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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccacttagtcataatttttttaacatttatcctaagtgttgcaaatttacttgatgaagttttgccttcccatttaacaaaaaagagattgcaa...

Basic information

species Zea mays
transcript GRMZM2G165418_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 5'ss of exon 7
TCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccacttagt--cataatttttttaacatttatcctaagtgttgcaaatttacttgatgaagttttgccttcccatttaacaaaaaagagattgcaa--
|||||||||||||| || |||||| ||||||| ||||| ||||| | ||||||||| || |||||||| ||||||||| ||||||||||||| ||||| ||||| |||| |||||  | || || ||  |  |||| | || |   |||  |||| |  |  || ||  | |   |   ||| |   |   |    ||   |  
TCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccatttagtaccttatttcttacatgatttgtgctcaactttg--aattaatgtactgcagcatgga--taaaattgattgatggaagctttcttaat

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA13G42800.2 (Glycine max), 5'ss of exon 7
TCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccacttagtcataatttttttaacatttatcctaagtgttgcaaatttacttgatgaagttttgccttcccatttaacaaaaaaga-gattgcaa
||||| |||||||| ||||||||| | |||||| ||||||| | ||  || || ||||| ||||||||||| |||||| |||| ||||| ||||| ||||||||      | |   | | | |  || |   ||| | | | || |       ||    |  ||  ||         || |     || | |  |||||| 
TCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACAGgtaagcttgataaaaaaaattatcctttattgttaacattattggtaacttggtaaaacactaaaattaattaatttatatggtttaagaaataattgca-

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 7
TCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccacttagtcataat-ttttttaacatttatcctaagtgttgcaaatttacttgatgaagttttgccttcccatttaacaaaaaagagattgcaa
||||| |||||| | ||||||||| | |||||| ||||||| | ||  || || ||||| ||||||||||| |||||| |||| ||||| ||||| ||||||||      | ||  | | | |  ||||   | ||   ||   ||  ||   | |     | || ||      |     |      | ||   |||||| 
TCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACAGgtaagcttgataagaaaaattatcctttagtgtatacattatcagtatcagggtaaaactctaaaattaattaatttatatagttcgagaaataattgca-

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 7
TCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccacttagtcataatttttttaacatttatcctaagtgttgcaaatttacttgatgaagttttgccttcccatttaacaaaaaagagattgcaa------
||||| |||||| | ||||||||| | |||||| ||||||| | ||  || || ||||| ||||||||||| |||||| |||| ||||| ||||| || ||||| |    ||    ||  | ||||||   | |     || ||||     || |  | |    || |    |  |||||||| |    | |  || ||       
TCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACTGgtaagt---tttcactattgtatttttatgctgtgctgaaactgttctctgttga--taacttggtataatttatccatttaa-agggcaaaacttacagtaccat

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA08G20830.2 (Glycine max), 5'ss of exon 7
TCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccacttagtcataatttttttaacatttatcctaagtgttgcaaatttacttgatgaagttttgccttcccatttaacaaaaaagagattgcaa-----
||||| |||||| | ||||||||| | |||||| ||||||| | ||  || || ||||| ||||||||||| |||||| |||| ||||| ||||| || ||||| |    ||    ||  | ||||||   | |     || ||||     || |  | |    || |    |  ||||||||     || |   |  |      
TCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACCGgtaagt---tttcactattgtatttttatgctgtgctgaaaatgttctctgttga--taacttggtataatttatccatttaaagggcaaaaacatatatacagt

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 7
TCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccacttagtcataatttttttaacatttatcctaagtgttgcaaatttacttgatgaagttttgccttccca--tttaacaaaaaagagattgcaa------------------------------------------------
|| || |||||||| ||| ||||| | ||||| |||||||| | || |||||| || || ||||||||||| ||||| ||||||||||| ||  |||| |||| | | ||||  || || ||| ||  |  ||  |    |  ||   |   ||  || ||          | |||    ||| |  |   |    || ||                                                 
TCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACAAACATGGAGGACTTAACTGgta-tgctacttc-tcctattttgttagatgttactttgtatggtcttaccattgattcatatgtcaacaacctccttacttttattatctatttttttcacgtttactgcttgtcgagcatgcttctaaatgctacatggtctgtgcag

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 5'ss of exon 7
TCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccacttagtcataatttttttaacatttatcctaagtgttgcaaatttacttgatgaagttttgccttcccatttaacaaaaaagagattgcaa------
||||| ||||||||||| |||||| | |||||||||||||| | ||| || || || ||||||||||||||||||||| |||||||||| |||||||| ||||   |  |  || | |   |     || |||    |||| ||  |    ||||  |  |||| |||     |   ||||||  |    |  ||   ||      
TCAGCTGATGATCTCCGGATAAATCTCTGGAACTTGGAAATTAGCAGTCAAAGTTTCAACATTGTTGATGTGAAGCCTGCAAACATGGAGGATCTAACTGgtagaact-cccagcctt--ctgaaagaaaattgtgtctaaatgg-gttgttttaacttctgaattttaagtgtt--atttaatgacttgggcatgttaaaaagaa

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 5'ss of exon 7
TCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccacttagtcataatttttttaacatttatcctaagtgttgcaaatttacttgatgaagttttgccttcccatttaacaaaaaagagattgcaa-----
||||| |||||||| || |||||  | |||||| ||||||| | ||  || || || || |||||||||||||||||||| |||||||| ||||| || ||||       ||||||     | ||| |  |||| | |||   |||     ||   ||  ||   | |   ||  | || ||    |   |   |||  |     
TCAGCTGATGATCTACGCATAAACCTTTGGAACCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTGAAGCCTACTAACATGGAGGATCTGACTGgtacggatttttagtc----ctctttcatgatttgttctactagttttgtcttccttttttgtcatctcttctggc-atgtacttcaggtggtgttgatattttg

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 7
TCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccacttagtcataatttttttaacatttatcctaagtgttgcaaatttacttgatgaagttttgccttccca--tttaacaaaaaag--agattgcaa-
||||| |||||||| ||||||||  | |||||||||||||| | || ||| ||||| || |||||||||||||||||| |||| ||||| |||||||| |||||    | ||| | || || || |  | ||| |       |  |     | || ||  ||    ||| ||    ||  ||||| | |   |  | ||||    
TCAGCTGATGATCTGCGAATAAACCTTTGGAACTTGGAAATTAGCAACCAAAGCTTCAATATTGTTGATGTGAAGCCTGCAAATATGGAGGATCTAACTGgtaaaatta-ttactaattatcttct-gatattcagtt---atactctgtgtgtattttgtgtgtcttttccaaggcacttttaatatatttgctaaattgacct

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|31352864|gb|CD437221.1|CD437221
EST:     GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAG                         AGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
genomic: GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccac ... catatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
EST: gi|211384024|gb|FL015619.1|FL015619
EST:     GAGNTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAG                         AGGTGATTACNTGNGCGGAGTTCCATCCATCCCATTGNAATACACTGGCCT
genomic: GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccac ... catatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
EST: gi|24934206|gb|CA452424.1|CA452424
EST:     GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAG                         AGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
genomic: GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccac ... catatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
EST: gi|211386654|gb|FL015627.1|FL015627
EST:     GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAG                         AGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
genomic: GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccac ... catatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
EST: gi|211386649|gb|FL015622.1|FL015622
EST:     GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAG                         AGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACNCTGGCCT
genomic: GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccac ... catatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
EST: gi|67025874|gb|CO454623.1|CO454623
EST:     GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAG                         AGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT
genomic: GAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccac ... catatttcagAGGTGATTACATGTGCGGAGTTCCATCCATCCCATTGTAATACACTGGCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccacttagtcataatttttttaacatttatcctaagtgttgcaaatttacttgatgaagttttgccttcccatttaacaaaaaagagattgcaa

- - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA