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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcatcttgtacaatctcctttctgaatatttggaaatgcaagatgctaatgcgatcttgaacacaaatacagGACAAACAAACATGGCCAGTGCTTGGAAATGTGAGTTCTGTCATTCTTCCCAAGTTACTGAG

Basic information

species Zea mays
transcript GRMZM2G052688_T01
intron # 6
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|91872021|gb|EB401978.1|EB401978
EST:     ATCATACCAGAGAATTGAAGAAGCNAAAAATCAA-TGGATCA-GTTCAAA                         GACAAACAAACATGGCCAGTGCTT
genomic: ATCATACCAGAGAATTGAAGAAGC-AAAAATCAAATG-ATCAAGTTCAAAgtaagtcatc ... acaaatacagGACAAACAAACATGGCCAGTGCTT
EST: gi|60396041|gb|DN228911.1|DN228911
EST:     TGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAGTTCAAA                         GACAAACAAACATGGCCAGTGCTTGGAAATGTGAGTTCTGTCATTCTTCCC
genomic: TGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAGTTCAAAgtaagtcatc ... acaaatacagGACAAACAAACATGGCCAGTGCTTGGAAATGTGAGTTCTGTCATTCTTCCC
EST: gi|88755916|gb|DY540057.1|DY540057
EST:     ACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAGTTCAAA                         GACAAACAAACATGGCCAGTGCTTGGAAATGTGAGTTCTGTCATTCTTCCC
genomic: ACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAGTTCAAAgtaagtcatc ... acaaatacagGACAAACAAACATGGCCAGTGCTTGGAAATGTGAGTTCTGTCATTCTTCCC
EST: gi|22935404|gb|BU571679.1|BU571679
EST:     TGATCATACCAGACAATTGAAGAAGCAAAAATCAAATGATCCAGTTCAAA                         GACAAACAAACATGGCCAGTGCTTGGAAATGTGAGTTCTGTCATTCTTCCC
genomic: TGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAGTTCAAAgtaagtcatc ... acaaatacagGACAAACAAACATGGCCAGTGCTTGGAAATGTGAGTTCTGTCATTCTTCCC
EST: gi|74233407|gb|DT641321.1|DT641321
EST:     TGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAGTTCAAA                         GACAAACAAACATGGCCAGTGCTTGGAAATGTGAGTTCTGTCATTCTTCCC
genomic: TGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAGTTCAAAgtaagtcatc ... acaaatacagGACAAACAAACATGGCCAGTGCTTGGAAATGTGAGTTCTGTCATTCTTCCC
EST: gi|87156124|gb|DY400913.1|DY400913
EST:     TGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCCAGTTCAAA                         GACAAACAAACATGGCCAGTGCTTGGAAATGTGAGTTCTGTCATTCTTCCC
genomic: TGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAGTTCAAAgtaagtcatc ... acaaatacagGACAAACAAACATGGCCAGTGCTTGGAAATGTGAGTTCTGTCATTCTTCCC

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), 48 (downstream exon)
Score: 50

AGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCAATGGATGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAGTTCAAAgtaagtcatc ... acaaatacagGACAAACAAACATGGCCAGTGCTTGGAAATGTGAGTTCTGTCATTCTTCCCAAGTTACTGAG


Block sizes: 35 (upstream exon), 39 (downstream exon)
Score: 17

AGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCAATGGATGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAGTTCAAAgtaagtcatc ... acaaatacagGACAAACAAACATGGCCAGTGCTTGGAAATGTGAGTTCTGTCATTCTTCCCAAGTTACTGAG


Block sizes: 41 (upstream exon), 37 (downstream exon)
Score: 6

AGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCAATGGATGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAGTTCAAAgtaagtcatc ... acaaatacagGACAAACAAACATGGCCAGTGCTTGGAAATGTGAGTTCTGTCATTCTTCCCAAGTTACTGAG


Block sizes: 46 (upstream exon), 16 (downstream exon)
Score: 8

AGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCAATGGATGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAGTTCAAAgtaagtcatc ... acaaatacagGACAAACAAACATGGCCAGTGCTTGGAAATGTGAGTTCTGTCATTCTTCCCAAGTTACTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctgaatatttggaaatgcaagatgctaatgcgatcttgaacacaaatacagGACAAACAAACATGGCCAGTGCTTGGAAATGTGAGTTCTGTCATTCTTCCCAAGTTACTGAG
                          tgctaat  putative branch site (score: 8)
     tgaatattt  TA-rich tract