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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttgcaactctacctactgatgttttttttttcttcctatcgctaagcacggtttgcagtgcactaactggaatgaatgccctcgtatttggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAATAAGGTGGAGGCGCGGCGCAGCCATCTTCCATGGGGGTGGGAGTCGAGG

Basic information

species Zea mays
transcript GRMZM2G077607_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077607_T07 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g48830.2 (Oryza sativa), 3'ss of exon 4
gctt-gcaactctacctactgatgttttttt-tttcttcctatcgctaagcacggtt--tgcagtgcactaactggaatgaatgccctcgtatttgg-tctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAATA--AGGTGGAGGCGCGGCGCAGCCATCTTCCATGGGGGTGGGAGTCGAGG
|||  |||  |  ||||| | |  |  |  | | ||   | |||         | ||  |   | |||||||| | ||      | |  || | ||  | |||||| ||| |||||||||||||||||||||||||||||||| |||||||||| |    || ||||||    ||| || || |      |   |  | | |     
gctcagcacatgcacctaatcacctagtagtatctccatccatcaaggtttctgcttaatctcgggcactaaccgaaa-----actcctgtttctgactatgcagAGGCGTAGAGGGCTGAAAGGGATGGAGAGCATGGACAGTGACTCGGAGTGACGGCAGCTGGAGGTCAAGCG-AGGCACCCAAAGCGAAAGGAGCAATAAGA-
















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|110522399|gb|EE026583.1|EE026583
EST:     TTTGACGAGGGGACGGTACGAGGTGCGGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: TTTGACGAGGGGACGGTACGAGGTGC-GGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|50337368|gb|CO532494.1|CO532494
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|50331099|gb|CO526225.1|CO526225
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|38687645|gb|CK144676.1|CK144676
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|91874845|gb|EB404802.1|EB404802
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|76908493|gb|DV162968.1|DV162968
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|71764405|gb|DR962342.1|DR962342
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|88753314|gb|DY537455.1|DY537455
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|148961771|gb|EE012548.2|EE012548
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|86474504|gb|DY240874.1|DY240874
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|211259122|gb|FL168237.1|FL168237
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|148939787|gb|EC884487.2|EC884487
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|148951901|gb|EC897677.2|EC897677
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|149078211|gb|EE166966.2|EE166966
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|94475460|gb|EB704418.1|EB704418
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|149084716|gb|EE174208.2|EE174208
EST:     ATTTGTCGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|71440678|gb|DR821728.1|DR821728
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|148933575|gb|EC877445.2|EC877445
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|101385251|gb|EB814671.1|EB814671
EST:     TTTGACGAGGGGACGGTTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGGCGGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTA
genomic: TTTGACGAGGGGACGG-TACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGA-GGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTA
EST: gi|148963706|gb|EE014774.2|EE014774
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|148953834|gb|EC899210.2|EC899210
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|76914201|gb|DV165443.1|DV165443
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|148963705|gb|EE014773.2|EE014773
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|148997313|gb|EE035808.2|EE035808
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|101385894|gb|EB814995.1|EB814995
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|78080307|gb|DV508719.1|DV508719
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|71434244|gb|DR815294.1|DR815294
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|14244188|gb|BG842258.2|BG842258
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|148956370|gb|EC902184.2|EC902184
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|71756828|gb|DR954765.1|DR954765
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|78079039|gb|DV507451.1|DV507451
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
EST: gi|94477672|gb|EB706630.1|EB706630
EST:     ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAG                         AAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA
genomic: ATTTGACGAGGGGACGGTACGAGGTGCGGGAGAAGAAATGCGTGAAGAAGgtataaatcg ... tggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcacggtttgcagtgcactaactggaatgaatgccctcgtatttggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAATAAGGTGGAGGCGCGGCGCAGCCATCTTCCATGGGGGTGGGAGTCGAGG
                 cactaac  putative branch site (score: 1)
                           aatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttgcaactctacctactgatgttttttttttcttcctatcgctaagcacggtttgcagtgcactaactggaatgaatgccctcgtatttggtctgcagAAGCGAAGAGGGCTGAAAGGGATGGAGAGCATGGACAGCGACTCGGAGTAATAAGGTGGAGGCGCGGCGCAGCCATCTTCCATGGGGGTGGGAGTCGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG