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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggctactcactggtttgtataatatactttgtttacatttattgcagagtcttctcgcagacttatgtactatatattcatatctattatgtcaatgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTTTCCAGTTTGGTGGAAATAATGTCATATTTGGTGGCAAGAAGGATGCACC

Basic information

species Zea mays
transcript GRMZM2G086484_T03
intron # 4
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|31351667|gb|CD436024.1|CD436024
EST:     ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTG                         GTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCACCTT
genomic: ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTGgtacggctac ... tgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTT
EST: gi|31361452|gb|CD445809.1|CD445809
EST:     ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTG                         GTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCACCTT
genomic: ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTGgtacggctac ... tgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTT
EST: gi|87156040|gb|DY400829.1|DY400829
EST:     ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTG                         GTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCACCTT
genomic: ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTGgtacggctac ... tgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTT
EST: gi|22546264|gb|BU098575.1|BU098575
EST:     ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTG                         GTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCACCTT
genomic: ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTGgtacggctac ... tgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTT
EST: gi|149014128|gb|EE043668.2|EE043668
EST:     CCGAACCTTTTTTCATCGCCTTCTCAGCNNNNNNNCACCAGATTACAGTG                         GTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCACCTT
genomic: CCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAA-CACCAGATTACAGTGgtacggctac ... tgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTT
EST: gi|94473209|gb|EB702167.1|EB702167
EST:     ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAA-CACCAGAATACAGTG                         GTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTT
genomic: ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTGgtacggctac ... tgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTT
EST: gi|76915806|gb|DV166129.1|DV166129
EST:     ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTG                         GTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAA
genomic: ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTGgtacggctac ... tgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAA
EST: gi|71311913|gb|DR792440.1|DR792440
EST:     ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTG                         GTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTT
genomic: ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTGgtacggctac ... tgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTT
EST: gi|13558335|gb|BG549691.1|BG549691
EST:     ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTG                         GTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTT
genomic: ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTGgtacggctac ... tgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTT
EST: gi|40334296|gb|CK368366.1|CK368366
EST:     ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTG                         GTATGTTTGCTGACAAGAAGAACACGTCCAGTGATTGCAGTAAACCAGCTT
genomic: ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTGgtacggctac ... tgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTT
EST: gi|88757793|gb|DY541934.1|DY541934
EST:     ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTG                         GTATGTTTGCTGACAAG
genomic: ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTGgtacggctac ... tgacatccagGTATGTTTGCTGACAAG
EST: gi|26558697|gb|CA830932.1|CA830932
EST:     ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTG                         GTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCACCTT
genomic: ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTGgtacggctac ... tgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTT
EST: gi|78105254|gb|DV523672.1|DV523672
EST:     ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTG                         GTATGTTTGCTGACAAGAAGAACACGTTCAGTGATAGCAGTAAACCA
genomic: ACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTGgtacggctac ... tgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCA

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), 42 (downstream exon)
Score: 168

AAGGCTCCAATTATGGCTTCTAGTTCTTCATCTTTTCAGAACTCAAGCTTACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTGgtacggctac ... tgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTTTCCAGTTTGGTGGAAATAATGTCATATTTGGTGGCAAGAAGGATGCACC


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 112

AAGGCTCCAATTATGGCTTCTAGTTCTTCATCTTTTCAGAACTCAAGCTTACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTGgtacggctac ... tgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTTTCCAGTTTGGTGGAAATAATGTCATATTTGGTGGCAAGAAGGATGCACC


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 101

AAGGCTCCAATTATGGCTTCTAGTTCTTCATCTTTTCAGAACTCAAGCTTACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTGgtacggctac ... tgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTTTCCAGTTTGGTGGAAATAATGTCATATTTGGTGGCAAGAAGGATGCACC


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 64

AAGGCTCCAATTATGGCTTCTAGTTCTTCATCTTTTCAGAACTCAAGCTTACCGAACCTTTTTTCATCGCCTTCTCAGCAAAAAACACCAGATTACAGTGgtacggctac ... tgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTTTCCAGTTTGGTGGAAATAATGTCATATTTGGTGGCAAGAAGGATGCACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctcgcagacttatgtactatatattcatatctattatgtcaatgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTTTCCAGTTTGGTGGAAATAATGTCATATTTGGTGGCAAGAAGGATGCACC
            ttatgtactatatatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggctactcactggtttgtataatatactttgtttacatttattgcagagtcttctcgcagacttatgtactatatattcatatctattatgtcaatgacatccagGTATGTTTGCTGACAAGAAGAACACGTCCAGTGATAGCAGTAAACCAGCTTTCCAGTTTGGTGGAAATAATGTCATATTTGGTGGCAAGAAGGATGCACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG