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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttagcatgagcagtgtctggaactgcatatgttaaatggtttacatatgtgcatatccttattccgtaatgctgatttcagttgttacgtgccaccagGTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGAATGGATCGGCAGTAACTTGAAGAAGGACAACGATCATGTGACCTGGGCT

Basic information

species Zea mays
transcript GRMZM5G831584_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G831584_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g64262.1 (Oryza sativa), 3'ss of exon 3
---gtttagcatgagcagtgtctggaactgcatatgttaaatggtttacatatg-tgcatatcc-ttat-tccgtaatgctgatttcagttgttacgtgccaccagGTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGAATGGATCGGCAGTAACTTGAAGAAGGACAACGATCATGTGACCTGGGCT
   |  |||||   |   || |   | |   || | |   | |    ||  ||| | ||| |   |||| ||| || || ||||  | |||      | |   |||||||||||||||||||||| ||| | | |||||||| |||||||||||||||||||| || || ||||| || |||||||| || |||||||| ||||| 
aaaggatagcaaatgttttggccctatcataatgtttatcaggaaggaccaatgattcatgtttgttatatccttagtgatgatgcctgtt------tactgtcagGTGGGTTGTCGACCACATGATCAACTTGGGATTTTCAAAGTCTCTTTCAGAATGGATTGGGAGCAACTTAAAAAAGGACAATGAACATGTGACATGGGCG
















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|31348702|gb|CD433059.1|CD433059
EST:     CGAGTCTTCCTTCTTCACTTCCATCACGCAA                         GTGGGCTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGA
genomic: CGAGTCTTCCTTCTTCACTTCCATCACGCAAgtactatctc ... gtgccaccagGTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGA
EST: gi|29545082|gb|CB605260.1|CB605260
EST:     CAGGTTTTGCAAACGCTAGCGAGTCTTCCTTCTTCACTTCCATCACGCAA                         GTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGA
genomic: CAGGTTTTGCAAACGCTAGCGAGTCTTCCTTCTTCACTTCCATCACGCAAgtactatctc ... gtgccaccagGTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGA
EST: gi|71418697|gb|DR804513.1|DR804513
EST:     CAGGTTTTGCAAACGCTAGCGAGTCTTCCTTCTTCACTTCCATCACGCAA                         GTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGA
genomic: CAGGTTTTGCAAACGCTAGCGAGTCTTCCTTCTTCACTTCCATCACGCAAgtactatctc ... gtgccaccagGTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGA
EST: gi|29577114|gb|CB617226.1|CB617226
EST:     CAGGTTTTGCAAACGCTAGCGAGTCTTCCTTCTTCACTTCCATCACGCAA                         GTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGA
genomic: CAGGTTTTGCAAACGCTAGCGAGTCTTCCTTCTTCACTTCCATCACGCAAgtactatctc ... gtgccaccagGTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGA
EST: gi|74241544|gb|DT649458.1|DT649458
EST:     CAGGTTTTGCAAACGCTAGCGAGTCTTCCTTCTTCACTTCCATCACGCAA                         GTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGA
genomic: CAGGTTTTGCAAACGCTAGCGAGTCTTCCTTCTTCACTTCCATCACGCAAgtactatctc ... gtgccaccagGTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGA
EST: gi|60342212|gb|DN209185.1|DN209185
EST:     CAGGTTTTGCAAACGCTAGCGAGTCTTCCTTCTTCACTTCCATCACGCAA                         GTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGA
genomic: CAGGTTTTGCAAACGCTAGCGAGTCTTCCTTCTTCACTTCCATCACGCAAgtactatctc ... gtgccaccagGTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGA
EST: gi|60395624|gb|DN228494.1|DN228494
EST:     CAGG-TTTGCAAACGCTAGCGAGTCTTCCTTCTTCACTTCCATCACGCAA                         GTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGA
genomic: CAGGTTTTGCAAACGCTAGCGAGTCTTCCTTCTTCACTTCCATCACGCAAgtactatctc ... gtgccaccagGTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGA
EST: gi|24763127|gb|CA398310.1|CA398310
EST:     GCGAGTCTTCCTTCTTCACTTCCATCACGCAA                         GTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGA
genomic: GCGAGTCTTCCTTCTTCACTTCCATCACGCAAgtactatctc ... gtgccaccagGTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgtgcatatccttattccgtaatgctgatttcagttgttacgtgccaccagGTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGAATGGATCGGCAGTAACTTGAAGAAGGACAACGATCATGTGACCTGGGCT
                          tgctgat  putative branch site (score: 3)
               ttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttagcatgagcagtgtctggaactgcatatgttaaatggtttacatatgtgcatatccttattccgtaatgctgatttcagttgttacgtgccaccagGTGGGTTGTCGACCACATGCTCAGCCTTGGATTTTCGAAGTCTCTTTCAGAATGGATCGGCAGTAACTTGAAGAAGGACAACGATCATGTGACCTGGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG