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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcaaggcagagctctttaaaaaaagttctaatgtgatgtgccctgatgaggcaacggtggcaacgctgcaagatttcttatactcttttgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTGAGCGATGGGTGGCATGCTACAGGCAACGGTG

Basic information

species Zea mays
transcript GRMZM2G337425_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G337425_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g16570.3 (Oryza sativa), 3'ss of exon 8
atgcaaggcagagctctttaaaaaaagttcta-at--gtgatgtgccctgatgaggcaacggtggcaacgctgcaagattt-cttatactctt--ttgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTGAGCGATGGGTGGCATGCTACAGGCAACGGTG
           |||| |  |   || | |  | ||  ||| | |    |  |   |  | |  ||     ||||||| ||| ||||   ||    ||||||| |||||||| | |||||||||||| |||||| ||||||||||||| ||||||||| | ||||||||||  || |||||||||||||||| |  ||   | | | 
-----gtttttagctttccatcgaaggattgacattggtgctattagttttttgtgtcatga-ggtgggactgcaaggtttacttactttcccacttgttttgcagTTTCATGCAAACTGCATCGATCCATGGTTGCGCCAACAGGGAACATGCCCAGTTTGCAAGCACCGTGTAAGCGATGGGTGGCATGGTGAAGCAGATGCTT

upper sequence: GRMZM2G337425_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA11G34130.2 (Glycine max), 3'ss of exon 8
--atgcaaggcaga-gctctttaaaaaaagttctaatgtgatgtgccctgatgaggcaacggtggcaacgctgcaagatttcttatactcttttgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTGAGCGATGGGTGGCATGCTACAGGCAACGGTG
  | | | | | || | ||  |||||  |||  | || |  |||       |    |     ||| |   |||  |  ||  ||||  | || | ||||  |||||||||  ||||||||||| || |||||||||||||| || ||||||||  | || ||    |  |   |   ||| |||  ||  |  ||  |   ||
acaagtatgtctgaagttcaataaaatcagtgttgatattctgtatttatttatctcgtgaatggta---ctgacaccttgtttatgtttttattttttgaagTTTCACGCTAACTGCATCGATCCCTGGCTGCGCCAACAAGGGACATGCCCTGTATGTAAATTTCGAGCTGGATCTGGTTGGAGTGACAATGGACATAATG

upper sequence: GRMZM2G337425_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA18G04160.1 (Glycine max), 3'ss of exon 9
--atgcaaggcagagctctttaaaaaaagttctaatgtgatgtgccctgatgaggcaacggtggcaacgctgcaagatttcttatactcttttgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTGAGCGATGGGTGGCATGCTACAGGCAACGGTG
  |||      | || ||  |||||  | |  | || |  ||     |  | |    | |          ||  |  ||  ||||  | || | ||||  ||||||||| ||| |||||||| || |||||||||||||| || ||||||||  | || ||    |  |   |   ||| |||  ||  |  ||  |   | 
acatgatgtctaaagttcaataaaatcattgttgatattctgcatt-tatttatctcatgtgaatggtattgacaccttgtttatgtttttattttttgaaGTTTCACGCAAATTGCATCGATCCCTGGCTGCGCCAACAAGGGACATGCCCTGTATGTAAATTTCGAGCTGGATCTGGTTGGAGTGACAATGGACATAAT-

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|1298525|gb|W21775.1|W21775
EST:     AGCAAGTCACGGTGGGTGATATGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCG-CAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|148928861|gb|EC873779.2|EC873779
EST:     AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|18164717|gb|BM334556.1|BM334556
EST:     AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|91056515|gb|EB166933.1|EB166933
EST:     AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|86467591|gb|DY233961.1|DY233961
EST:     AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|71760470|gb|DR958407.1|DR958407
EST:     AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|78083978|gb|DV512371.1|DV512371
EST:     AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|18166650|gb|BM336489.1|BM336489
EST:     AGCAAGTCACGGTTGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATG
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATG
EST: gi|78085072|gb|DV513465.1|DV513465
EST:     AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|76288197|gb|DV027765.1|DV027765
EST:     AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|86467324|gb|DY233694.1|DY233694
EST:     AGCAAGTCACGGTGGGTGATTTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgaggcaacggtggcaacgctgcaagatttcttatactcttttgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTGAGCGATGGGTGGCATGCTACAGGCAACGGTG
 ccctgat  putative branch site (score: 4)
                              tttcttatactctttt  putative PPT
                             atttcttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcaaggcagagctctttaaaaaaagttctaatgtgatgtgccctgatgaggcaacggtggcaacgctgcaagatttcttatactcttttgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTGAGCGATGGGTGGCATGCTACAGGCAACGGTG

atgcaag
- - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - -tgtgatg
- - - - - - - - - - - - - - - - - - - - - -cctgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgcaa