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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGTCTGAAGGTTGCCATGATGAGTCCTGGTTTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttctttcagtatatatttcgaccacgtgtgattctgattatgcttaggccccgtttgtttcgttggaattgaattctattttaataattataattt...

Basic information

species Zea mays
transcript GRMZM2G111713_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111713_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g45300.1 (Oryza sativa), 5'ss of exon 5
GTTGGTCTGAAGGTTGCCATGATGAGTCCTGGTTTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttctttcagtatatatttcgaccacgtgtgattctgattatgcttaggccccgtttgtttcgttggaattgaattctattttaataattataattt
|| ||| ||||||||| ||||||||| |||||||| ||||||||||| ||||||   |||||||  || ||||||||||||||||     || || | ||||||| ||||   | || ||    | | |    |   |  |  ||  |||   |||  |  | ||  |   |||| |      
GTCGGTATGAAGGTTGTCATGATGAGCCCTGGTTTTGTATATGAGCCATACAGCATTCGGGAACCAATCCCCTTCTGGAAAAGgtgaaa-ttacattctatattttgacctt-tatgcttt--gtcacgt---gaatcaatacgta-cgt--aaatcaatctgtacat-ggtaatcag-----
















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|211131767|gb|FL358660.1|FL358660
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
EST: gi|211177445|gb|FL359118.1|FL359118
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
EST: gi|211361987|gb|FL325579.1|FL325579
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTCTACACTAAGTGGCTGGAGAAGGACAAAGGAG
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTT-TACACTAAGTGGCTGGAGAAGGACAAAGGAG
EST: gi|211093125|gb|FL308869.1|FL308869
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTG
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTG
EST: gi|211532039|gb|FL347052.1|FL347052
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGT
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGT
EST: gi|71443106|gb|DR824156.1|DR824156
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
EST: gi|50337823|gb|CO532949.1|CO532949
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
EST: gi|211043460|gb|FL324042.1|FL324042
EST:     TTCGTATATGAGCCGTACAGCCCACGGGA-CGCATTCC-TTCTGGGAAAG                         ATGGTTTACACTA
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTA
EST: gi|101389514|gb|EB816695.1|EB816695
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
EST: gi|211526596|gb|FL367655.1|FL367655
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAGGACAA-GGAGGACATCA
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCA
EST: gi|61119623|gb|DN560584.1|DN560584
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
EST: gi|211208019|gb|FL322438.1|FL322438
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
EST: gi|211140827|gb|FL324953.1|FL324953
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCTCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAG
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAG
EST: gi|211442630|gb|FL341621.1|FL341621
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAA-G                         ATGGTTTACCCTTAGTGGCTGGAGAAAGACAAAGGAGGACATCATTTTTGG
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTT-GG
EST: gi|89758224|gb|DY687488.1|DY687488
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
EST: gi|88758133|gb|DY542274.1|DY542274
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
EST: gi|211061706|gb|FL341836.1|FL341836
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAAGGACAA-GGAGGACATCATTTTGG
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAA-GGACAAAGGAGGACATCATTTTGG
EST: gi|148938688|gb|EC883024.2|EC883024
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
EST: gi|71420010|gb|DR804975.1|DR804975
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
EST: gi|211412583|gb|FL353839.1|FL353839
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAGGACAAAG
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAG
EST: gi|148989211|gb|EE031705.2|EE031705
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
EST: gi|32913045|gb|CF017857.1|CF017857
EST:     TTCGTATATGAGCCGTACAGGCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
EST: gi|91048124|gb|EB158542.1|EB158542
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
EST: gi|76923558|gb|DV169546.1|DV169546
EST:     TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAG                         ATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA
genomic: TTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGA

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: 47 (upstream exon), 49 (downstream exon)
Score: 86

GTTGGTCTGAAGGTTGCCATGATGAGTCCTGGTTTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 46

GTTGGTCTGAAGGTTGCCATGATGAGTCCTGGTTTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 45

GTTGGTCTGAAGGTTGCCATGATGAGTCCTGGTTTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 85

GTTGGTCTGAAGGTTGCCATGATGAGTCCTGGTTTCGTATATGAGCCGTACAGCCCACGGGAACGCATTCCCTTCTGGAAAAGgtttttcttt ... tgtgaattagATGGTTTACACTAAGTGGCTGGAGAAGGACAAAGGAGGACATCATTTTGGAG