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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccctatgtgcatggtgcatcctgtagatatgatacacatattgcttatgactcttcagacatagagaggtatacccgactaattcagaacttattttcagGTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGGAGCAGTCCTTGGTAGGCTCCAGCATACTGGCAACTTCTGGGTATAACTC

Basic information

species Zea mays
transcript GRMZM2G017923_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017923_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g55000.1 (Oryza sativa), 3'ss of exon 3
ccctatgtgcatggtgcatcctgtagatat--gatacacatattgcttatgactcttcagacatagagaggtatacccgactaattcagaacttattttcagGTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGGAGCAGTCCTTGGTAGGCTCCAGCATACTGGCAACTTCTGGGTATAACTC
   ||| |   ||     ||||  | ||||  |||   |   ||| || || | |||   ||||| ||    ||    ||||||| || || ||||  |||||||||||||| |||  |    || |||||| ||||||||| ||||| ||| |||||||||||||||| ||||||||||||||  |||||||| || | ||
-tttatatctttgtgttttcctacacatataagatgtcccagttggttctgcccctt-gcacataaagtatcatgtgtgactaatccaaaaattatcctcagGTATTGTAATTCCTATTCTGTCCCTGAAGCAATTCACTCCGACTAGATGGCAGCAGTCCTTGGTAGGATCCAGCATACTGGCTGCTTCTGGGCATCATTC
















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|71775037|gb|DR972915.1|DR972915
EST:     CTTCCTACAGCAGCGATGTCGATTTGGTGGTAACTGCCGCATGTCTCATG                         GTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGG
genomic: CTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATGgtatgttaat ... ttattttcagGTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGG
EST: gi|78088366|gb|DV516759.1|DV516759
EST:     CTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG                         GTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGG
genomic: CTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATGgtatgttaat ... ttattttcagGTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGG
EST: gi|149081356|gb|EE170470.2|EE170470
EST:     CTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG                         GTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGG
genomic: CTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATGgtatgttaat ... ttattttcagGTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGG
EST: gi|149073984|gb|EE162314.2|EE162314
EST:     CTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG                         GTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGG
genomic: CTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATGgtatgttaat ... ttattttcagGTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGG
EST: gi|74245804|gb|DT653718.1|DT653718
EST:     CTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG                         GTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGG
genomic: CTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATGgtatgttaat ... ttattttcagGTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGG
EST: gi|149110259|gb|EE190315.2|EE190315
EST:     CTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG                         GTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGG
genomic: CTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATGgtatgttaat ... ttattttcagGTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGG
EST: gi|148932219|gb|EC875717.2|EC875717
EST:     CTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG                         GTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGG
genomic: CTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATGgtatgttaat ... ttattttcagGTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGG
EST: gi|148999333|gb|EE036269.2|EE036269
EST:     CTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG                         GTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGG
genomic: CTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATGgtatgttaat ... ttattttcagGTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgactcttcagacatagagaggtatacccgactaattcagaacttattttcagGTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGGAGCAGTCCTTGGTAGGCTCCAGCATACTGGCAACTTCTGGGTATAACTC
                               gactaat  putative branch site (score: 2)
                                            cttattttc  putative PPT
                                          aacttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccctatgtgcatggtgcatcctgtagatatgatacacatattgcttatgactcttcagacatagagaggtatacccgactaattcagaacttattttcagGTATTGTAATGCCTTCTAAAGCCTTGAAGCGATTCACTCCAACTAGGTGGGAGCAGTCCTTGGTAGGCTCCAGCATACTGGCAACTTCTGGGTATAACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG