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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagcatatcttgcttcttcctcctgtttataccatgctgagtaatcatgctgacttgtttcttctcttcattgttggtgtattcttgctaatcttcagTTGTCCATTTTGTCGGAAG

Basic information

species Zea mays
transcript GRMZM5G804772_T01
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|76910497|gb|DV163897.1|DV163897
EST:     GAATTTGAAGG                         TTGTCCATTTTGTCGGAAG
genomic: GAATTTGAAGGgtacagcata ... taatcttcagTTGTCCATTTTGTCGGAAG




















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), 49 (downstream exon)
Score: 149

CTTGGAAGGTGAAAGAGGAATCAAAAATAGGACAGTGCAAACGACCAGAAAAGCCTATCGAGATATATGAATTTGAAGGgtacagcata ... taatcttcagTTGTCCATTTTGTCGGAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 214

CTTGGAAGGTGAAAGAGGAATCAAAAATAGGACAGTGCAAACGACCAGAAAAGCCTATCGAGATATATGAATTTGAAGGgtacagcata ... taatcttcagTTGTCCATTTTGTCGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

CTTGGAAGGTGAAAGAGGAATCAAAAATAGGACAGTGCAAACGACCAGAAAAGCCTATCGAGATATATGAATTTGAAGGgtacagcata ... taatcttcagTTGTCCATTTTGTCGGAAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 106

CTTGGAAGGTGAAAGAGGAATCAAAAATAGGACAGTGCAAACGACCAGAAAAGCCTATCGAGATATATGAATTTGAAGGgtacagcata ... taatcttcagTTGTCCATTTTGTCGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatgctgacttgtttcttctcttcattgttggtgtattcttgctaatcttcagTTGTCCATTTTGTCGGAAG
                                          tgctaat  putative branch site (score: 106)
                                      ttcttgct  CT-rich tract
                                    tattctt  TA-rich tract