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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtgtgcaagagagtgtatgcatccatttatcttatcctctacctatttcattcaggtcaccaaagtttgtccctgctttgttttttttgtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAG

Basic information

species Zea mays
transcript GRMZM2G110143_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110143_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g37960.1 (Oryza sativa), 3'ss of exon 4
ctgtgtgcaagagagtgtatgcatccattta--tcttatcctctacctatttcattcaggtcaccaaagtttgtccctgctt-tgttttttttgtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAG
 |||||  ||      | |  |||   |||   | ||||||||||| ||| | | | | ||||   |  |||     || || |||| ||    | ||||||| |  ||||||||| ||| ||| | ||||||||||||| | ||||||||||| |||||||| ||||||| |||
ttgtgttgaactttaagaa-acatttgttttgttattatcctctacttatgtaaatgaagtcat--atctttaattttgtttatgttcttccaatctctgtagACGAAAAGGAAGGATCATAGAAGAGGTTGAGAAATCACGGGACAGGTCAAGAAGCCGTAGCCCAAGGCGAAG
















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|89757947|gb|DY687314.1|DY687314
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|149005364|gb|EE039916.2|EE039916
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|149107293|gb|EE189175.2|EE189175
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|4152004|gb|AI372138.1|AI372138
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGA
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGA
EST: gi|76290040|gb|DV029608.1|DV029608
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|32833902|gb|CD973580.1|CD973580
EST:     ACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: ACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|211277772|gb|FL330870.1|FL330870
EST:     AACATCANTGGTGCATGTTTGCAAAGTACGGCCCCCAATGCTGTGCCAAT                         CCCCCAAGGAAGGGTCAAAGAGGGGGGTTGAGAAATCA
genomic: AACATCA-TGGTGCA-GTTTGCAAAGTACGGCCCC-AATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGG-TTGAGAAATCA
EST: gi|50335677|gb|CO530803.1|CO530803
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|78076983|gb|DV505417.1|DV505417
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|50325433|gb|CO520559.1|CO520559
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|74243434|gb|DT651348.1|DT651348
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|211347504|gb|FL349161.1|FL349161
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTC
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTC
EST: gi|89756357|gb|DY686407.1|DY686407
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|74237054|gb|DT644968.1|DT644968
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|71420359|gb|DR805069.1|DR805069
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|71321797|gb|DR797591.1|DR797591
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|31558121|gb|CD527333.1|CD527333
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|211253499|gb|FL469937.1|FL469937
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|211208282|gb|FL335694.1|FL335694
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATC
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATC
EST: gi|32835620|gb|CD975298.1|CD975298
EST:     GTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: GTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|74241218|gb|DT649132.1|DT649132
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|30307256|gb|CD001929.1|CD001929
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|60400418|gb|DN233225.1|DN233225
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|50328942|gb|CO524068.1|CO524068
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|149101748|gb|EE287365.2|EE287365
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|71325769|gb|DR799565.1|DR799565
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
EST: gi|50328977|gb|CO524103.1|CO524103
EST:     AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT                         CCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG
genomic: AGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAATgtgagtaggc ... gtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttcattcaggtcaccaaagtttgtccctgctttgttttttttgtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAG
                          tccctgctttgttttt  CT-rich tract
                                 tttgttttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtgtgcaagagagtgtatgcatccatttatcttatcctctacctatttcattcaggtcaccaaagtttgtccctgctttgttttttttgtgtctgtagCCACAAAGGAAGGGTCAAAGAGGGGGTTGAGAAATCAAGAGACAGGTCAAGGAGCCGTAGTCCAAGGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG