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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaatacttgcatgactgtttactactctctgaattgctctcattcactgttttcagcatttgttattttatgattttttatgcattgatag

Basic information

species Zea mays
transcript GRMZM2G410515_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G410515_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 5'ss of exon 4
GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgata--aatacttgcatgactgtttactactctctgaattgctctcattcactgttttcagcatttgttattttatgattttttatgcattgatag-------------------------------------------------
|||| |||||| ||||||| || || ||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||| | |     || |||  |||  ||  |   | | | |   ||  ||    |   | ||||  |      |||| |||  |  |  ||| || || |||                                                 
GATTAGCTGGTTTATCAACGGCAAAATATCTGGCAGATGCTGGTCATAAACCCATATTGCTTGAGGCAAGGGATGTTTTGGGTGGAAAGgttttactcttatgcttttatg-ttgcatttaattttttttgttattcattctttttttttttggttgcctttatcttaatagctcatattcactgttagtagcatttgtggattattgtttttttttttggggaaatgccttgaacag

upper sequence: GRMZM2G410515_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA18G00720.1 (Glycine max), 5'ss of exon 3
GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaatacttgcatgactgtttactactctctgaattgctctcattcactgttttcagcatttgttattttatga---ttttttatgcattgatag-------
||||||||||| ||||||| || || ||| |||| |||||||| |||||||| |||||||| || |||||||| ||| | ||||||||||| |      || ||  ||  || |   | |     | | |||   ||| | | ||         ||  ||||||||  |   | ||| ||| | | | |        
GATTGGCTGGTTTATCAACTGCAAAATATTTGGCTGATGCTGGGCATAAACCTATATTGCTGGAAGCAAGAGACGTTCTAGGTGGAAAGgttttcctgctaatttaatccctttcggcaa-----taagttg---tcacttagtgcgccttcttttcattattttaacaagctgtttaatgaaataagaaatttgtt

upper sequence: GRMZM2G410515_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA11G36810.1 (Glycine max), 5'ss of exon 3
GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaatacttgcatgactgtttactactctctgaattgctctcattcactgttttcagcat-ttgttattttatgattttttatgcattgatag-------
||||||||||| ||||||| || || ||| |||| |||||||| |||||||| |||||||| || |||||||| ||| | ||||||||||| |      || ||   | |    ||||   ||  | | ||| || | ||   ||  ||| ||   || || |   ||| | ||| ||| | | | |        
GATTGGCTGGTTTATCAACTGCAAAATATTTGGCTGATGCTGGGCATAAACCTATATTGCTGGAAGCAAGAGACGTTCTAGGTGGAAAGgttttcctgctaatt---taatctcttacg--tcaattagttg-tcactttgtgtgcattctgctcattattttagcatgctgtttaatgaaataagaaatttgtt

upper sequence: GRMZM2G410515_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT4G14210.2 (Arabidopsis thaliana), 5'ss of exon 4
GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgt---ctgataaat---acttgcatgactgtttactactctctgaattgctctcattcactgttttcagcatttgttattttatgattttttatgcattgatag---
||||||||||  | ||||| || ||||| ||||| ||||| || || |||||  | |||||||| |||||||||||| | |||||||||||    ||||   |   |||| |   | |  ||| |  | | || |||  ||||||||     ||  |  ||||| |  ||    |    |    || | ||     
GATTGGCTGGATTGTCAACTGCAAAGTACCTGGCTGATGCAGGCCACAAACCTCTGTTGCTTGAAGCAAGAGATGTTCTTGGTGGAAAGgtactttgattggtctcactttccgaattacttattgttgtttgcatt--tctcattc-----ttatatgatttgctgattcccaaaggctgtaccaattatgtttg

upper sequence: GRMZM2G410515_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 5'ss of exon 4
GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaatacttgcatgactgtttactactctctgaattgctctcattcactgttttcagcatttgttattttatgattttttatgcattgatag-----
| ||||||||| | || || || || ||| |||||||||| || || || || |||||| | || |||||||||||||| ||||||||||| |   | || ||    |   | |   |  || | | | ||    ||||| |   | |   || | |  | |  ||| |  ||  |    |           
GTTTGGCTGGTTTGTCTACTGCAAAATATTTGGCAGATGCAGGTCACAAGCCTATATTGTTGGAAGCAAGAGATGTTTTAGGTGGAAAGgtttatgagatgctc---tatttttgcccctctttttaatttttagtcattaaacttctcttgcttattctgtcatataaaattcaaactttctccccttatt

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|211417839|gb|FL018169.1|FL018169
EST:     CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG                         GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
genomic: CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
EST: gi|211005245|gb|FL018195.1|FL018195
EST:     CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG                         GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
genomic: CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
EST: gi|211002469|gb|FL018188.1|FL018188
EST:     CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG                         GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
genomic: CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
EST: gi|211417840|gb|FL018170.1|FL018170
EST:     CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG                         GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
genomic: CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
EST: gi|211417848|gb|FL018178.1|FL018178
EST:     CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG                         GTAGCTGCTTGGAAGGATGAAGATGGAGNAT-GGTACGAGACTGGGCTTCA
genomic: CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAG-ATTGGTACGAGACTGGGCTTCA
EST: gi|211002475|gb|FL018194.1|FL018194
EST:     CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG                         GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
genomic: CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
EST: gi|71765383|gb|DR963320.1|DR963320
EST:     CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG                         GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
genomic: CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
EST: gi|211005249|gb|FL018199.1|FL018199
EST:     TGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGGTGGAAAG                         GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
genomic: TGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGG-TGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
EST: gi|211417844|gb|FL018174.1|FL018174
EST:     TGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGGTGGAAAA                         GTAGCTGCTTGGAAGG
genomic: TGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGG-TGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGG
EST: gi|211417847|gb|FL018177.1|FL018177
EST:     TGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTTGGGTGGAAAA                         GTAGCTGCTTGGAAGGATGATGATGGAGATTGGTACGAGACTGGGCTTCAT
genomic: TGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTT-GGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
EST: gi|211002464|gb|FL018183.1|FL018183
EST:     CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG                         GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
genomic: CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
EST: gi|76294009|gb|DV033577.1|DV033577
EST:     CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG                         GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
genomic: CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
EST: gi|78075888|gb|DV504322.1|DV504322
EST:     CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG                         GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
genomic: CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
EST: gi|211417850|gb|FL018180.1|FL018180
EST:     CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG                         GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
genomic: CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
EST: gi|211415305|gb|FL018166.1|FL018166
EST:     TGGACATAAACCCATATTGCTTGAGGCAAAGAGATGTTTTGGGTGGAAAG                         GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
genomic: TGGACATAAACCCATATTGCTTGAGGCAA-GAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
EST: gi|211417841|gb|FL018171.1|FL018171
EST:     CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG                         GTAGCTGCTTGGAAG
genomic: CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaatacttgcatgactgtttactactctctgaattgctctcattcactgttttcagcatttgttattttatgattttttatgcattgatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA