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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcccttgcttttatttcatatccattaagagtgtgcatcaagagcattcatttgcaatagtcagtatcttttcaaaatgtttttgttctaactcgctgataactaaactttttgtcaattttctttccctcaaacactcgttaattttattttaacccatttcagGTAAGTTTCAGTGATTGGTTCATGTCCAAAGGGGGTACTCGGGAGAGTATCACAAGAATGTGGGATCCTGTTGCTTACGCTTTGGGTTTCATTGACTGTG

Basic information

species Zea mays
transcript GRMZM2G454952_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G454952_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g10490.1 (Oryza sativa), 3'ss of exon 6
gtaagtatcccttgcttttatttcatatccattaagagtgtgcatcaagagcattcatttgcaatagtcagtatcttttcaaaatgtttttgttctaactcgctgataactaaactttttgtcaattttctttccctcaaacactcgttaattt-tattttaacccatttcagGTAAGTTTCAGTGATTGGTTCATGTCCAAAGGGGGTACTCGGGAGAGTATCACAAGAATGTGGGATCCTGTTGCTTACGCTTTGGGTTTCATTGACTGTG
                                                                ||  || |||    |  |||| |  | |  ||   |   | || |  |||      ||  ||    | |  || ||      ||||||||  |  |  ||   ||||||||||||||||| ||||||||| |||| ||||| |||||||| ||||| |||||||| ||||||||||||||||| || ||| | ||||||||||||||||
----------------------------------------------------------------taaaca-tatgcactataaatatcgtagaactg--ttattaatgaa-aaatcagaggtagatagcttctatctaaag-----gttaatttgcaagtgtacttttttcagGTAAGTTTCAGCGATTGGTTCTTGTCGAAAGGTGGTACTCGAGAGAGCATCACAAGGATGTGGGATCCTGTTGCCTATGCTCTTGGTTTCATTGACTGTG

upper sequence: GRMZM2G454952_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G04870.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaagtatcccttgcttttatttcatatccattaagagtgtgcatcaagagcattcatttgcaatagtcagtatcttttcaaaatgtttttgttctaactcgctgataactaaactttttgtcaattttctttccctcaaacactcgttaattttattttaacccattt--cagGTAAGTTTCAGTGATTGGTTCATGTCCAAAGGGGGTACTCGGGAGAGTATCACAAGAATGTGGGATCCTGTTGCTTACGCTTTGGGTTTCATTGACTGTG
                                                                                               |||     |||||||      || |    || |    | |         ||  ||| |||  |  ||  | |||  ||| ||||||||   ||||||||| |||| ||||| || || ||||  ||||||   ||||||||||||||||||||||| ||| | |||||||| ||||| |
----------------------------------------------------------------------------------------------gtaaagaa-tgataacctgttcttcttctcatctgtactactatttgtgttctctaaattttctgaaatactttttgcagATAAGTTTCTCGGATTGGTTCCTGTCAAAAGGTGGGACACGGGCAAGTATCCAGAGAATGTGGGATCCTGTTGCTTATGCTCTAGGTTTCATAGACTGCG
















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|211117968|gb|FK980643.1|FK980643
EST:     CTCTGGTTGATCCTGATGGTGCATTGCAGCAAGTGCGGGACTTGGATGAT                         ATAAAGTT-CAGTGGATTGGT-CATGTCCAAA
genomic: CTCTGGTTGATCCTGATGGTGCATTGCAGCAAGTGCGGGACTTGGATGATgtaagtatcc ... cccatttcagGTAA-GTTTCAGTG-ATTGGTTCATGTCCAAA
EST: gi|211117183|gb|FK980637.1|FK980637
EST:     CTCTGGTTGATCCTGATGGTGCATTGCAGCAAGTGCGGGACTTGGATGAT                         ATAAGTTTCAGTGATTGGTTCATGTCCCAAGGGG-TACTCGGGAGAGTATC
genomic: CTCTGGTTGATCCTGATGGTGCATTGCAGCAAGTGCGGGACTTGGATGATgtaagtatcc ... cccatttcagGTAAGTTTCAGTGATTGGTTCATGTCCAAAGGGGGTACTCGGGAGAGTATC

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: 45 (upstream exon), 45 (downstream exon)
Score: 80

TGATAAAGCAAGAAATGCAGTTGCTCTTGCCCTTAGTCCAGTTGTTCGGGCTCTGGTTGATCCTGATGGTGCATTGCAGCAAGTGCGGGACTTGGATGATgtaagtatcc ... cccatttcagGTAAGTTTCAGTGATTGGTTCATGTCCAAAGGGGGTACTCGGGAGAGTATCACAAGAATGTGGGATCCTGTTGCTTACGCTTTGGGTTTCATTGACTGTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 199

TGATAAAGCAAGAAATGCAGTTGCTCTTGCCCTTAGTCCAGTTGTTCGGGCTCTGGTTGATCCTGATGGTGCATTGCAGCAAGTGCGGGACTTGGATGATgtaagtatcc ... cccatttcagGTAAGTTTCAGTGATTGGTTCATGTCCAAAGGGGGTACTCGGGAGAGTATCACAAGAATGTGGGATCCTGTTGCTTACGCTTTGGGTTTCATTGACTGTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 104

TGATAAAGCAAGAAATGCAGTTGCTCTTGCCCTTAGTCCAGTTGTTCGGGCTCTGGTTGATCCTGATGGTGCATTGCAGCAAGTGCGGGACTTGGATGATgtaagtatcc ... cccatttcagGTAAGTTTCAGTGATTGGTTCATGTCCAAAGGGGGTACTCGGGAGAGTATCACAAGAATGTGGGATCCTGTTGCTTACGCTTTGGGTTTCATTGACTGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 345

TGATAAAGCAAGAAATGCAGTTGCTCTTGCCCTTAGTCCAGTTGTTCGGGCTCTGGTTGATCCTGATGGTGCATTGCAGCAAGTGCGGGACTTGGATGATgtaagtatcc ... cccatttcagGTAAGTTTCAGTGATTGGTTCATGTCCAAAGGGGGTACTCGGGAGAGTATCACAAGAATGTGGGATCCTGTTGCTTACGCTTTGGGTTTCATTGACTGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtcaattttctttccctcaaacactcgttaattttattttaacccatttcagGTAAGTTTCAGTGATTGGTTCATGTCCAAAGGGGGTACTCGGGAGAGTATCACAAGAATGTGGGATCCTGTTGCTTACGCTTTGGGTTTCATTGACTGTG
                                       ttttaac  putative branch site (score: 345)
                                             cccatttc  CT-rich tract
                              ttaattttattttaac  TA-rich tract