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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCCTTTGAATGAGAAGTTTGATCCAAATAGGCACTATGCCATTTTCCAAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcatttcttaatgctactttttgtttactagcaaacatggccatgtgttgcaatggaacttacaagttgttgtgtgattcttgtgccaattgaact...

Basic information

species Zea mays
transcript GRMZM2G002440_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002440_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g25090.2 (Oryza sativa), 5'ss of exon 5
TGATCCTTTGAATGAGAAGTTTGATCCAAATAGGCACTATGCCATTTTCCAAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcatttct--taatgctactttttgtttactagcaaacatggccatgtgttgcaatggaacttacaagtt-gttgtgtgattcttgtgccaattgaact
||||||  | |||||||| ||||||||||||| |||   |||  ||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||  |||   ||||  |  | |  | ||  || |   | |   | | ||    ||  |  | | |||||  | |   | |      ||    |||    
TGATCCACTTAATGAGAAATTTGATCCAAATAAGCATGCTGCGCTTTTCCAAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctcttccgataattttggtatagggtttttacccc-ctttctcttctgaaataagagctcattcaagtccggtacttaacctcaatgtttgttggt--
















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|5922290|gb|AW055579.1|AW055579
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
EST: gi|5739690|gb|AI947266.1|AI947266
EST:     ATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: ATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
EST: gi|50332490|gb|CO527616.1|CO527616
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
EST: gi|37394200|gb|CF634371.1|CF634371
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
EST: gi|5819185|gb|AI987391.1|AI987391
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
EST: gi|13237180|gb|BG355194.1|BG355194
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
EST: gi|67042408|gb|CO468663.1|CO468663
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
EST: gi|18659614|gb|BM500430.1|BM500430
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
EST: gi|32934212|gb|CF039024.1|CF039024
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
EST: gi|5607682|gb|AI901349.1|AI901349
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
EST: gi|88754856|gb|DY538997.1|DY538997
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGGTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
EST: gi|21828625|gb|BQ703309.1|BQ703309
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
EST: gi|74234069|gb|DT641983.1|DT641983
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
EST: gi|5343189|gb|AI795374.1|AI795374
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTC
EST: gi|16378404|gb|BI992428.1|BI992428
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATCCTTTGAATGAGAAGTTTGATCCAAATAGGCACTATGCCATTTTCCAAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcatttcttaatgctactttttgtttactagcaaacatggccatgtgttgcaatggaacttacaagttgttgtgtgattcttgtgccaattgaact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT