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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttggtaccccgcggcgcatcggattgtgcgacagtatacagtacaataggcggtgaacaaggatttagggcggcggctgacacgatctcgtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGG

Basic information

species Zea mays
transcript GRMZM2G090647_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090647_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g37832.1 (Oryza sativa), 3'ss of exon 1
-----gttggtaccccgcggcgcatcggattgtgcgacagtatacagtacaataggcggtgaacaaggatttagggcggcggctgacacgatctcgtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGG
     | ||| |      |||  || || |||        | |   ||    | |  ||||        | ||  || ||  |   ||      | |     |||||||||||||| |||||||| ||| | |||||||||||||| |||||||||||||||||||||||||| |||||||| |||
ctagagatggcatgttagggca-atgggtttgattttttttgtgt-gtttttttgatggtgtttgcccttatactgctgcatc-atcata--tacatatatacagGTGGTGGCTCTGAACGAATCTGTGGCGGGGAGCGTCAAGTCGGTCTTCAAGCCCTGGGAGCAGCGCCTCGACACCTCTGGG
















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|211391416|gb|FL107759.1|FL107759
EST:     ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAG                         GTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
genomic: ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAGgtcctgtaat ... gtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
EST: gi|211394035|gb|FL107766.1|FL107766
EST:     ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAG                         GTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
genomic: ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAGgtcctgtaat ... gtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
EST: gi|78074482|gb|DV502916.1|DV502916
EST:     ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAG                         GTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
genomic: ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAGgtcctgtaat ... gtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
EST: gi|113702250|gb|EE679754.1|EE679754
EST:     ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAG                         GTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
genomic: ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAGgtcctgtaat ... gtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
EST: gi|20301430|gb|BQ164373.1|BQ164373
EST:     ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAG                         GTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
genomic: ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAGgtcctgtaat ... gtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
EST: gi|211396668|gb|FL107792.1|FL107792
EST:     ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAG                         GTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
genomic: ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAGgtcctgtaat ... gtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
EST: gi|211391414|gb|FL107757.1|FL107757
EST:     ACAACTGCGCCGCCGACTGGTCGCTCTACA-CCACATCGACGTCCCCAAG                         GTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
genomic: ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAGgtcctgtaat ... gtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
EST: gi|211391419|gb|FL107762.1|FL107762
EST:     ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAG                         GTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
genomic: ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAGgtcctgtaat ... gtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
EST: gi|211391417|gb|FL107760.1|FL107760
EST:     ACAACTGCGCCGCNGACTGGTCGCTCTACAACCACATCGACGTCCCCAAG                         GTGGTGGCTCTCAACGAATCGGTGCC-GGGAGCGTCAAGTCCGTCTTCAAG
genomic: ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAGgtcctgtaat ... gtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
EST: gi|71770110|gb|DR968047.1|DR968047
EST:     ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAG                         GTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
genomic: ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAGgtcctgtaat ... gtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
EST: gi|211396658|gb|FL107782.1|FL107782
EST:     ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAG                         GTGGTGGCTCTCAATGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
genomic: ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAGgtcctgtaat ... gtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
EST: gi|211394041|gb|FL107772.1|FL107772
EST:     ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAG                         GTGGTGGCTCTCAACGAATCGGTGCCCGGGGAGCGTCAAGTCCGTCTTCAA
genomic: ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAGgtcctgtaat ... gtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGG-AGCGTCAAGTCCGTCTTCAA
EST: gi|211394048|gb|FL107779.1|FL107779
EST:     ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAG                         GTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
genomic: ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAGgtcctgtaat ... gtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
EST: gi|211391420|gb|FL107763.1|FL107763
EST:     ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAG                         GTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
genomic: ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAGgtcctgtaat ... gtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
EST: gi|211396659|gb|FL107783.1|FL107783
EST:     ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAG                         GTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
genomic: ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAGgtcctgtaat ... gtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
EST: gi|20507306|gb|BQ279572.1|BQ279572
EST:     ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAG                         GTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG
genomic: ACAACTGCGCCGCCGACTGGTCGCTCTACAACCACATCGACGTCCCCAAGgtcctgtaat ... gtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataggcggtgaacaaggatttagggcggcggctgacacgatctcgtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGG
                              ggctgac  putative branch site (score: 3)
                  attta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtaccccgcggcgcatcggattgtgcgacagtatacagtacaataggcggtgaacaaggatttagggcggcggctgacacgatctcgtgcgcgcagGTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG