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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTCCCTAGACCCCAAGCAATTCTTGGGTGTTGCTTCAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttgtctgtctatctgtgacagcatgagaatctgtcccaatcttcgcaacttacaggttttcatcctgaactttttcag

Basic information

species Zea mays
transcript GRMZM2G147191_T02
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147191_T02 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os09g28570.1 (Oryza sativa), 5'ss of exon 17
GTTTCCCTAGACCCCAAGCAATTCTTGGGTGTTGCTTCAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttgtctgtctatctgtgacagcatgagaatctgtcccaatcttcgcaa-------cttacaggttttcatcctg-aactttttcag
|||||||| ||||| ||| ||||| ||||||| ||||| |     |||||||| ||||||||||||||||||||||||||||||||||||  | | |  | |       |||    ||  || ||||| |  |||||| |||        | | || ||||  | ||| ||| ||| |||
GTTTCCCTTGACCCGAAGAAATTCGTGGGTGTAGCTTCTGCGCCTGATGCGGTAGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtacca-tcgcttat------atgatgaaatatgattctgttcttatcttctcaaatgtgacttaatagatttttcttctggaacctttccag
















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|76282583|gb|DV022151.1|DV022151
EST:     CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
genomic: CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttg ... actttttcagGTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
EST: gi|76282582|gb|DV022150.1|DV022150
EST:     CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
genomic: CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttg ... actttttcagGTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
EST: gi|211538275|gb|FL465653.1|FL465653
EST:     CAGTCGTAGATGCGGTCGAATATYTTCATTCTGGCAARAGTGTTGGCAAG                         GTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
genomic: CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttg ... actttttcagGTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
EST: gi|211530863|gb|FL078324.1|FL078324
EST:     CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
genomic: CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttg ... actttttcagGTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
EST: gi|58029381|gb|CX724808.1|CX724808
EST:     CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
genomic: CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttg ... actttttcagGTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
EST: gi|6672154|gb|AW282329.1|AW282329
EST:     CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
genomic: CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttg ... actttttcagGTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
EST: gi|13557631|gb|BG548987.1|BG548987
EST:     CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
genomic: CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttg ... actttttcagGTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
EST: gi|211368048|gb|FL471710.1|FL471710
EST:     CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
genomic: CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttg ... actttttcagGTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
EST: gi|91868064|gb|EB399901.1|EB399901
EST:     CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
genomic: CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttg ... actttttcagGTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
EST: gi|101384702|gb|EB814397.1|EB814397
EST:     CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
genomic: CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttg ... actttttcagGTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
EST: gi|60357940|gb|DN224913.1|DN224913
EST:     CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
genomic: CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttg ... actttttcagGTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
EST: gi|16380053|gb|BI993288.1|BI993288
EST:     CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAG                         GTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA
genomic: CAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttg ... actttttcagGTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAA

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), 48 (downstream exon)
Score: 149

GTTTCCCTAGACCCCAAGCAATTCTTGGGTGTTGCTTCAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttg ... actttttcagGTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAATCCATGGACATGATGCGCATTGTCTTCCATGGTCACGTAGGTTATTGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 334

GTTTCCCTAGACCCCAAGCAATTCTTGGGTGTTGCTTCAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttg ... actttttcagGTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAATCCATGGACATGATGCGCATTGTCTTCCATGGTCACGTAGGTTATTGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 412

GTTTCCCTAGACCCCAAGCAATTCTTGGGTGTTGCTTCAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttg ... actttttcagGTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAATCCATGGACATGATGCGCATTGTCTTCCATGGTCACGTAGGTTATTGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 735

GTTTCCCTAGACCCCAAGCAATTCTTGGGTGTTGCTTCAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttg ... actttttcagGTCGTTGTGTGTATTGATCCATCATACGGTCAGATCGTTGCAAAATTATAATCCATGGACATGATGCGCATTGTCTTCCATGGTCACGTAGGTTATTGTC


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTCCCTAGACCCCAAGCAATTCTTGGGTGTTGCTTCAGTCGTAGATGCGGTCGAATATCTTCATTCTGGCAAGAGTGTTGGCAAGgtataagttgtctgtctatctgtgacagcatgagaatctgtcccaatcttcgcaacttacaggttttcatcctgaactttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA