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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcatatcttctgacataataaaaaatttcatgctaccaatactggatgcttcttacatatgactgattcacttttcatgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT

Basic information

species Zea mays
transcript GRMZM2G098569_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 4
gtaa-tcatatcttctgacataataaaaaatttcatgctaccaatactggatgcttcttacatatgactgattcacttttcatgtttt--cagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT
|||| |  |||||||||||||   | | | | |   |  |  ||||||| | ||||||  |  ||| |   ||   | ||  ||||||   |||||||||| ||||| |||||||| ||| ||||||||||||| ||||| || ||||| ||||||||||| || || || |||||||||||
gtaagttgtatcttctgacatg-cacatattgttgggaaaaaaatactgtacgcttctccctgatgcccagttgtatgtttttgttttgttagGTTGAGTTTAAGACTGCTTCAGGTCAATTGTTGGATCTTATTACTACTCATGAGGGAGAAAAGGATCTCACAAAGTACAACTTGACAGT
















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|76293424|gb|DV032992.1|DV032992
EST:     ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
EST: gi|71306846|gb|DR789579.1|DR789579
EST:     ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
EST: gi|76293423|gb|DV032991.1|DV032991
EST:     CTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: CTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
EST: gi|211448759|gb|FL324438.1|FL324438
EST:     ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
EST: gi|148951738|gb|EC897493.2|EC897493
EST:     ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGGTGGATCTTATCACTAC
genomic: ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTAC
EST: gi|149100779|gb|EE186873.2|EE186873
EST:     ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
EST: gi|148950117|gb|EC895653.2|EC895653
EST:     ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
EST: gi|71310911|gb|DR791758.1|DR791758
EST:     ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
EST: gi|211504975|gb|FL314285.1|FL314285
EST:     ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
EST: gi|71310909|gb|DR791757.1|DR791757
EST:     AAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAG                         GTAGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: AAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
EST: gi|148964886|gb|EE015748.2|EE015748
EST:     ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
EST: gi|78117582|gb|DV535969.1|DV535969
EST:     ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAG                         GTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC
genomic: ACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCAC

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), 49 (downstream exon)
Score: 111

AAATGATGGGATTATCCTTCGCAATCATATCTCACGAATCCTTCAACGCCACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 562

AAATGATGGGATTATCCTTCGCAATCATATCTCACGAATCCTTCAACGCCACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 488

AAATGATGGGATTATCCTTCGCAATCATATCTCACGAATCCTTCAACGCCACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 191

AAATGATGGGATTATCCTTCGCAATCATATCTCACGAATCCTTCAACGCCACTTCAAAGGAAAGCCATATTATGTTGATATCATTGACTTGTTCAACGAGgtaatcatat ... atgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctaccaatactggatgcttcttacatatgactgattcacttttcatgttttcagGTTGAGTTCAAGACAGCTTCAGGGCAAATGTTGGATCTTATCACTACCCACGAGGGTGAAAAGGATCTAACTAAATATAACTTGACAGT
                                       cttttcatgttttc  CT-rich tract
                     ttacatat  TA-rich tract