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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acggtacactgcactgtttacagagtgaagtttgaaatatgggatgtgatgaataacactgctggagatagcctaatatccctttcctttgtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGAAGGGAAGCTCCCACTGAATC

Basic information

species Zea mays
transcript GRMZM2G368908_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G368908_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 6
acggtacactgcactgtttacagagtgaagtttgaaatatgggatgtgatgaataacactgctggagatagcctaatatccctttcct-----ttgtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGAAGGGAAGCTCCCACTGAATC
          | | | |||    ||   | | || | | |  |     |  | |  |  |  |    ||  ||||||||  | ||  |     ||||||   ||||| || |||||||||||||||||||| ||||| || ||||||||||||||||||||  | || || ||||||||||||||||||||||||||||||||||
----------gtaatatttcacaag---aatatgcattttcagcct--acaagttgctttatt----atgccctaatatatcctttatcattgttgtcattaaagGTAACCAGCAAGCTTGCAGCCTTGAAAGGACTGGACGCAAGGCTCAGGGAGATCCGTGGGTACTTAGATCTTGTAATTGAAGGGAAGCTCCCACTGAATC
















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|60340869|gb|DN207842.1|DN207842
EST:     ACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG
genomic: ACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAGgtaatatgtc ... gtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG
EST: gi|60355241|gb|DN222214.1|DN222214
EST:     ACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG
genomic: ACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAGgtaatatgtc ... gtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG
EST: gi|60399723|gb|DN232533.1|DN232533
EST:     CCTTTTAAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG
genomic: CCTTTT-AAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAGgtaatatgtc ... gtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG
EST: gi|108824177|gb|EC278185.1|EC278185
EST:     ACCTTTTAAGGGATGTAAAGGACACAACCATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG
genomic: ACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAGgtaatatgtc ... gtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG
EST: gi|32857775|gb|CD997456.1|CD997456
EST:     GGACACAACCATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG
genomic: GGACACAACCATAAGCACACTTGCTACAGAGgtaatatgtc ... gtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG
EST: gi|87153027|gb|DY397816.1|DY397816
EST:     ACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG
genomic: ACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAGgtaatatgtc ... gtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG
EST: gi|16925720|gb|BM078788.1|BM078788
EST:     CATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG
genomic: CATAAGCACACTTGCTACAGAGgtaatatgtc ... gtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG
EST: gi|110520623|gb|EE024807.1|EE024807
EST:     ACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG                         GTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG
genomic: ACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAGgtaatatgtc ... gtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatgaataacactgctggagatagcctaatatccctttcctttgtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGAAGGGAAGCTCCCACTGAATC
                               tatccctttcctttgt  CT-rich tract
                                              tcaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acggtacactgcactgtttacagagtgaagtttgaaatatgggatgtgatgaataacactgctggagatagcctaatatccctttcctttgtcaaataagGTCACTAGCAAGCTTGCAGCCTTGAAGGGACTAGATGCAAGGCTCAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGAAGGGAAGCTCCCACTGAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - -actgcac
- - - - - - - - - - - - - - - - - - - - - - tgtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgctg