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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggattaaatactttgtagccttatgaatttaactcaaggaaacttgtgacatcatattaattcaagcctgtatggctacttgaaacatatgcagGAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGACCAATCAACTCGAGTCTGCAATGTGCTTGTACTCCTTAAG

Basic information

species Zea mays
transcript AC191251.3_FGT005
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC191251.3_FGT005 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g57130.1 (Oryza sativa), 3'ss of exon 2
-------------------------------------gtggattaaatactttgtagccttatgaatttaactcaaggaaacttgtgacatcatattaattcaagcctgtatggctacttgaaacatatgcagGAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGACCAATCAACTCGAGTCTGCAATGTGCTTGTACTCCTTAAG
                                     || || ||   |  ||    | |    ||   || |||    |   | | |     |  | ||||| |  | | ||  |  ||   | | |||||||| ||||||||||| |||| || |||||||||||||  |||||||   |     ||||  || ||||||||||  |||| ||| ||| ||
gtaggttacaattcttcatgttgtttaagtcagtgtggttgagtacgaatgttagttcttccgaaaagaaattcatttgagtctttcatggttttctcattca-gtttatttg--tggtttggata-atgcagGAGATTGTGTCAATCTATCCATCACTTTCACCCCCAACATTATCTCCAGGGGCTTCAAACCGTGTCTGCAATGCACTTGCACTTCTTCAG
















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|71757156|gb|DR955093.1|DR955093
EST:     TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG                         GAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGAC
genomic: TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAGgtggattaaa ... acatatgcagGAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGAC
EST: gi|148981581|gb|EE027738.2|EE027738
EST:     TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG                         GAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGAC
genomic: TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAGgtggattaaa ... acatatgcagGAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGAC
EST: gi|211005972|gb|FL170680.1|FL170680
EST:     TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG                         GAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGGA
genomic: TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAGgtggattaaa ... acatatgcagGAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTG-A
EST: gi|211005967|gb|FL170675.1|FL170675
EST:     TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG                         GAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGAC
genomic: TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAGgtggattaaa ... acatatgcagGAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGAC
EST: gi|50336378|gb|CO531504.1|CO531504
EST:     TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG                         GAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGAC
genomic: TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAGgtggattaaa ... acatatgcagGAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGAC
EST: gi|211005968|gb|FL170676.1|FL170676
EST:     TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG                         GAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGAC
genomic: TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAGgtggattaaa ... acatatgcagGAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGAC
EST: gi|211003194|gb|FL170674.1|FL170674
EST:     TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG                         GAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGAC
genomic: TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAGgtggattaaa ... acatatgcagGAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGAC
EST: gi|211005974|gb|FL170682.1|FL170682
EST:     TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG                         GAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGAC
genomic: TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAGgtggattaaa ... acatatgcagGAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGAC
EST: gi|211005971|gb|FL170679.1|FL170679
EST:     TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG                         GAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGAC
genomic: TTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAGgtggattaaa ... acatatgcagGAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGAC

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: 47 (upstream exon), 49 (downstream exon)
Score: 55

AAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAGgtggattaaa ... acatatgcagGAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGACCAATCAACTCGAGTCTGCAATGTGCTTGTACTCCTTAAG


Block sizes: 42 (upstream exon), 45 (downstream exon)
Score: 11

AAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAGgtggattaaa ... acatatgcagGAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGACCAATCAACTCGAGTCTGCAATGTGCTTGTACTCCTTAAG


Block sizes: 39 (upstream exon), 39 (downstream exon)
Score: 10

AAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAGgtggattaaa ... acatatgcagGAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGACCAATCAACTCGAGTCTGCAATGTGCTTGTACTCCTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

AAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAGgtggattaaa ... acatatgcagGAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGACCAATCAACTCGAGTCTGCAATGTGCTTGTACTCCTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacttgtgacatcatattaattcaagcctgtatggctacttgaaacatatgcagGAAATTGTGTCAATTTATCGATTACTTTCACCCCCACAATTATCTTTTGACCAATCAACTCGAGTCTGCAATGTGCTTGTACTCCTTAAG
               tattaat  putative branch site (score: 52)
           atcatattaattcaa  TA-rich tract