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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctgatgatcaactgtatgatgttggtattctatgaatttaattgttgagcttactttactctatgagaatccacaacacaaccag

Basic information

species Zea mays
transcript GRMZM2G120517_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120517_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g35520.2 (Oryza sativa), 5'ss of exon 9
GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtga-----------------------tctctgatgatcaactg-tatgatgttgg--tattctatga--atttaattgttgagcttacttt-------actctatgagaatccacaacacaaccag
|| || ||||||||| ||||||||||||| |||||| | |||||||||||||| ||||||||||||||||  ||||||||||                         ||     || |||   | |  |  | |  |||   | ||  |||| |   ||||  | | | |       ||| | ||||||| |||  ||||  |||
GAGATAAAAGAGAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCTGCATTATTTGAGGACCCAACATTCAAGgtgaataatgcttaaactgtactctcacttcccgaaataaaccaatctcgtactaggatatgtcaggatcatttgaaaattgaaataattattgaactaactgtctgagaattcaccgcacattcag
















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|4887369|gb|AI677468.1|AI677468
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|7162396|gb|AW520018.1|AW520018
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|60342201|gb|DN209174.1|DN209174
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|24934386|gb|CA452604.1|CA452604
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|71327463|gb|DR800349.1|DR800349
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|67022725|gb|CO451474.1|CO451474
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|7216381|gb|AW562503.1|AW562503
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|101393103|gb|EB818482.1|EB818482
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|60397958|gb|DN230774.1|DN230774
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|74246091|gb|DT654005.1|DT654005
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|7204636|gb|AW559169.1|AW559169
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|60349847|gb|DN216820.1|DN216820
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|5740004|gb|AI947694.1|AI947694
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGCCCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGCCCAAGACGCATTCTTCAGAGACTCC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|211351874|gb|FK984289.1|FK984289
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|76920121|gb|DV168019.1|DV168019
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|76292512|gb|DV032080.1|DV032080
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|211216297|gb|FL460273.1|FL460273
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|60342528|gb|DN209501.1|DN209501
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|71759931|gb|DR957868.1|DR957868
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|14244899|gb|BG842837.2|BG842837
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|88753851|gb|DY537992.1|DY537992
EST:     TTTTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGATTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
EST: gi|7145161|gb|AW506642.1|AW506642
EST:     TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAG                         GTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC
genomic: TTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctg ... acacaaccagGTCTATGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATATCAAAGAGAAACGAGATCAGGATCTTCTGGTCCTACCTACAGATGCTGCTTTATTTGAGGACCCAAAGTTCAAGgtgatctctgatgatcaactgtatgatgttggtattctatgaatttaattgttgagcttactttactctatgagaatccacaacacaaccag

- - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - GCTGCT