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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttcttataaatatatgcatagttgaattgaatctgagttaatattactgaagttaaagaaataagcattacaactattccagGTGATGGATATTCTAGGGCCCAGCCTTTGGGATGTCTGGAATTCATTTGGGCAGTT

Basic information

species Zea mays
transcript GRMZM2G116086_T01
intron # 5
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|67028330|gb|CO457079.1|CO457079
EST:     ACCATGGGTTCATTACAAAGGTCGACAAGGAGATTACTATGTTCTG                         GTGATGGATATTCTAGGGCCCAGCCTTTGGGATGTCTGGAATTCATTTGGG
genomic: ACCATGGGTTCATTACAAAGGTCGACAAGGAGATTATTATGTTCTGgttagttctt ... actattccagGTGATGGATATTCTAGGGCCCAGCCTTTGGGATGTCTGGAATTCATTTGGG
EST: gi|87155883|gb|DY400672.1|DY400672
EST:     GTACCATGGGTTCATTACAAAGGTCGACAAGGAGATTATTATGTTCTG                         GTGATGGATATTCTAGGGCCCAGCCTTTGGGATGTCTGGAATTCATTTGGG
genomic: GTACCATGGGTTCATTACAAAGGTCGACAAGGAGATTATTATGTTCTGgttagttctt ... actattccagGTGATGGATATTCTAGGGCCCAGCCTTTGGGATGTCTGGAATTCATTTGGG
EST: gi|9731560|gb|BE510312.1|BE510312
EST:     GTGTACCATGGGTTCATTACAAAGGTCGACAAGGAGATTATTATGTTCTG                         GTGATGGATATTCTAGGGCCCAGCCTTTGGGATGTCTGGAATTCATTTGGG
genomic: GTGTACCATGGGTTCATTACAAAGGTCGACAAGGAGATTATTATGTTCTGgttagttctt ... actattccagGTGATGGATATTCTAGGGCCCAGCCTTTGGGATGTCTGGAATTCATTTGGG
EST: gi|211111190|gb|FL061237.1|FL061237
EST:     GTGTACCATGGGTTCATTACAAAGGTCGACAAGGAGATTACTATGTTCTG                         GTGATGGATATTCTAGGGCCCAGCCTTTGGGATGT
genomic: GTGTACCATGGGTTCATTACAAAGGTCGACAAGGAGATTATTATGTTCTGgttagttctt ... actattccagGTGATGGATATTCTAGGGCCCAGCCTTTGGGATGT
EST: gi|26559656|gb|CA831891.1|CA831891
EST:     GTACCATGGGTTCATTACAAAGGTCTACAAGGAGATTATTATGTTCTG                         G-GATGGATATTCTAGGGCCCAGCCTTTGGGATGTCTGGAATTCATTTGGG
genomic: GTACCATGGGTTCATTACAAAGGTCGACAAGGAGATTATTATGTTCTGgttagttctt ... actattccagGTGATGGATATTCTAGGGCCCAGCCTTTGGGATGTCTGGAATTCATTTGGG

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), 47 (downstream exon)
Score: 421

TGCTCTGAACGGGTGTTATGGTGTACCATGGGTTCATTACAAAGGTCGACAAGGAGATTATTATGTTCTGgttagttctt ... actattccagGTGATGGATATTCTAGGGCCCAGCCTTTGGGATGTCTGGAATTCATTTGGGCAGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 371

TGCTCTGAACGGGTGTTATGGTGTACCATGGGTTCATTACAAAGGTCGACAAGGAGATTATTATGTTCTGgttagttctt ... actattccagGTGATGGATATTCTAGGGCCCAGCCTTTGGGATGTCTGGAATTCATTTGGGCAGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 342

TGCTCTGAACGGGTGTTATGGTGTACCATGGGTTCATTACAAAGGTCGACAAGGAGATTATTATGTTCTGgttagttctt ... actattccagGTGATGGATATTCTAGGGCCCAGCCTTTGGGATGTCTGGAATTCATTTGGGCAGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 642

TGCTCTGAACGGGTGTTATGGTGTACCATGGGTTCATTACAAAGGTCGACAAGGAGATTATTATGTTCTGgttagttctt ... actattccagGTGATGGATATTCTAGGGCCCAGCCTTTGGGATGTCTGGAATTCATTTGGGCAGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatctgagttaatattactgaagttaaagaaataagcattacaactattccagGTGATGGATATTCTAGGGCCCAGCCTTTGGGATGTCTGGAATTCATTTGGGCAGTT
        agttaat  putative branch site (score: 642)
                                              ctattcc  putative PPT
          ttaatattactgaagt  TA-rich tract