACTCCAG                         GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
genomic: TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
EST: gi|71445883|gb|DR826933.1|DR826933
EST:     TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAG                         GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
genomic: TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
EST: gi|211374623|gb|FK958603.1|FK958603
EST:     TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCGG                         GAGATTATATCCATTTACCCGGCACTATCACCCCCCACACTGGCACCTGGA
genomic: TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
EST: gi|31356490|gb|CD440847.1|CD440847
EST:     TTGCTCCGCTGCTTTGGTANNNNNNNGGCACAATTGCTGCGTTACTCCAG                         GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
genomic: TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
EST: gi|211374624|gb|FK958604.1|FK958604
EST:     TGCTCCGCTGCTTTGGCATTCATTTGGCACAATTTGCTGCGTTACTCCAG                         GAGATTATATCCATT
genomic: TGCTCCGCTGCTTTGGCACTCATTTGGCACAATT-GCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATT
EST: gi|76936740|gb|DV174858.1|DV174858
EST:     TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAG                         GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
genomic: TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
EST: gi|31354815|gb|CD439172.1|CD439172
EST:     TTGCTCCGCTGCTTTGGCATTCATTTGGCACAATTGCTGCGTTACTCCAG                         GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
genomic: TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
EST: gi|74233595|gb|DT641509.1|DT641509
EST:     TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAG                         GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
genomic: TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
EST: gi|91056772|gb|EB167190.1|EB167190
EST:     TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAG                         GAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA
genomic: TTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGA

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: 168

AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG


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

AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG


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

AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 135

AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatat ... acatatacagGAGATTATATCCATTTACCCGTCACTATCACCCCCCACACTGTCACCTGGAGCATCAAACCGAGTTTGCAATGCTCTTGCACTTCTGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAGgtatgcatattttctggcccttcaatagataacattttaatacctgtaaattgtaatgataaaggactagtatataggtttgaggatacttcattccttt

- - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC