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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcatgccgcatggcccccctcaagccctcaacactcttactcctcacgcgcatttgccttcctgtgaatcctgtgatacgcattcatcccgatagatgacaatgtagggaataatacgggctcatattaattcttttctgcatccgtcggtcgatctcctctctagATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTTGAACAGCTCTTCAAGGAGACGGGGAACTTCTCCAAGAAATTCCAAG

Basic information

species Zea mays
transcript GRMZM2G134752_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134752_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g42820.1 (Oryza sativa), 3'ss of exon 1
gtacgcatgccgcatggcccccctcaagccctcaacactcttactcctcacgcgcatttgccttcctgtgaatcctgtgatacgcattcatcccgatagatgacaatgtagggaataatacgggctcatattaattcttttctgcatccgtcggtcgatct---cctctctagATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTTGAACAGCTCTTCAAGGAGACGGGGAACTTCTCCAAGAAATTC---CAAG
                                                                  | || ||  | ||  |   ||    || |  | |||    |  ||    || || |   | | || || | |    |   ||  ||     || |   | |||  ||||  | | ||||||||| ||||| || || ||||||||||||||||||||||| ||||||||||| |||||||||| |||||| |||||||||   ||||
-----------------------------------------------------------------gtatgtata-tatggcatcgatcggccctgcaacatg----ttcagtttttattaggtaattaaatcaactatcacatttttcgttcaaaacatttacgcatctgcagATGTGTAACTACTCTTCGATGGATGGTGTCCTGTACTGCAAGACGCACTTTGAGCAGCTCTTCAAAGAGACGGGGAGCTTCTCAAAGAAATTCTCGCAAG

upper sequence: GRMZM2G134752_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT3G61230.1 (Arabidopsis thaliana), 3'ss of exon 1
gtacgcatgccgcatggcccccctcaagccctcaacactcttactcctcacgcgcatttgccttcctgtgaatcctgtgatacgcattcatcccgatagatgaca-atgtagggaataatacgggctcatattaattcttttctgcatccgtcggtcgatctcctctctagATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTTGAACAGCTCTTCAAGGAGACGGGGAACTTCTCCAAGAAATTCCAAG---
                                                                     | |||     ||   | ||   | | || | |  |  ||| |   || || ||           ||    |||||               |||||| |  ||||  | | |||||| |||||||| || ||| |||| |||||||| || ||||||||||||||||| ||  | || || |||  |||||| ||||||    
---------------------------------------------------------------------gtatctatctatcttccttttcctccattgttccctcatgaaaaaaaaaacacaaa-----gagaacatctttct---------------tctccttttcagATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAG

upper sequence: GRMZM2G134752_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
gtacgcatgccgcatggcccccctcaagccctcaacactcttactcctcacgcgcatttgccttcctgtgaatcctgtgatacgcattcatcccgatagatgacaatgtagggaataatacgggctcatattaattcttttctgcatccgtcggtcgatctcctctctagATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTTGAACAGCTCTTCAAGGAGACGGGGAACTTCTCCAAGAAATTCCAAG---
                                                                                   ||| ||||    |   ||     |||  |   |  || |   ||||||||  ||     |  |||  |  || |||  |      |||| |||| ||| || ||||||||||| ||| ||||||||||||| || ||||| || |||||||||||  | || || |||  ||| || || |||    
---------------------------------------------------------------------------------gtgcactcatt---actcattttcttgttagatcttctatga--tcatattatatcaacaatttatctatgtgttgatggc------agATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG

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|21330224|gb|BQ485605.1|BQ485605
EST:     CGTACCACAAGACCTGCTTCAAATGCAGCCACTGCAAGGGCGTCCTCTCG                         ATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTT
genomic: CGTACCACAAGACCTGCTTCAAATGCAGCCACTGCAAGGGCGTCCTCTCGgtacgcatgc ... tcctctctagATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTT
EST: gi|26455015|gb|CA826598.1|CA826598
EST:     CGTACCACAAGACCTGCTTCAAATGCAGCCACTGCAAGGGCGTCCTCTCG                         ATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTT
genomic: CGTACCACAAGACCTGCTTCAAATGCAGCCACTGCAAGGGCGTCCTCTCGgtacgcatgc ... tcctctctagATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTT
EST: gi|21329770|gb|BQ485151.1|BQ485151
EST:     CGTACCACAAGACCTGCTTCAAATGCAGCCACTGCAAGGGCGTCCTCTCG                         ATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTT
genomic: CGTACCACAAGACCTGCTTCAAATGCAGCCACTGCAAGGGCGTCCTCTCGgtacgcatgc ... tcctctctagATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTT
EST: gi|87154920|gb|DY399709.1|DY399709
EST:     AAATGCAGCCACTGCAAGGGCGTCCTCTCG                         ATTAGCAGCTACTCTTCCATGGACGGCAGTTCTGTACTGCAAGACGCACTT
genomic: AAATGCAGCCACTGCAAGGGCGTCCTCTCGgtacgcatgc ... tcctctctagATTAGCAGCTACTCTTCCATGGACGGC-GTTCTGTACTGCAAGACGCACTT
EST: gi|89106608|gb|DY576825.1|DY576825
EST:     CGTACCACAAGACCTGCTTCAAATGCAGCCACTGCAAGGGCGTCCTCTCG                         ATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTT
genomic: CGTACCACAAGACCTGCTTCAAATGCAGCCACTGCAAGGGCGTCCTCTCGgtacgcatgc ... tcctctctagATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTT
EST: gi|26455135|gb|CA826718.1|CA826718
EST:     CGTACCACAAGACCTGCTTCAAATGCAGCCACTGCAAGGGCGTCCTCTCG                         ATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTT
genomic: CGTACCACAAGACCTGCTTCAAATGCAGCCACTGCAAGGGCGTCCTCTCGgtacgcatgc ... tcctctctagATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTT
EST: gi|37659524|gb|CF752086.1|CF752086
EST:     CGTACCACAAGACCTGCTTCAAATGCAGCCACTGCAAGGGCGTCCTCTCG                         ATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTC
genomic: CGTACCACAAGACCTGCTTCAAATGCAGCCACTGCAAGGGCGTCCTCTCGgtacgcatgc ... tcctctctagATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatacgggctcatattaattcttttctgcatccgtcggtcgatctcctctctagATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTTGAACAGCTCTTCAAGGAGACGGGGAACTTCTCCAAGAAATTCCAAG
             tattaat  putative branch site (score: 2)
                                       tcgatctcctctct  putative PPT
          tcatattaattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcatgccgcatggcccccctcaagccctcaacactcttactcctcacgcgcatttgccttcctgtgaatcctgtgatacgcattcatcccgatagatgacaatgtagggaataatacgggctcatattaattcttttctgcatccgtcggtcgatctcctctctagATTAGCAGCTACTCTTCCATGGACGGCGTTCTGTACTGCAAGACGCACTTTGAACAGCTCTTCAAGGAGACGGGGAACTTCTCCAAGAAATTCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA