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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgagccatcttgcatgaatttcacctctctactatctctctccgttaaggcatgaacgatccacttaccttgcattcatctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGCCCCCGGAGGGCCAACCTTCGTCCCACTCCAGCGTTCCACAGGAAAAATA

Basic information

species Zea mays
transcript GRMZM2G375904_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375904_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os05g43570.3 (Oryza sativa), 3'ss of exon 13
gtaatgagccatcttgc-atgaatttcacctctctactatctctctccgttaaggcatgaacgatccacttaccttgcattcatctctgaa-cagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGCCCCC---GGAGGGCCAACCTTCGTCCCACTCCAGCGTTCCACAGGAAAAATA
||| |||||  | ||   |   |||    |  | ||| | |     |||||      |  | |||    ||| ||||| || |||  | || ||||||| ||||| ||||| |||||||||||||| |||||||||| |||||||||||    |||||| |||||||| || ||||||| | ||||||  ||| |   
gtattgagcactattattacctattggttccttatac-accatgtaccgttt-----ttcatgatatgtttaacttgcttttatccttaaaacagAGAGCATGGATGAAGATGAGCCTGTTCAAGGAAGTTTCTTAAATATGTTGCCCCATAAGGAGGGGCAACCTTCATCTCACTCCACCATTCCACCAGAACA---
















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|5895617|gb|AW036863.1|AW036863
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTG                         AGAGGATGGACGGAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
EST: gi|28187719|gb|CB179329.1|CB179329
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTG                         AGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
EST: gi|5901099|gb|AW042199.1|AW042199
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTG                         AGAGGATGGACGGAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
EST: gi|33285627|gb|CF075422.1|CF075422
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTG                         AGAGGATGGACNAAGAGGAGCCTGTTCA-GGGA
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGA
EST: gi|211195854|gb|FL001022.1|FL001022
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTG                         AGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
EST: gi|32934179|gb|CF038991.1|CF038991
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGGCCAACCATCAAGACAATGTTTG                         AGAGGATGGACGGAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
EST: gi|149049839|gb|EE048526.2|EE048526
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTG                         AGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
EST: gi|32870336|gb|CF010018.1|CF010018
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTG                         AGAGGATGGACGGAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTAT
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTAT
EST: gi|5597186|gb|AI891179.1|AI891179
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTG                         AGAGGATGGACGGAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC

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), 47 (downstream exon)
Score: 125

CAGAGTTGAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGCCCCCGGAGGGCCAACCTTCGTCCCACTCCAGCGTTCCACAGGAAAAATA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 186

CAGAGTTGAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGCCCCCGGAGGGCCAACCTTCGTCCCACTCCAGCGTTCCACAGGAAAAATA


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

CAGAGTTGAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGCCCCCGGAGGGCCAACCTTCGTCCCACTCCAGCGTTCCACAGGAAAAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 226

CAGAGTTGAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGCCCCCGGAGGGCCAACCTTCGTCCCACTCCAGCGTTCCACAGGAAAAATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctctccgttaaggcatgaacgatccacttaccttgcattcatctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGCCCCCGGAGGGCCAACCTTCGTCCCACTCCAGCGTTCCACAGGAAAAATA
                           cacttac  putative branch site (score: 226)
                                        ttcatctct  putative PPT