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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtatgccgctgctcaacagactttttgatggaagatctgcaatcatttttgtggattgcatttacactcttttttttttgcctttttgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG

Basic information

species Zea mays
transcript GRMZM5G845755_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G845755_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 7
gtaaagtatgccgctgctcaacagactttttgatggaagatctgcaatcatttttgtggattgcatttacactcttttttttttgcctttttgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG
||| | |      |   |  | |     |   ||| |||| ||  | |  ||  | || |||  | ||      |||||||||            ||||||||| ||||||||||| ||| |||||||||||||||| ||||||||||| ||||| || |  |||
gtata-tgaattacaatt--atatgtgatgcaatgcaagacctctagtt-ttaatatgaattaaaattttgacatttttttttcat---------atgcagGCACAGCAGGAAACCTTGGTCAAAGTTTATTAATGCTGACAACCAACATCTAGTATCCCCAGAG
















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|6465600|gb|AW191195.1|AW191195
EST:     -ACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|5846756|gb|AI999839.1|AI999839
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|32846294|gb|CD985975.1|CD985975
EST:     ACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: ACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|194717129|gb|FK934282.1|FK934282
EST:     GTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: GTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|29945847|gb|CB815850.1|CB815850
EST:     AGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|94476026|gb|EB704984.1|EB704984
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|31359089|gb|CD443446.1|CD443446
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|60354727|gb|DN221700.1|DN221700
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|32849734|gb|CD989415.1|CD989415
EST:     ACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATACAGACAACCAACACCT
genomic: ACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|60345260|gb|DN212233.1|DN212233
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|4609748|gb|AI600587.1|AI600587
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|60350778|gb|DN217751.1|DN217751
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|61117731|gb|DN558692.1|DN558692
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|61117730|gb|DN558691.1|DN558691
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|113626902|gb|DW790797.1|DW790797
EST:     TTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: TTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|61117732|gb|DN558693.1|DN558693
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|113860692|gb|DW979642.1|DW979642
EST:     CTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAAAGCAGACAACCAACACCT
genomic: CTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|61117733|gb|DN558694.1|DN558694
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|148990947|gb|EE032376.2|EE032376
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACCCCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT

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: 387

GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 243

GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatttttgtggattgcatttacactcttttttttttgcctttttgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG
                 catttacactcttttt  CT-rich tract
                        actctttttttttt  TA-rich tract