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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagctagctcaaatttctccttgcattctgacagttctatttatctttttagtcaagctataatttgacgttgagggtgtcttcacccttcagTGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGTGCTCGGCTGCGTGATGTGCATTGCAGGGTCTGTGGTCATTGTTATCCAC

Basic information

species Zea mays
transcript GRMZM2G120175_T04
intron # 3
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|148934736|gb|EC878785.2|EC878785
EST:     GCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAG                         TGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGT
genomic: GCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAGgttagctagc ... cacccttcagTGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGT
EST: gi|149085221|gb|EE174729.2|EE174729
EST:     GCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAG                         TGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGT
genomic: GCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAGgttagctagc ... cacccttcagTGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGT
EST: gi|148943741|gb|EC888811.2|EC888811
EST:     GCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAG                         TGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGT
genomic: GCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAGgttagctagc ... cacccttcagTGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGT
EST: gi|71423545|gb|DR806069.1|DR806069
EST:     GCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAG                         TGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGT
genomic: GCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAGgttagctagc ... cacccttcagTGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGT
EST: gi|76287458|gb|DV027026.1|DV027026
EST:     GCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAG                         TGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGT
genomic: GCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAGgttagctagc ... cacccttcagTGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGT
EST: gi|76281094|gb|DV020662.1|DV020662
EST:     GCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAG                         TGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGT
genomic: GCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAGgttagctagc ... cacccttcagTGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGT
EST: gi|148963641|gb|EE014691.2|EE014691
EST:     GCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAG                         TGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGT
genomic: GCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAGgttagctagc ... cacccttcagTGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGT

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: 48 (upstream exon), 48 (downstream exon)
Score: 27

TGATTGTAGGTGAGATTGCCAATTTCGTGGCATATGCTTTCGCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAGgttagctagc ... cacccttcagTGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGTGCTCGGCTGCGTGATGTGCATTGCAGGGTCTGTGGTCATTGTTATCCAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 87

TGATTGTAGGTGAGATTGCCAATTTCGTGGCATATGCTTTCGCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAGgttagctagc ... cacccttcagTGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGTGCTCGGCTGCGTGATGTGCATTGCAGGGTCTGTGGTCATTGTTATCCAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 83

TGATTGTAGGTGAGATTGCCAATTTCGTGGCATATGCTTTCGCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAGgttagctagc ... cacccttcagTGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGTGCTCGGCTGCGTGATGTGCATTGCAGGGTCTGTGGTCATTGTTATCCAC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 64

TGATTGTAGGTGAGATTGCCAATTTCGTGGCATATGCTTTCGCCCCCGCTGTTCTGGTTACTCCCCTTGGAGCACTCAGCATAATTGTTAGgttagctagc ... cacccttcagTGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGTGCTCGGCTGCGTGATGTGCATTGCAGGGTCTGTGGTCATTGTTATCCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttatctttttagtcaagctataatttgacgttgagggtgtcttcacccttcagTGCAGTGCTGGCTCATTTCATTCTGAACGAGAGGCTGCATGCCCTCGGGGTGCTCGGCTGCGTGATGTGCATTGCAGGGTCTGTGGTCATTGTTATCCAC
                        atttgac  putative branch site (score: 64)
                                       tgtcttcacccttc  putative PPT
                    tataatttga  TA-rich tract