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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGTTCGCCAATCATTTGATGTGATTGTCAATGGAATTGAGCAATGCATTGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaattatgtctgctttctgggacaattagattttctcaaacactaccgaaataatttagcattttttaaatccattcagttatcctctaatttaa...

Basic information

species Zea mays
transcript GRMZM2G180732_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180732_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g43520.2 (Oryza sativa), 5'ss of exon 3
TTTGTTCGCCAATCATTTGATGTGATTGTCAATGGAATTGAGCAATGCATTGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaattatgtctgctttctgggacaattagattttctcaaa--cactaccgaaataa--tttagcattttttaaatccat---tcagttatcctctaatttaa
|||||||||||||| |||||||| |||||  |||| || |||||| |||||||||||||||| ||||| ||||  ||||||||||| | |||||| |||||||||||||||  | |  |   |||   |   |   |||  ||||  | |  ||| |   |  ||| ||   | || |||  ||   | | |||  || |       
TTTGTTCGCCAATCCTTTGATGTAATTGTTGATGGCATCGAGCAAAGCATTGTTGAAGCTCATAACAACCTCCGTCCTGGGAAAATATTTGTGAATAAAGgtataaaattagcttt--tgcttggactagccaaggttttccaaaaccgcctccggagccaatttttgctgctgtttaattaatgagtaaattacactttgg-----
















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|71321470|gb|DR797436.1|DR797436
EST:     TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAG                         GTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCT
genomic: TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCT
EST: gi|211192374|gb|FL184214.1|FL184214
EST:     TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAG                         GTGACATCCTTGATGCCGGTGTGAATCG
genomic: TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCG
EST: gi|211298319|gb|FL250320.1|FL250320
EST:     TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAG                         GTGACATCCTTGATGCCGGTGTGAATCGCAGCCCAAGTGCATACCTAAATA
genomic: TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
EST: gi|74240745|gb|DT648659.1|DT648659
EST:     TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAG                         GTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
genomic: TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
EST: gi|211189959|gb|FL184194.1|FL184194
EST:     TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAG                         GTGACATCCTTGATGCCGGTGTGAATCGCAGCCCAAGTGCATACCTAAATA
genomic: TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
EST: gi|211189960|gb|FL184195.1|FL184195
EST:     TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAG                         GTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
genomic: TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
EST: gi|211298318|gb|FL250319.1|FL250319
EST:     TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAG                         GTGACATCCTTGATGCCGGTGTGAATCGCAGCCCAAGTGCATACCTAAATA
genomic: TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
EST: gi|211192371|gb|FL184211.1|FL184211
EST:     TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAG                         GTGACATCCTTGATGCCGGTGTGAATCGCANCCCAAGTGCATACCTAAATA
genomic: TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
EST: gi|71426638|gb|DR807688.1|DR807688
EST:     TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAG                         GTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
genomic: TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
EST: gi|211192367|gb|FL184207.1|FL184207
EST:     TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAG                         GTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
genomic: TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
EST: gi|71323344|gb|DR798328.1|DR798328
EST:     TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAG                         GTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
genomic: TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
EST: gi|211189962|gb|FL184197.1|FL184197
EST:     TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAG                         GTGACATCCTTGATGCCGGTGTGAATCGCAGCCCAAGTGCATACCTAAATA
genomic: TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
EST: gi|211189967|gb|FL184202.1|FL184202
EST:     TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAG                         GTGACATCCTTGATGCCGGTGTGAATCGCAGCCCAAGTGCATACCTAAATA
genomic: TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
EST: gi|211189964|gb|FL184199.1|FL184199
EST:     TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAG                         GTGACATCCTTGATGCCGGTGTGAATCGCAGCCCAAGTGCATACCTAAATA
genomic: TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
EST: gi|31363574|gb|CD447931.1|CD447931
EST:     TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAG                         GTGACCTCCTTGATGCCGGTGTGAATCGCAGCCCAAGTGCATATCTAAATA
genomic: TGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATA

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), 49 (downstream exon)
Score: 147

TTTGTTCGCCAATCATTTGATGTGATTGTCAATGGAATTGAGCAATGCATTGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATAACCCCGCTGAAGAGAGAGGCAAGTATAAGTACAATGTTGATAAAGAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

TTTGTTCGCCAATCATTTGATGTGATTGTCAATGGAATTGAGCAATGCATTGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATAACCCCGCTGAAGAGAGAGGCAAGTATAAGTACAATGTTGATAAAGAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

TTTGTTCGCCAATCATTTGATGTGATTGTCAATGGAATTGAGCAATGCATTGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATAACCCCGCTGAAGAGAGAGGCAAGTATAAGTACAATGTTGATAAAGAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 420

TTTGTTCGCCAATCATTTGATGTGATTGTCAATGGAATTGAGCAATGCATTGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaatt ... tgattttcagGTGACCTCCTTGATGCCAGTGTGAATCGCAGCCCAAGTGCATATCTAAATAACCCCGCTGAAGAGAGAGGCAAGTATAAGTACAATGTTGATAAAGAAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGTTCGCCAATCATTTGATGTGATTGTCAATGGAATTGAGCAATGCATTGTTGAAGCTCACAACAATCTCCACCCTGGGAAAATCTATGTGAACAAAGgtataaaattatgtctgctttctgggacaattagattttctcaaacactaccgaaataatttagcattttttaaatccattcagttatcctctaatttaa

- - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA