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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatccccgtaaaaaaacgcaacttcaattgcatcatttaccgaacaatcctggcagatgattagtctggctatcgtaacatatatctcgcagCACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTG

Basic information

species Zea mays
transcript GRMZM2G044629_T01
intron # 8
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|40337292|gb|CK371362.1|CK371362
EST:     GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTG                         CACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAAT
genomic: GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTGgtaatccccg ... tatctcgcagCACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAAT
EST: gi|149014175|gb|EE043721.2|EE043721
EST:     GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTG                         CACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAA
genomic: GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTGgtaatccccg ... tatctcgcagCACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAA
EST: gi|148958334|gb|EC904558.2|EC904558
EST:     GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTG                         CACTGAAGTCCNAGAAGTTGATGGA
genomic: GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTGgtaatccccg ... tatctcgcagCACTGAAGTCCAAGAAGTTGATGGA
EST: gi|32941368|gb|CF046187.1|CF046187
EST:     GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTG                         CACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAAT
genomic: GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTGgtaatccccg ... tatctcgcagCACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAAT
EST: gi|37397991|gb|CF636304.1|CF636304
EST:     GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTG                         CACTG-AGTCCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAA
genomic: GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTGgtaatccccg ... tatctcgcagCACTGAAGT-CCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAA

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: 40 (upstream exon), 48 (downstream exon)
Score: 91

GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTGgtaatccccg ... tatctcgcagCACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTG


Block sizes: 40 (upstream exon), 47 (downstream exon)
Score: 139

GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTGgtaatccccg ... tatctcgcagCACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 220

GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTGgtaatccccg ... tatctcgcagCACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 167

GTAGCAAAGGCTCCTGATGGCAACGGTGGAGTTTATGCTGgtaatccccg ... tatctcgcagCACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccgaacaatcctggcagatgattagtctggctatcgtaacatatatctcgcagCACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTG
                                   tcgtaac  putative branch site (score: 167)
                                      taacatatat  TA-rich tract