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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gctagatctcttcctttgttgcctggagtatttcattacacagatatagagaaacaagtattagttgtcatagatttggtccaatgttctgtagttagcggctaatgtatcttttcatcttttttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGAGAGCTGCTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAA

Basic information

species Zea mays
transcript GRMZM2G391936_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 3'ss of exon 12
gctagatctcttcctttgttgcctggagtatttcattacacagatatagagaaacaagtattagttgtcatagatttggtccaatgttctgtagttagcggctaatgtatcttttcatcttttttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGAGAGCTGCTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAA
                    | | |   | ||   || ||| | || |        || || |     ||  |   ||| |     |||   | |||      |    || |||   |    ||  |||||||||||| ||||||||||| |||||||  ||||| ||||   ||||||||||||| ||||| || |||||||| ||||||||||| || || ||||||||||
--------------------gtcagatattttcattttcactgctaga--------agcataaaacaccaacggaatggcc-----ttcca-aatta-----cataaaatatttctgttccattgtcctgcagGATACAGTAATGCTTGGTGCTGATTTCTATGAGACTGATCTGGAAAGAGGAGAACTGCTGGCTGAAGGAAAGGTTCCTATTGGAATCGGGGAGAATACAA

upper sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 12
gctagatctcttcctttgttgcctggagtatttcattacacagatatagagaaacaagtattagttgt-catagatttggtccaatgttc-----tgtagttagcggctaatgtatctttt----catcttttttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGAGAGCTGCTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAA
                                          || ||| |  || |  | || || |  |||| ||||||| |  |  |      ||   | | |   |  | || ||| |    |||     ||   |||||||||| || |||||||| ||||||||||||||||| |  |  |||   | ||  ||  | || ||||||| |||||| ||||| || ||||| |||||||
------------------------------------------gaaatataataatat-tcttggtggaacataaatttggtacgtttcttacgtgtgccctcatctagttctataacttctagcgcattacacttatatgcagGATACAGTGATGCTTGGTGCTGATTATTATGAAACCGATGCAGAAGTGGCAGCACTCTTAGCTGAAGGAAGAGTTCCAATTGGAATAGGAGAAAATACAA
















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|71757054|gb|DR954991.1|DR954991
EST:     ATAGTGTTGTTGGAGTTCGTTTTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|13236975|gb|BG354989.1|BG354989
EST:     CGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: CGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|71324302|gb|DR798853.1|DR798853
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|27753904|gb|BM378096.1|BM378096
EST:     TGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: TGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|24763417|gb|CA398592.1|CA398592
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|211232745|gb|FL322840.1|FL322840
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|110195335|gb|EC877232.1|EC877232
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|13558450|gb|BG549806.1|BG549806
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|13126504|gb|BG317074.1|BG317074
EST:     TTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAGCTGCCGTGGAAAGAGGA
genomic: TTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|211470047|gb|FL442813.1|FL442813
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|18178292|gb|BM379502.1|BM379502
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|71429962|gb|DR811012.1|DR811012
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|93281647|gb|EB673911.1|EB673911
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|71323466|gb|DR798382.1|DR798382
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|89763297|gb|DY690558.1|DY690558
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|31363279|gb|CD447636.1|CD447636
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTCCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|32850355|gb|CD990036.1|CD990036
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|16377759|gb|BI992107.1|BI992107
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCCCCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|31348918|gb|CD433275.1|CD433275
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|12967897|gb|BG264844.1|BG264844
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|50335821|gb|CO530947.1|CO530947
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|31362917|gb|CD447274.1|CD447274
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
EST: gi|78103575|gb|DV522003.1|DV522003
EST:     ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAG                         GATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA
genomic: ATAGTGTTGTTGGAGTTCGTTCTCGGATAGGCTCCAATGTGCACCTCAAGgctagatctc ... ttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccaatgttctgtagttagcggctaatgtatcttttcatcttttttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGAGAGCTGCTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAA
                     ggctaat  putative branch site (score: 3)
                           tgtatcttttcatctt  CT-rich tract
                                 ttttcatctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctagatctcttcctttgttgcctggagtatttcattacacagatatagagaaacaagtattagttgtcatagatttggtccaatgttctgtagttagcggctaatgtatcttttcatcttttttccctgcagGATACTGTAATGCTTGGCGCTGATTATTATGAAACTGCCGTGGAAAGAGGAGAGCTGCTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA