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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTTCTTACTTGGTCTTGTCTATGCGGCAGTGACACCATTTTTGCTCCCTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagcatatcataaatgtcctcatgtgttttctttagcattgcatctggcattgtgttgtttatcgtgctgtgctacatttgcatgcgcataattatacatattagttagtgtgttgcatttgtttggttagaaattgacttaccctgatgcataacttacacagcttaactgtttcag

Basic information

species Zea mays
transcript GRMZM2G064189_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064189_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g35050.4 (Oryza sativa), 5'ss of exon 10
GTATTTCTTACTTGGTCTTGTCTATGCGGCAGTGACACCATTTTTGCTCCCTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagcatatcataaatgtcctcatgtgttttctttagcattgcatctggcattgtgttgtttatcgtgctgtgctacatttgcatgcgcataattatacatattagttagtgtgttgcatttgtttggttagaaattgacttaccctgatgcataacttacacagcttaactgtttcag
|||||||| || || ||||||||||| | ||||||||||||||||| ||||| |||| |||||||||||||| || || || |||||||| |||||||||| || | | | | | | | || | | || | | ||| | || | | | || || | | | || ||||| |
CTATTTCTTGCTCGGACTTGTCTATGCTGTGGTGACACCATTTTTGCTTCCTTTCATATTAATATTCTTTGGGTTAGCATATGTGGTATACCGTCACCAGgtaa-taaccctttggaacactttgtgatttttagcactttgtgattaatcatgaatctgtccatcttttgttttggggtgc---caagtgaaagtaattcttg--------------------------------------------------------------------------------
















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|78021094|gb|DV489481.1|DV489481
EST:     TGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: TGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|5846752|gb|AI999835.1|AI999835
EST:     CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|5847484|gb|AW000563.1|AW000563
EST:     CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|40336310|gb|CK370380.1|CK370380
EST:     CTTTTGTATTGGTATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|5055562|gb|AI734449.1|AI734449
EST:     CTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|211159706|gb|FL164258.1|FL164258
EST:     CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|67022912|gb|CO451661.1|CO451661
EST:     CTTTTGTATTGATATTCTTTGGGGTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|37392989|gb|CF633749.1|CF633749
EST:     CTTTTGTATTGGTATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|74035115|gb|DT535605.1|DT535605
EST:     CTTTTGTATTGGTATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAAGGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|211159704|gb|FL164256.1|FL164256
EST:     CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|60338400|gb|DN205373.1|DN205373
EST:     CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA

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: 100

GTATTTCTTACTTGGTCTTGTCTATGCGGCAGTGACACCATTTTTGCTCCCTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

GTATTTCTTACTTGGTCTTGTCTATGCGGCAGTGACACCATTTTTGCTCCCTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 224

GTATTTCTTACTTGGTCTTGTCTATGCGGCAGTGACACCATTTTTGCTCCCTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

GTATTTCTTACTTGGTCTTGTCTATGCGGCAGTGACACCATTTTTGCTCCCTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC