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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtcgaacttacattcaacagtcagcttttactgctattctcaagaaccgaccaaagtttaatgtcctgttcactattcag

Basic information

species Zea mays
transcript GRMZM2G081188_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081188_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g66350.1 (Oryza sativa), 5'ss of exon 2
GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtcgaacttacattcaacagtcagcttttactgctattctcaaga------accgaccaaagtttaatgtcctgttcactattcag
||| | ||||||||||||||||||||||| ||||||||||| ||||| || ||||||||||| ||||| || || |||||||||||||| || |||||||||||||   ||||||   ||||   |||   | | ||| ||      || |       |  ||  ||  ||| | |  | |  |    | ||
GAAGTTATGGCATTCATAAGATCATATGTTGTGCCTGAAGGCTTTCCGGATAGTGTTACTCCGTCATACGTCCCATACATGACCTGGAGAGCCCTGAAGgtatatttcggaacttgtgttcacttgtcgtttgtgacttctgaatcaaatacatcatgctaacttaaaattattatttt-tgtatcccttag

upper sequence: GRMZM2G081188_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA07G40210.1 (Glycine max), 5'ss of exon 2
GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtata---ttgtcgaacttaca-ttcaacagtcagcttttactgctattctcaagaaccgaccaaagtttaatgtcctgttcactattcag
||| |  |  | ||| | | ||| ||||| || || ||||| || || || |||||||||||||| ||||| || |||||||| ||||||||||| |||||||    |||||   |||  | ||  |||  || ||     |||  |  |  ||  || | ||   |||    |  |             
GAAGTCCTCTCTTTCGTTACATCCTATGTTGTCCCCGAAGGTTTCCCTGATAGTGTTACTCCTTCTTATGTCCCCTACATGACATGGAGGGCTCTTAAGgtatccttttgtctttcttctacttttacacacacctacctgtgccttcattcagctcc-atcatcatttgtaattgtag-----------

upper sequence: GRMZM2G081188_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA17G00580.1 (Glycine max), 5'ss of exon 1
-GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtcgaacttacattcaacagtca--gcttttac-tgctattctcaagaaccgaccaaagtttaatgtcctgttcactattcag-----
 ||| |  | || ||| | | ||| ||||| || || ||||| ||||| || ||||||| |||||| ||||| || |||||||| ||||||||||| ||||||| |  |     |    || | |    |   |||||||    |   |||   |  | | ||   |  |   || |  ||| |  | |      
TGAAGTCCTCGCTTTCGTTACATCCTATGTTGTCCCCGAAGGTTTTCCTGATAGTGTTATTCCTTCCTATGTCCCCTACATGACATGGAGGGCTCTTAAGgtatgtaatatgtatgttgtttatcttgtactacttttacacattcagctcttaactccatcatcatc-atcatcatcatcatttgtaattgtag

upper sequence: GRMZM2G081188_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv12s0035g01870.t01 (Vitis vinifera), 5'ss of exon 2
GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtcgaactt------acattcaacagtcagcttttactgctattctcaagaaccgaccaaagtttaatgtcc-tgttcactattcag-------------------------------------------------------------------------------------
||  | ||| ||||||||||||| ||||||||||| || || || || || |||||||||||||||||||| || |||||| | ||||| ||| | |||||||  | |     ||      | |    | || | |  |||  |   |      ||| ||  |  |  |||   |  |  |   | |||  |                                                                                      
GAGTTGATGTCATTCATAAGATCCTATGTGGTGCCCGAGGGATTCCCGGATAGTGTTACTCCTTCATATGTGCCATACATGTCATGGAGAGCTTTAAAGgtattctcttacgtttggtgctataccataaaggcgggcttttttaggaaat--gagagccatctcatatttggagaacacggatattatgaatattacaaaacattctacgtctaatttatgtgaagtggggttgctgccctaaaatacaatactgatgaatttcatgttcattgtag

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|211292640|gb|FL058746.1|FL058746
EST:     CAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAAG                         CATTTCTT-GGTGGAGCGATGGGAGTGTTTACGA
genomic: CAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAA-Ggtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGA
EST: gi|211299060|gb|FL058784.1|FL058784
EST:     CAGTGTTACTCCTTCATATGTACCTTACATGACCTGGGAGG-CTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
genomic: CAGTGTTACTCCTTCATATGTACCTTACATGACCTGG-AGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
EST: gi|148945695|gb|EC890968.2|EC890968
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
EST: gi|211292628|gb|FL058734.1|FL058734
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGG
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGG
EST: gi|148953714|gb|EC899078.2|EC899078
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
EST: gi|32837137|gb|CD976815.1|CD976815
EST:     ACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGGGTGTTTACGACAAGAACCTTGCTGAGT
genomic: ACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
EST: gi|211288358|gb|FL058718.1|FL058718
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGAGTGTTTACGAACA-GAACCTTGCTGAG
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGA-CAAGAACCTTGCTGAG
EST: gi|211290496|gb|FL058728.1|FL058728
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGAGTG
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTG
EST: gi|211296915|gb|FL058767.1|FL058767
EST:     CAGTNGT-ACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
genomic: CAGT-GTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
EST: gi|149076159|gb|EE164750.2|EE164750
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
EST: gi|211292635|gb|FL058741.1|FL058741
EST:     ACAGTGGTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGAAGCGATGGGAGTGTT-ACGACAAGAAC-TTGCTGA
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGA
EST: gi|211296923|gb|FL058775.1|FL058775
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
EST: gi|211290489|gb|FL058721.1|FL058721
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         AATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAAC
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAAC
EST: gi|211290499|gb|FL058731.1|FL058731
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGAGTGTT
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTT
EST: gi|211290497|gb|FL058729.1|FL058729
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTTGCTGAG
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTT-GCTGAG
EST: gi|211294779|gb|FL058757.1|FL058757
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTTGCTGAG
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTT-GCTGAG
EST: gi|31353527|gb|CD437884.1|CD437884
EST:     TACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTCTT-GTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAG
genomic: TACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCT-TTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAG
EST: gi|148958478|gb|EC904716.2|EC904716
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
EST: gi|148966241|gb|EE017202.2|EE017202
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
EST: gi|211288350|gb|FL058710.1|FL058710
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGG
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGG
EST: gi|211296919|gb|FL058771.1|FL058771
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGAGTGTTTACGAC
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGAC
EST: gi|211288352|gb|FL058712.1|FL058712
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTG
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTG
EST: gi|211517299|gb|FK997845.1|FK997845
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAA                         CATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAAT
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
EST: gi|211296912|gb|FL058764.1|FL058764
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
EST: gi|149012213|gb|EE042512.2|EE042512
EST:     ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAG                         CATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT
genomic: ACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtc ... cactattcagCATTTCTTTGGTGGAGCGATGGGAGTGTTTACGACAAGAACCTTGCTGAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAATAATGGCATTCATAAGATCATATGTGGTGCCTGAAGGGTTTCCAGACAGTGTTACTCCTTCATATGTACCTTACATGACCTGGAGGGCTCTGAAGgtatattgtcgaacttacattcaacagtcagcttttactgctattctcaagaaccgaccaaagtttaatgtcctgttcactattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG