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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccagtttacactgcttcactttatttatttttctttcctatcatgacccctaagtattatattgaaatctacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG

Basic information

species Zea mays
transcript GRMZM2G006130_T06
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 8
gtaccagtttac--------actgcttcactttatttatttttct--ttcctatcatg----acccctaagtattatatt-----------------gaaatctacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
|||| |||||||        | | || |  || ||||  || ||   | |  |||||      ||  | |||  ||||||                 ||| || || ||||||||| | ||||| ||||||||||||||||||||||| ||||||||||
gtactagtttacttgacattattcctgcctttcattttcttatcacgtcctaatcatatattgcctttgagttctatatttttctaatgaaaactttgaactccacatcaaagCTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG

upper sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 8
-------------------------------gtaccagttta-cactgcttcactttat-ttatttttctttcctatcatgacccctaagtattatattgaaatctacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
                                 |     ||| |||| | | |   ||| ||   |||   | ||||  |     ||||  |  |  ||||| ||||| ||||||||| | ||||||||||| ||||||||||||||||| || |||||||
gtaccagtttagttgacattatttccgcccttcattttcttatcactccctaatcatatattgcctttgaattctatttttttttctaatgaaaaatttgaactctacatcaaagCTTTCTGAGGACCTGGGCGCTGCCCCAATCTGGGTGTTTAACAATG
















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|211350735|gb|FL044608.1|FL044608
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCA
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCA
EST: gi|211350729|gb|FL044602.1|FL044602
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGGACCTGGGTGCTGCCCCAA
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGG-ACCTGGGTGCTGCCCCAA
EST: gi|211350733|gb|FL044606.1|FL044606
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAAGGACCTGGGTGCTG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGA-GGACCTGGGTGCTG
EST: gi|211221447|gb|FL389601.1|FL389601
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
EST: gi|211350724|gb|FL044597.1|FL044597
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGT
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGT
EST: gi|211350722|gb|FL044595.1|FL044595
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGN-CCTTGGGGTGCTGCCCCA-TCTGGGTATTCAACAATGGAA
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCT-GGG-TGCTGCCCCAATCTGGGTATTCAACAATGGAA
EST: gi|211350723|gb|FL044596.1|FL044596
EST:     GTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGGTCCTTCAG                         CTTGCGGAGGACCTGGG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGG
EST: gi|211353135|gb|FL044612.1|FL044612
EST:     TTTGGCATTACTGGACTGATGATGGGCTTAGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAA
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAA
EST: gi|21331549|gb|BQ486930.1|BQ486930
EST:     GTGGCATTACTGGACTGATGATGGGNC-TGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTGGCATTACTGGACTGATGATGGG-CTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
EST: gi|32929408|gb|CF034220.1|CF034220
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
EST: gi|211350730|gb|FL044603.1|FL044603
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGAC
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGAC
EST: gi|211353132|gb|FL044609.1|FL044609
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCC
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCC
EST: gi|32924613|gb|CF029425.1|CF029425
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
EST: gi|18963147|gb|BM660266.1|BM660266
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
EST: gi|18661865|gb|BM501621.1|BM501621
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
EST: gi|211350725|gb|FL044598.1|FL044598
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
EST: gi|32923839|gb|CF028651.1|CF028651
EST:     TACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
EST: gi|211350728|gb|FL044601.1|FL044601
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATNATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCC
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCC
EST: gi|211150003|gb|FL374637.1|FL374637
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
EST: gi|211079656|gb|FL402147.1|FL402147
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAN                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
EST: gi|18654845|gb|BM499650.1|BM499650
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
EST: gi|32929966|gb|CF034778.1|CF034778
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
EST: gi|32924017|gb|CF028829.1|CF028829
EST:     TACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
EST: gi|32924051|gb|CF028863.1|CF028863
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
EST: gi|32924183|gb|CF028995.1|CF028995
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
EST: gi|211350731|gb|FL044604.1|FL044604
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTA
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTA
EST: gi|211353136|gb|FL044613.1|FL044613
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATGG
EST: gi|32924623|gb|CF029435.1|CF029435
EST:     TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
EST: gi|32928349|gb|CF033161.1|CF033161
EST:     TACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAG                         CTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
genomic: TACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagttt ... tacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttttctttcctatcatgacccctaagtattatattgaaatctacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG
                          taagtattatattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccagtttacactgcttcactttatttatttttctttcctatcatgacccctaagtattatattgaaatctacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC