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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTCCATCGCCATTGTCGGCGCAAGCAAAGGGGCGGAGCAGCATGGCGGGGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgcccaatcctccgcctccctcatcttggcgatcccaccattgcccgggcacatatctactttccttatttggcaccgggttttttccgagaa...

Basic information

species Zea mays
transcript GRMZM2G448715_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G448715_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 5'ss of exon 1
ATCTCCATCGCCATTGTCGGCGCAAGCAAAGGGGCGGAGCAGCATGGCGGGGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgcccaatcctccgcctccctcatcttggcgatcccaccattgcccgggcacatatctactttccttatttggcaccgggttttttccgagaa----
|   |||   | |    ||  | |||   | |   ||  |   |||||||||||||| ||| ||||||||||||||||||| ||||||||||||||||||||  | |   || ||||||  ||||||||   ||  | |     ||   |  ||    |  ||||  |||| |  ||     ||   | |  |||| |      
AAGCCCAAGCCGACCCCCGAGGGAAGGGGAAGACGGGGCCGAGATGGCGGGGCGCTACGACAGCAACCCCTTCGAGGAGGACGACGTGAACCCTTTCTCGgt--gaggaacccatcctctccctccctccctttctccacgttcccgccgggcgca-gcggatctggtttcgtgtttccttgccct-tctcctccgtgcgcgtt

upper sequence: GRMZM2G448715_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA07G31090.1 (Glycine max), 5'ss of exon 1
-ATCTCCATCGCCATTGTCGGCGCAAGCAAAGGGGCGGAGCAGCATGGCGGGGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgcccaatcctccgcctccctcatcttggcgatcccaccattgcccgggcacatatctactttccttatttggcaccgggttttttccgagaa-
 | |  |  |  ||  |||  |  |          |  |    |||||| || ||||||||| | ||||||||||| |||||||| || ||||||||||| ||| |  |      |  | |  ||   |   |   |   |       |   | ||| |       | ||    | ||  | || |||| |  ||  ||   
TAGCCTCTGCAACAGAGTCT-CAGATCTCTGCATTCCAATTCCCATGGCTGGTCGCTATGACAGTAACCCCTTCGATGAGGAAGAAGTTAACCCTTTCTCTgtaagtccttattttgttgctgcttttt-gccaaagttgtgattttgtgaactgggtatgctcaaagttgtgattttgtgaactgggtatgctcaaagttg
















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|211023196|gb|FK976150.1|FK976150
EST:     GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCG                         CAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
genomic: GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttggtagCAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
EST: gi|24462488|gb|BM660019.1|BM660019
EST:     GGCGCTATGACGGCAACCCCTTCGAGGANGAAGACGTGAACCCTTTCTCG                         CAACAAACGCGCGGTAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
genomic: GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttggtagCAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
EST: gi|91048315|gb|EB158733.1|EB158733
EST:     GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCG                         CAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
genomic: GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttggtagCAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
EST: gi|33770808|gb|CF273102.1|CF273102
EST:     GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCG                         CAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
genomic: GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttggtagCAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
EST: gi|211223444|gb|FL382580.1|FL382580
EST:     GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCG                         CAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
genomic: GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttggtagCAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
EST: gi|28188216|gb|CB179826.1|CB179826
EST:     GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCCTTCTCG                         CAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
genomic: GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttggtagCAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
EST: gi|76931490|gb|DV172743.1|DV172743
EST:     GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCG                         CAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
genomic: GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttggtagCAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
EST: gi|211023197|gb|FK976151.1|FK976151
EST:     GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCG                         CAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
genomic: GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttggtagCAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
EST: gi|211046010|gb|FL422511.1|FL422511
EST:     GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCG                         CAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
genomic: GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttggtagCAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
EST: gi|211023203|gb|FK976157.1|FK976157
EST:     GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCG                         CAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
genomic: GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttggtagCAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
EST: gi|37621984|gb|CF675037.1|CF675037
EST:     GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCG                         CAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
genomic: GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttggtagCAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
EST: gi|211025647|gb|FK976165.1|FK976165
EST:     GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCG                         CAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
genomic: GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttggtagCAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
EST: gi|211219781|gb|FL407453.1|FL407453
EST:     GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCG                         CAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
genomic: GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttggtagCAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
EST: gi|89251197|gb|DY622983.1|DY622983
EST:     GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCG                         CAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
genomic: GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttggtagCAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
EST: gi|37621886|gb|CF674939.1|CF674939
EST:     GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCG                         CAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG
genomic: GGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgc ... tccttggtagCAACAAACGCGCGGCAAGGCTGGCGGGCAATCCAACTTTGGCGGTGGCGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTCCATCGCCATTGTCGGCGCAAGCAAAGGGGCGGAGCAGCATGGCGGGGCGCTATGACGGCAACCCCTTCGAGGAGGAAGACGTGAACCCTTTCTCGgtacgcgcgcccaatcctccgcctccctcatcttggcgatcccaccattgcccgggcacatatctactttccttatttggcaccgggttttttccgagaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcgccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctccgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccctca