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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCTCGAGCTCGGCAAGAGCGGCAAGGACCGCGTCGCCACTACCTCCGCCTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctccttcccttctcttgttcggttcctcgtttagatctgcgaacgctgtggtggttctgaatgatgatggttgggacggattcgtgcag

Basic information

species Zea mays
transcript GRMZM2G077669_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077669_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA04G41090.1 (Glycine max), 5'ss of exon 1
GGGCTCGAGCTCGGCAAGAGCGGCAAGGACCGCGTCGCCACTACCTCCGCCTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctccttcccttctcttgttcggttcctcgtttagatctgcgaacgctgtggtggttctgaatgatgatggttggga--cggattcgtgcag-------
|   | |||||  |||||| |  |||||| ||  ||  |||  | ||||| ||||| |||||||||||||||||| |||||||||| |||||||||||| ||||    ||  || |||||||   |  | ||  |  | |||||| |   |  | |  | | ||| |       |  ||      |  |||      |       
GTTATGGAGCTGAGCAAGAACAACAAGGATCGAATCAACACCTCTTCCGCATTCAATTCCTTCAAGAACAACTACCTCCTCGTCTATTCCCTCATGATGGgtacaga-tctgtctcttctctc--ttagatc--cactcagatcttctctcattctccttgatctaaccttcctttctttcatttctcatttccattgccagctt

upper sequence: GRMZM2G077669_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA06G13760.2 (Glycine max), 5'ss of exon 1
GGGCTCGAGCTCGGCAAGAGCGGCAAGGACCGCGTCGCCACTACCTCCGCCTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacg--ccctccttcccttctcttgttcggttcctcgtttagatctgcgaacgctgtggtggttctgaatgatgatggttgggacggattcgtgcag--
| |   |||||  ||||||||  |||||||||  ||  |||  | ||||| ||||| |||||||||||||||||| || ||||||| |||||||||||| ||||    |   |||| ||    | | ||   ||     | |  ||      | || |  |    |       | ||   |       |||  |  |   
GTGACGGAGCTGAGCAAGAGCAACAAGGACCGAATCAACACCTCTTCCGCATTCAATTCCTTCAAGAACAACTACCTCATCGTCTATTCCCTCATGATGGgtacagatctgtcttctctctcttagatccactcagatctaacctcatttccctctttattccacccattacttcatttctcattttcatttttttatcg

upper sequence: GRMZM2G077669_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT1G64650.1 (Arabidopsis thaliana), 5'ss of exon 1
GGGCTCGAGCTCGGCAAGAGCGGCAAGGACCGCGTCGCCACTACCTCCGCCTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctccttcccttctcttgttcggttcctcgtttagatctgcgaacgctgtggtggttctgaatgatgatggttgggacggattcgtgcag-------------------------------------------------------------------------
||  | |||||  ||||      ||| |||||| |   |||  |||||||||||||||||||||||||||||||  ||||||||||||| ||||||||| ||  |  |||  | |    |||  |   | |||   ||  ||| |    |     | |||    ||  ||||  ||   || | | ||   || |                                                                          
GGCTTGGAGCTGAGCAAATCGAACAAAGACCGCATTAACACCTCCTCCGCCTTCAACTCCTTCAAGAACAACTATCTCCTCGTCTACTCTCTCATGATGGgttagttctcactaca---tctgatcacgatccattttctgatttctatagagcttagtgtcggtgtgtgatt-tgaccggaatgaatgaatgaatgctcccaatgattgattgattgtccatagatcctaaaatccaacaatgaatttatgtccctggcggcatttag

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|78179671|gb|DV550044.1|DV550044
EST:     CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|12047314|gb|BF729453.1|BF729453
EST:     CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|211181672|gb|FL010880.1|FL010880
EST:     CTTTAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|149009314|gb|EE041383.2|EE041383
EST:     CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|211344699|gb|FL214759.1|FL214759
EST:     ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|211184075|gb|FL010888.1|FL010888
EST:     CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|211181671|gb|FL010879.1|FL010879
EST:     CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|50336619|gb|CO531745.1|CO531745
EST:     CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|211184079|gb|FL010892.1|FL010892
EST:     CTTTAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|211184074|gb|FL010887.1|FL010887
EST:     CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|211184069|gb|FL010882.1|FL010882
EST:     CTTTAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|149016972|gb|EE154301.2|EE154301
EST:     CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|211184070|gb|FL010883.1|FL010883
EST:     CTTTAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|211184080|gb|FL010893.1|FL010893
EST:     CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|31354966|gb|CD439323.1|CD439323
EST:     CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|211184071|gb|FL010884.1|FL010884
EST:     CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|148980798|gb|EE027354.2|EE027354
EST:     CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCCTACGTCTACTACCTCTACAGCCAGTAC
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCC-TACGTCTACTACCTCTACAGCCAGTAC
EST: gi|74236381|gb|DT644295.1|DT644295
EST:     CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|149030377|gb|EE286314.2|EE286314
EST:     CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|78110935|gb|DV529333.1|DV529333
EST:     CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
EST: gi|211184076|gb|FL010889.1|FL010889
EST:     CTTTAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG

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: 115

GGGCTCGAGCTCGGCAAGAGCGGCAAGGACCGCGTCGCCACTACCTCCGCCTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATC


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 132

GGGCTCGAGCTCGGCAAGAGCGGCAAGGACCGCGTCGCCACTACCTCCGCCTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 201

GGGCTCGAGCTCGGCAAGAGCGGCAAGGACCGCGTCGCCACTACCTCCGCCTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 248

GGGCTCGAGCTCGGCAAGAGCGGCAAGGACCGCGTCGCCACTACCTCCGCCTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctc ... attcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCTCGAGCTCGGCAAGAGCGGCAAGGACCGCGTCGCCACTACCTCCGCCTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccctccttcccttctcttgttcggttcctcgtttagatctgcgaacgctgtggtggttctgaatgatgatggttgggacggattcgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC