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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actacccattttccttaaccagtcagaatattttgaacttgcccaattatttgtgtttctttgtaagactgctgatttgtgctactgtttttggttacagAGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAGTGTTCCCGTCAACTACGGTGGTTACAACCCTCCAAATTATCCTCCGCAA

Basic information

species Zea mays
transcript GRMZM2G156638_T02
intron # 13
splice site 3'
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|16925759|gb|BM078827.1|BM078827
EST:     TTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACC--A-                         A--AGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG
genomic: TTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAAGgtattgccac ... ttggttacagAGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG
EST: gi|113703304|gb|EE680808.1|EE680808
EST:     TTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAAG                         AGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG
genomic: TTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAAGgtattgccac ... ttggttacagAGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG
EST: gi|33100101|gb|CF060061.1|CF060061
EST:     GTACCGACAAACCAAAG                         AGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG
genomic: GTACCAACAAACCAAAGgtattgccac ... ttggttacagAGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG
EST: gi|211523712|gb|FL481395.1|FL481395
EST:     TTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAAG                         AGCAGWTCAATTATTYCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG
genomic: TTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAAGgtattgccac ... ttggttacagAGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG
EST: gi|14244490|gb|BG842508.2|BG842508
EST:     TTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAAG                         AGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG
genomic: TTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAAGgtattgccac ... ttggttacagAGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG
EST: gi|28986772|gb|CB351302.1|CB351302
EST:     TTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAAG                         AGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG
genomic: TTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAAGgtattgccac ... ttggttacagAGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG
EST: gi|14204013|gb|BG837690.1|BG837690
EST:     TTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAWG                         WKYWKWTCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG
genomic: TTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAAGgtattgccac ... ttggttacagAGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG
EST: gi|71758986|gb|DR956923.1|DR956923
EST:     TTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAAG                         AGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG
genomic: TTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAAGgtattgccac ... ttggttacagAGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG
EST: gi|8102613|gb|AW927416.1|AW927416
EST:     TTCCAAGGCCACGTTTTCGCTACATCTAACCCTGTACCAACAAACCAAAG                         AGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG
genomic: TTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAAGgtattgccac ... ttggttacagAGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAG

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: 61

ACTTTGGAGATGCAACTGGCCAAGGGAGTGGATCTATCAGGTCAGCAAATTTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAAGgtattgccac ... ttggttacagAGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAGTGTTCCCGTCAACTACGGTGGTTACAACCCTCCAAATTATCCTCCGCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 114

ACTTTGGAGATGCAACTGGCCAAGGGAGTGGATCTATCAGGTCAGCAAATTTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAAGgtattgccac ... ttggttacagAGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAGTGTTCCCGTCAACTACGGTGGTTACAACCCTCCAAATTATCCTCCGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 162

ACTTTGGAGATGCAACTGGCCAAGGGAGTGGATCTATCAGGTCAGCAAATTTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAAGgtattgccac ... ttggttacagAGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAGTGTTCCCGTCAACTACGGTGGTTACAACCCTCCAAATTATCCTCCGCAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 58

ACTTTGGAGATGCAACTGGCCAAGGGAGTGGATCTATCAGGTCAGCAAATTTCCAAGGCCACGTCTTCGCTACATCTAACCCTGTACCAACAAACCAAAGgtattgccac ... ttggttacagAGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAGTGTTCCCGTCAACTACGGTGGTTACAACCCTCCAAATTATCCTCCGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatttgtgtttctttgtaagactgctgatttgtgctactgtttttggttacagAGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAGTGTTCCCGTCAACTACGGTGGTTACAACCCTCCAAATTATCCTCCGCAA
                        tgctgat  putative branch site (score: 58)
                                       ctgttttt  putative PPT
          tttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actacccattttccttaaccagtcagaatattttgaacttgcccaattatttgtgtttctttgtaagactgctgatttgtgctactgtttttggttacagAGCAGATCAATTATTTCATGTGTCTTCTCAAGGATTGAGTGCCCATTCCAGTGTTCCCGTCAACTACGGTGGTTACAACCCTCCAAATTATCCTCCGCAA

- - - - - - - - - - - - - - - - - - -cttgccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctactg