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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgaaagatgccgattctatcattgcaatgtgagagagggcttccagttgagttgttaaggttaaggtgttttgttttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGGCAGAGGCCGACAGTTAGCAAGAAGGATCTGGAGGTGCATGAGAGGTTCA

Basic information

species Zea mays
transcript GRMZM2G126860_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126860_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 7
gtaacgaaagatgccgattctatcattgca-atgtgagagagggcttccagttgagttgttaaggttaaggtgttttgttttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGGCAGAGGCCGACAGTTAGCAAGAAGGATCTGGAGGTGCATGAGAGGTTCA
||||       || |  |||   || |||  |||| |||   ||||||   |    ||   ||| || |  | |  ||||    |||||||| ||||||||||| ||||||||||| ||||| ||||| ||| |  | |||||||| |||||||| |||||||| ||  |||||||||| || ||||| |
gtaagattgattgacatttcctccactgcgcatgttagaagaggcttctgat--gattagcaagattta--tttcctgtt----atgtagATCCTTCCACCACCAATCTCAAGGACAGATTTCGAGAAAGTCCTCGCCAGGCAGAGACCGACAGTGAGCAAGAAAGACTTGGAGGTGCACGAAAGGTTTA

upper sequence: GRMZM2G126860_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g04814.4 (Oryza sativa), 3'ss of exon 7
gtaacgaaagatgccgattctatcattgca-atgtgagagagggcttccagttgagttgttaaggttaaggtgttttgttttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGGCAGAGGCCGACAGTTAGCAAGAAGGATCTGGAGGTGCATGAGAGGTTCA
||||       || |  |||   || |||  |||| |||   ||||||   |    ||   ||| || |  | |  ||||    |||||||| ||||||||||| ||||||||||| ||||| ||||| ||| |  | |||||||| |||||||| |||||||| |                        
gtaagattgattgacatttcctccactgcgcatgttagaagaggcttctgat--gattagCAAGATTTA--TTTCCTGTT----ATGTAGATCCTTCCACCACCAATCTCAAGGACAGATTTCGAGAAAGTCCTCGCCAGGCAGAGACCGACAGTGAGCAAGAAAG------------------------
















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|78118803|gb|DV537187.1|DV537187
EST:     CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|37377679|gb|CF625466.1|CF625466
EST:     CTGCACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATTCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTA-TCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAG
EST: gi|78120339|gb|DV538723.1|DV538723
EST:     CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|40335376|gb|CK369446.1|CK369446
EST:     CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|194717076|gb|FK934229.1|FK934229
EST:     GTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: GTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|32851418|gb|CD991099.1|CD991099
EST:     CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|37387153|gb|CF630769.1|CF630769
EST:     CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|211094373|gb|FL362897.1|FL362897
EST:     CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGA
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGA
EST: gi|211356932|gb|FL335286.1|FL335286
EST:     CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|71758799|gb|DR956736.1|DR956736
EST:     CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|94473141|gb|EB702099.1|EB702099
EST:     CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|83278917|gb|DV942925.1|DV942925
EST:     CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|211035900|gb|FL445344.1|FL445344
EST:     CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|40334257|gb|CK368327.1|CK368327
EST:     CTGCACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|88753790|gb|DY537931.1|DY537931
EST:     CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCCCCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|37381596|gb|CF627695.1|CF627695
EST:     CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|12972290|gb|BG267908.1|BG267908
EST:     CAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|149073557|gb|EE161858.2|EE161858
EST:     CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|37396249|gb|CF635412.1|CF635412
EST:     CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|149081425|gb|EE170542.2|EE170542
EST:     CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
EST: gi|60343814|gb|DN210787.1|DN210787
EST:     CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAG                         ATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG
genomic: CTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGG

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), 44 (downstream exon)
Score: 83

CAAGGCAGACGGTGACATGTGGATGCCATGTGGACCAAAACAACCGGGGTCTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGGCAGAGGCCGACAGTTAGCAAGAAGGATCTGGAGGTGCATGAGAGGTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

CAAGGCAGACGGTGACATGTGGATGCCATGTGGACCAAAACAACCGGGGTCTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGGCAGAGGCCGACAGTTAGCAAGAAGGATCTGGAGGTGCATGAGAGGTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

CAAGGCAGACGGTGACATGTGGATGCCATGTGGACCAAAACAACCGGGGTCTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGGCAGAGGCCGACAGTTAGCAAGAAGGATCTGGAGGTGCATGAGAGGTTCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 87

CAAGGCAGACGGTGACATGTGGATGCCATGTGGACCAAAACAACCGGGGTCTGTACAGACCACAATGCAGGAGCTTGCATCCAAGGGCCTCGCTGCAAAGgtaacgaaag ... ttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGGCAGAGGCCGACAGTTAGCAAGAAGGATCTGGAGGTGCATGAGAGGTTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagagagggcttccagttgagttgttaaggttaaggtgttttgttttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGGCAGAGGCCGACAGTTAGCAAGAAGGATCTGGAGGTGCATGAGAGGTTCA
                                      ttttgtttt  CT-rich tract
                                      ttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacgaaagatgccgattctatcattgcaatgtgagagagggcttccagttgagttgttaaggttaaggtgttttgttttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGGCAGAGGCCGACAGTTAGCAAGAAGGATCTGGAGGTGCATGAGAGGTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG