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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgctttcctttgtcaaatcttttggcttacgagtgcctggttttctgctgactattgtgtttggttgtttcttttgttttaatagGAAAATAATGATTGGGTTGAATGGCAAACAAATGTGCTGGTCAAACGCAATGAAGTGGAGAATGTTTATCATTGGGCTTGTGG

Basic information

species Zea mays
transcript GRMZM2G149321_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149321_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g40340.1 (Oryza sativa), 3'ss of exon 12
--------------------gttcgctttcctttgtcaaatcttttggcttacga-gtgcctg-gttttctgctgactattgtgtttggttgtttcttttgttttaatagGAAAATAATGATTGGGTTGAATGGCAAACAAATGTGCTGGTCAAACGCAATGAAGTGGAGAATGTTTATCATTGGGCTTGTGG
                     ||  ||   |  | |  ||| |||||   || || || |||| ||| |||||| ||| |   |         || |||| |   |||||||||||| ||| |||||||| ||||||||| |||| || ||||| || ||||| |||||||||||||||||||||||||||||
gtgatatttcctttctttccattgactcaacagtctttaattttttgaactatgaagtacctgagttctctgctcactgtctcg-------aattattttttaacaatagGAAAATAGTGAGTGGGTTGACTGGCAAACAGATGTTCTAGTCAAGCGTAATGAGGTGGAGAATGTTTATCATTGGGCTTGTGG
















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|211428993|gb|FL402814.1|FL402814
EST:     TTCAGTTGGGCAATAGTAACAACACAATCCAGGCTCACTTACAG                         GAAAATAATGATTGGGTTGAATGGCAAACAAATGTGCTGGTCAAACGCAAT
genomic: TTCAGTTGGGCAATAGTAACAACACAATCCAGGCTCACTTACAGgttcgctttc ... gttttaatagGAAAATAATGATTGGGTTGAATGGCAAACAAATGTGCTGGTCAAACGCAAT
EST: gi|211426577|gb|FL408870.1|FL408870
EST:     AACTTATTCAGTTGGGCAATAGTAACAACACAATCCAGGCTCACTTACAG                         GAAAATAATGATTGGGTTGAATGGCAAACAAATGTGCTGGTCAAACGCAAT
genomic: AACTTATTCAGTTGGGCAATAGTAACAACACAATCCAGGCTCACTTACAGgttcgctttc ... gttttaatagGAAAATAATGATTGGGTTGAATGGCAAACAAATGTGCTGGTCAAACGCAAT
EST: gi|211266310|gb|FL390568.1|FL390568
EST:     TTCAGTTGGGCAATAGTAACAACACAATCCAGGCTCACTTACAG                         GAAAATAATGATTGGGTTGAATGGCAAACAAATGTGCTGGTCAAACGCAAT
genomic: TTCAGTTGGGCAATAGTAACAACACAATCCAGGCTCACTTACAGgttcgctttc ... gttttaatagGAAAATAATGATTGGGTTGAATGGCAAACAAATGTGCTGGTCAAACGCAAT

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: 354

AACCCCTCCAAGAATTGGAAATGTTGGTCACATGACAAGAATAGCCAATAAACTTATTCAGTTGGGCAATAGTAACAACACAATCCAGGCTCACTTACAGgttcgctttc ... gttttaatagGAAAATAATGATTGGGTTGAATGGCAAACAAATGTGCTGGTCAAACGCAATGAAGTGGAGAATGTTTATCATTGGGCTTGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 245

AACCCCTCCAAGAATTGGAAATGTTGGTCACATGACAAGAATAGCCAATAAACTTATTCAGTTGGGCAATAGTAACAACACAATCCAGGCTCACTTACAGgttcgctttc ... gttttaatagGAAAATAATGATTGGGTTGAATGGCAAACAAATGTGCTGGTCAAACGCAATGAAGTGGAGAATGTTTATCATTGGGCTTGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 290

AACCCCTCCAAGAATTGGAAATGTTGGTCACATGACAAGAATAGCCAATAAACTTATTCAGTTGGGCAATAGTAACAACACAATCCAGGCTCACTTACAGgttcgctttc ... gttttaatagGAAAATAATGATTGGGTTGAATGGCAAACAAATGTGCTGGTCAAACGCAATGAAGTGGAGAATGTTTATCATTGGGCTTGTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 294

AACCCCTCCAAGAATTGGAAATGTTGGTCACATGACAAGAATAGCCAATAAACTTATTCAGTTGGGCAATAGTAACAACACAATCCAGGCTCACTTACAGgttcgctttc ... gttttaatagGAAAATAATGATTGGGTTGAATGGCAAACAAATGTGCTGGTCAAACGCAATGAAGTGGAGAATGTTTATCATTGGGCTTGTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtgcctggttttctgctgactattgtgtttggttgtttcttttgttttaatagGAAAATAATGATTGGGTTGAATGGCAAACAAATGTGCTGGTCAAACGCAATGAAGTGGAGAATGTTTATCATTGGGCTTGTGG
               tgctgac  putative branch site (score: 294)
                                  ttgtttcttttgtttt  putative PPT
                                     tttcttttgttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgctttcctttgtcaaatcttttggcttacgagtgcctggttttctgctgactattgtgtttggttgtttcttttgttttaatagGAAAATAATGATTGGGTTGAATGGCAAACAAATGTGCTGGTCAAACGCAATGAAGTGGAGAATGTTTATCATTGGGCTTGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA