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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatttcctctacatatccttgttcaatcggtgggtcttgctttctgactgcaatacatacatgtaccgattgcag

Basic information

species Zea mays
transcript GRMZM2G148130_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G148130_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g47770.1 (Oryza sativa), 5'ss of exon 5
ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatttcctctacatatcct--tgttcaatcggtgggtcttgctttctgactgcaatacatacatgt-accgattgcag---
|||||||||||||||||||||| || || ||||| || |||||| | |||||||| || || || ||| |||| ||||||||||||||||||| | |  | | ||   |   ||  |||| ||  ||  | || ||| | |||||   | || ||   | | |    |||  |   
ATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAGgttatagagcttcactgtgtcctctcctgtttaaatgg-agatcatgcat-ctgaccatattatatgtttattatatgttggtgcag

upper sequence: GRMZM2G148130_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA01G37480.1 (Glycine max), 5'ss of exon 5
ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatt-tcctctacatatcct-tgttcaatcggtgggtcttgctttctgactgcaatacata--catgtaccgattgcag---------------
||||||||||||| || |||||||| || ||||| || ||||||||||| ||||| ||  | || ||||| || |||||| |  ||||||| | |  || |   | |   ||| | | ||       |   | |||   | |||    | |||     ||| ||     |||                 
ATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAGgtgagaatttattaaccatgaatcttgtattttcctaattccttttgtgctatgataagattactggaccatataggacatgctatatttttaaccaagg

upper sequence: GRMZM2G148130_T03 (Zea mays), 5'ss of exon 5
lower sequence: AT1G75440.1 (Arabidopsis thaliana), 5'ss of exon 5
ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgt-tacatatttcctctacatatccttgttcaatcggtgggtcttgctttctgactgcaa-tacatacatgtaccgattgcag-------------
|||| |||||||| |||||||| ||||| ||||| || ||||||||||| || |||||  | || ||||| || |||||  | | ||||||    | |  || |  ||  | | ||  |  ||         |  |||| |  ||| |  |  |     ||  || |||                
ATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAGgtacttacagctcttacactcaccattaatatataaactttgatctctttgttgctgaagctgaaccttcgtctcgcttggcttgttttgttgcag

upper sequence: GRMZM2G148130_T03 (Zea mays), 5'ss of exon 5
lower sequence: Vv18s0001g13180.t01 (Vitis vinifera), 5'ss of exon 5
ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatttcctctacatatcctt-gttcaatcggtgggtcttgctttctgactgcaatacatacatgt-----accgattgcag-------------------------------------
||||  | ||||| || ||||||||||| ||||| || ||||| ||||||||||||||| | || ||| | || |||||| | |  ||||||   |      | |  |  |  |  |||   |       || |   |||| | |        ||  | |      || |||  ||                                     
ATATTCTATATGATTCATGGTCCCCAGCCATGACAGTTAGTTCAATCTGTATCAGCATACTCTCCATGTTATCGAGCTCAACTGTGAAGgtttggttcaaattgtcaaagttttaagttttttaaacccctcctttcttcttaattttgcttttatctttttccagcctattttagtgtgagagcattactcatgagttttttcattgtgcag

upper sequence: GRMZM2G148130_T03 (Zea mays), 5'ss of exon 5
lower sequence: Vv04s0023g02620.t01 (Vitis vinifera), 5'ss of exon 5
ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgtta-----catatttcct--------ctacatatccttgttcaatcgg---tgggtcttgctttctgactgcaatacatacatgtaccgattgcag----
|||| |||||||| || ||||||||||| ||||| || ||||||||||| ||||||||  | || ||||| || |||||| | |  ||||||      ||| |||| |         | ||||||||| |    ||     |     | | ||||    ||| ||  || ||  |  |    |||     
ATATTTTGTATGATTCTTGGTCCCCAGCCATGACAGTTAGTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAGgttcttgtccatctttcttactagcactttcatatccttctcggttcacaattcaacttggttttccttgtgctatg-attcaattctctggggcaaagct

upper sequence: GRMZM2G148130_T03 (Zea mays), 5'ss of exon 5
lower sequence: PP1S211_21V6.1 (Physcomitrella patens), 5'ss of exon 5
ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatttcctctacatatccttgttcaatcggtgggtctt--gctttctgactgcaatacatacatgtaccgattgcag------------------
||||  | |||||||| ||||| ||||||||||| || ||||||||||| ||||||||  | || ||| |||| || ||| | |  |||||    | |    | | || |      | ||     ||  | ||  |  |   |  || || | ||           ||  ||                  
ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtactttttaaagtttccacactagcctccacgtattgaattttcagtatatcgcatgtaaaa-atggggactgttcttttagtgtcctgctttctaactt

upper sequence: GRMZM2G148130_T03 (Zea mays), 5'ss of exon 5
lower sequence: PP1S193_49V6.1 (Physcomitrella patens), 5'ss of exon 5
ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatattt-cctctacatatcctt--gttcaatcggtgggtcttgctttctgact---gcaatacatacatgtaccgattgcag--------------
|||||||||||||||| ||||| |||||||||||||| || || ||||| ||||||||  | |||||| | || || ||| |||  |||||  | | ||  |||  || | | |    ||| ||||  ||| |          || |   | ||||| ||||  ||  ||                    
ATATATTGTATGACTCTTGGTCACCAGCAATGACTGTGAGCTCCATCTGCATCAGCATCCTCTCTATGTTATCTAGTTCAACAGTGAAGgtatcctgttaacctgaacttgttcacacgtttaatctttggatagaaaagcgcgagtaaagaaatac-tacacttaatgacattgttttatgttgacttc

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|88755064|gb|DY539205.1|DY539205
EST:     GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG                         CAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
genomic: GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatt ... ccgattgcagCAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
EST: gi|88757761|gb|DY541902.1|DY541902
EST:     GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG                         CAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
genomic: GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatt ... ccgattgcagCAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
EST: gi|71427893|gb|DR808943.1|DR808943
EST:     GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG                         CAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
genomic: GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatt ... ccgattgcagCAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
EST: gi|89754929|gb|DY685543.1|DY685543
EST:     GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG                         CAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
genomic: GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatt ... ccgattgcagCAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
EST: gi|211054652|gb|FL411716.1|FL411716
EST:     GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG                         CAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCNNATGGGAG
genomic: GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatt ... ccgattgcagCAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCA-ATGGGAG
EST: gi|71445359|gb|DR826409.1|DR826409
EST:     GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG                         CAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
genomic: GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatt ... ccgattgcagCAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
EST: gi|5714133|gb|AI944118.1|AI944118
EST:     GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG                         CAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
genomic: GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatt ... ccgattgcagCAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
EST: gi|71445358|gb|DR826408.1|DR826408
EST:     GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG                         CAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
genomic: GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatt ... ccgattgcagCAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
EST: gi|76292123|gb|DV031691.1|DV031691
EST:     GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG                         CAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
genomic: GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatt ... ccgattgcagCAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
EST: gi|86475096|gb|DY241466.1|DY241466
EST:     GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG                         CAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
genomic: GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatt ... ccgattgcagCAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
EST: gi|84980323|gb|DW530672.1|DW530672
EST:     GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG                         CAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
genomic: GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatt ... ccgattgcagCAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
EST: gi|78115399|gb|DV533787.1|DV533787
EST:     GTTCTATTTGTATCAGCATATTATTTATGCTGTCCAGCTCCCCAGCAAAG                         CAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
genomic: GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatt ... ccgattgcagCAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
EST: gi|211318355|gb|FL450740.1|FL450740
EST:     GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG                         CAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG
genomic: GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatt ... ccgattgcagCAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGgttacatatttcctctacatatccttgttcaatcggtgggtcttgctttctgactgcaatacatacatgtaccgattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG