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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttctttacacctgatgatccatctggcctttccctcaacggtcaatgcccatcacctttcatgaattatagaacactactaatgttttgttgctgacccactgtgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTTTTCCCTGATGCATCACGTTGTCATGGGTGATGATCCAGAGGTGAAGGCT

Basic information

species Zea mays
transcript GRMZM2G102231_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102231_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g14580.1 (Oryza sativa), 3'ss of exon 3
gtaagtt--tctttacacctgatg-atccatctg-gcctttccctcaacggtc--aatgcccatcacctttcatgaattatagaacactactaatgttttgttgctgacccactgtgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTTTTCCCTGATGCATCACGTTGTCATGGGTGATGATCCAGAGGTGAAGGCT
|||| ||   | | |   |  ||  ||   |||| | |||   | | | | ||   |||  |        |    ||||| |    |  ||   || || |||  |     | |||| ||| ||||||||| ||||| |||||||| |||||||| ||||| ||| ||||||||||| | |||||||| || ||||| ||||| ||||||||||| |||||| ||
gtaatttatccatgatgaccaatatattgctctgagtcttgtgcactatgttcctgatgaaccctgtgcctttcaaattaga----atcacgtttgattcgttctttcttta-tgtggctt-cagATCCCACAAACGTCATTTTGCCCTGAAGACGCAGAACCACAAGGAAATGTTTACACTGATGCACCATGTTGTGATGGGGGATGATCCAGATGTGAAGACT
















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|211004136|gb|FL435012.1|FL435012
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|211016904|gb|FL048021.1|FL048021
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|14245028|gb|BG842966.2|BG842966
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|71438331|gb|DR819381.1|DR819381
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|50325634|gb|CO520760.1|CO520760
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|50338089|gb|CO533215.1|CO533215
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|44901216|gb|CK827761.1|CK827761
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTCGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|5649953|gb|AI920313.1|AI920313
EST:     ATCTT-ATGCCAA-GGAG-ACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: ATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
EST: gi|149013686|gb|EE043136.2|EE043136
EST:     TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGG                         ATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT
genomic: TTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTT

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), 49 (downstream exon)
Score: 31

GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTTTTCCCTGATGCATCACGTTGTCATGGGTGATGATCCAGAGGTGAAGGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTTTTCCCTGATGCATCACGTTGTCATGGGTGATGATCCAGAGGTGAAGGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 58

GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTTTTCCCTGATGCATCACGTTGTCATGGGTGATGATCCAGAGGTGAAGGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 36

GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTGTTGCGACAGGgtaagtttct ... tgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTTTTCCCTGATGCATCACGTTGTCATGGGTGATGATCCAGAGGTGAAGGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgaattatagaacactactaatgttttgttgctgacccactgtgtcttacagATCCCATAAACGCCATTTTGCACTGAAGACCCAGAATCACCAGGAAATGTTTTCCCTGATGCATCACGTTGTCATGGGTGATGATCCAGAGGTGAAGGCT
     aattatagaa  TA-rich tract