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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgatgaaattataatgttcttttgtactggcattatcttagctgagcttacatttttttcttttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAAACCGATGACATACTGATAGGGGACAGTCAAAGTAGTTGGAATTGGAACC

Basic information

species Zea mays
transcript GRMZM2G152319_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152319_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g13790.1 (Oryza sativa), 3'ss of exon 12
gtacttgatgaaattataatgttcttttgtactggcattatcttagctgagcttacatttt-----tttcttttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAAACCGATGACATACTGATAGGGGACAGTCAAAGTAGTTGGAATTGGAACC
|||||  |  ||  |   ||       |||  |    | ||  | |    ||| | |  |      | |  | || || |||||||||||||| |||||| ||||||||||||||||| ||| || ||| ||  | |||||| ||||  |||||||||| || | |||||||||  | |   
gtactatacaaatgtcctatccatacctgttttcttttcatggt-gtaatgctcataactaaacaatcttctctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCATGCTGATGACTTACTCCTAGGGGACAGCCAGAATAGTTGGAACCGCATGA

upper sequence: GRMZM2G152319_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g56234.2 (Oryza sativa), 3'ss of exon 12
gtacttgatgaa-attataatgtt--cttttgta----ctggcattatct--tagctgagcttacatttt----tttcttttctt--ggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAAACCGATGACATACTGATAGGGGACAGTCAAAGTAGTTGGAATTGGAACC
||||| ||   | ||  ||    |  || || ||    || | || ||||   | |  || | | |  ||    | |||| ||||  |  || |||||||||| |||||||||||||| || |||||  |||||||||| ||| | || ||| ||||  |||| |||||||| | |||||||||| | |   
gtactagacagatatcctatccctgcctgttttagtttctagtataatctatcaacacagatcataacttactatgtcttctctttggatagGCTGATTCACTTGGACCACTGGACTTAGAGATACCATCCGTGAGATACCAAGCTGAGGACTTACTCTTAGGAGACAGTCAGAATAGTTGGAATCGCATGA
















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|6022224|gb|AW067152.1|AW067152
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|6952326|gb|AW424394.1|AW424394
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCTGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|6195038|gb|AW147142.1|AW147142
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCTGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|6827796|gb|AW331439.1|AW331439
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCTGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|6166619|gb|AW144883.1|AW144883
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCTGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|21987664|gb|BQ779192.1|BQ779192
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|6057103|gb|AW091508.1|AW091508
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|32945441|gb|CF050260.1|CF050260
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCTGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|71431160|gb|DR812210.1|DR812210
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|78025210|gb|DV493597.1|DV493597
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|6166618|gb|AW144882.1|AW144882
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCTGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|93281627|gb|EB673891.1|EB673891
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 79

TGATGACGCCAAAGACGAAGAGGAGTTTTATGCTAAATCACCACCTCGAAATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAAACCGATGACATACTGATAGGGGACAGTCAAAGTAGTTGGAATTGGAACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 59

TGATGACGCCAAAGACGAAGAGGAGTTTTATGCTAAATCACCACCTCGAAATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAAACCGATGACATACTGATAGGGGACAGTCAAAGTAGTTGGAATTGGAACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 91

TGATGACGCCAAAGACGAAGAGGAGTTTTATGCTAAATCACCACCTCGAAATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAAACCGATGACATACTGATAGGGGACAGTCAAAGTAGTTGGAATTGGAACC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 55

TGATGACGCCAAAGACGAAGAGGAGTTTTATGCTAAATCACCACCTCGAAATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAAACCGATGACATACTGATAGGGGACAGTCAAAGTAGTTGGAATTGGAACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttgtactggcattatcttagctgagcttacatttttttcttttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAAACCGATGACATACTGATAGGGGACAGTCAAAGTAGTTGGAATTGGAACC
                           agcttac  putative branch site (score: 55)
                             cttacatttttttctt  CT-rich tract
                              ttacatttttttcttt  TA-rich tract