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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgcatactccatttatcccgcatggggattttgtttgtttcaattgcttttctcacccatgagaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTAATCTCACGTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGA

Basic information

species Zea mays
transcript GRMZM2G160958_T01
intron # 5
splice site 3'
intron type U2

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|87156312|gb|DY401101.1|DY401101
EST:     AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAA                         GAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGG
genomic: AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAGgtattgcata ... agaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGG
EST: gi|20802444|gb|BQ293494.1|BQ293494
EST:     AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAG                         GAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
genomic: AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAGgtattgcata ... agaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
EST: gi|37398767|gb|CF636701.1|CF636701
EST:     AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAG                         GAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
genomic: AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAGgtattgcata ... agaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
EST: gi|61119151|gb|DN560112.1|DN560112
EST:     AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAG                         GAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
genomic: AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAGgtattgcata ... agaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
EST: gi|60352451|gb|DN219424.1|DN219424
EST:     AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAG                         GAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
genomic: AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAGgtattgcata ... agaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
EST: gi|149090595|gb|EE179908.2|EE179908
EST:     AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAG                         GAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
genomic: AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAGgtattgcata ... agaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
EST: gi|78543710|gb|DV621208.1|DV621208
EST:     AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAG                         GAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
genomic: AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAGgtattgcata ... agaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
EST: gi|78108033|gb|DV526451.1|DV526451
EST:     AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAG                         GAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
genomic: AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAGgtattgcata ... agaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
EST: gi|113702255|gb|EE679759.1|EE679759
EST:     AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAG                         GAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
genomic: AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAGgtattgcata ... agaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
EST: gi|32912724|gb|CF017536.1|CF017536
EST:     AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAG                         GAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
genomic: AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAGgtattgcata ... agaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
EST: gi|71328875|gb|DR801120.1|DR801120
EST:     AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAG                         GAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
genomic: AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAGgtattgcata ... agaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
EST: gi|76291051|gb|DV030619.1|DV030619
EST:     GTTCATCAGTCGGAAG                         GAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
genomic: GTTCATCAGTCGGAAGgtattgcata ... agaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
EST: gi|78115180|gb|DV533568.1|DV533568
EST:     AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAG                         GAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA
genomic: AATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAGgtattgcata ... agaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTA

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), 48 (downstream exon)
Score: 201

CCTAAAGAAGAGCAATTCCAATGGCCTTCTTTATGGTCTCATTTCTTTCCAATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAGgtattgcata ... agaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTAATCTCACGTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 97

CCTAAAGAAGAGCAATTCCAATGGCCTTCTTTATGGTCTCATTTCTTTCCAATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAGgtattgcata ... agaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTAATCTCACGTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 115

CCTAAAGAAGAGCAATTCCAATGGCCTTCTTTATGGTCTCATTTCTTTCCAATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAGgtattgcata ... agaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTAATCTCACGTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 121

CCTAAAGAAGAGCAATTCCAATGGCCTTCTTTATGGTCTCATTTCTTTCCAATCTTCCCCCCACAGAGACAAGGGTAGCAAATGGTTCATCAGTCGGAAGgtattgcata ... agaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTAATCTCACGTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccgcatggggattttgtttgtttcaattgcttttctcacccatgagaaatacagGAATGGCCCTTCGACATGTACCCGCCATGGGCTCATGGCCCTGGATACGTAATCTCACGTGACATCGCTAAGTTTGTAGTCCAAGGCCACCAGGAACTGA
                                 ttctcac  putative branch site (score: 121)
           attttgttt  TA-rich tract