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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAGgtaactgtgtatatctctcctccttttcggctttagtgattattcatatctggtttcctatgaacatatatttgagaacattagtcatgtgattgtagtc...

Basic information

species Arabidopsis thaliana
transcript AT3G04500.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G04500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 2
ATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAGgtaa-ctgtgtatatctctcctc-----cttttcggctttagtgattattcat--atctggtttcctatgaacatatatttgagaacattagtcatgtgattgtagtc
| ||||| || ||||||||||| ||||| || |||||||| |||||||||||||| |||||||||||| |  | || ||  ||||||| ||||| | ||||| | |   || | | |||       ||| |  |    |    |||||||   |||   ||     |   ||  |  |    ||  || || |||| ||       
ACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcccatttttatccaaaaaagcttatttgtagcaaaacttattcaacgatccaattattgtttgccaggttctctgaaa--tttgttatgtaata------

upper sequence: AT3G04500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G068255_T02 (Zea mays), 5'ss of exon 1
--ATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAGgtaa-ctgtgtatatctctcctc-----cttttcggctttagtgattattcat--atctggtttcctatgaacatatatttgagaacattagtcatgtgattgtagtc
  | ||||| || ||||||||||| ||||| || |||||||| |||||||||||||| |||||||||||| |  | || ||  ||||||| ||||| | ||||| | |   || | | |||       ||| |  |    |    |||||||   |||   ||     |   ||  |  |    ||  || || |||| ||       
AGACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaacggcccatttttatccaaaaaagcttatttgtagcaaaacttattcaacgatccaattattgtttgccaggttctctgaaa--tttgttatgtaata------

upper sequence: AT3G04500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G016106_T02 (Zea mays), 5'ss of exon 1
--ATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAGgtaactgtgtatatctctcctccttttcggctt--tagtgattattcatatctggtttcctatgaacatatatttgagaacattagtcatgtgattgtagtc--
  | ||||| || ||||||||||| ||||| || |||||||| |||||||||||||| |||||||||||  |  | || ||  ||||||| ||||| | |||||     |||  || |    |     |||||  | ||    |  | | |        | |   |    |||   | | |  | ||||  |  || |||    
AGACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTATCCAAAGCATTCTCACGGTTTCCATCCTTCAACATGGCAAGGgtaa----atatccctttttatccaaaaggcttatttgtagcaaaacttgttcaacaatccaattattgttatgcaatacctattgtcaaattcttttaggggc

upper sequence: AT3G04500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G016106_T01 (Zea mays), 5'ss of exon 2
ATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAGgtaactgtgtatatctctcctccttttcggctt--tagtgattattcatatctggtttcctatgaacatatatttgagaacattagtcatgtgattgtagtc--
| ||||| || ||||||||||| ||||| || |||||||| |||||||||||||| |||||||||||  |  | || ||  ||||||| ||||| | |||||     |||  || |    |     |||||  | ||    |  | | |        | |   |    |||   | | |  | ||||  |  || |||    
ACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTATCCAAAGCATTCTCACGGTTTCCATCCTTCAACATGGCAAGGgtaa----atatccctttttatccaaaaggcttatttgtagcaaaacttgttcaacaatccaattattgttatgcaatacctattgtcaaattcttttaggggc

upper sequence: AT3G04500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G30900.2 (Glycine max), 5'ss of exon 3
ATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAGgtaactgtgtatatctctcctccttttcggctttagtgattattcatatctggtttccta---tgaacatatatttgagaacatt-agtcatgtgattgtagtc
|||| ||||| || |||||||| |||||||| ||||| ||||||||||||||||| || ||||||||| |  |||| ||  |||| || |||||    |||| || ||     |||    |   |   || || || ||| | ||   ||   | |||   ||| ||| | ||        || ||   | || ||| |   
ATGATTATCGGCTCTTCTGTGGGGATCTTGGTAACGAGGTGAATGATGATGTTCTCTCAAAAGCATTTTCACGATTTCCTTCCTTTAACATGGCACGAgtaagtgggttctcatctaactcgaattctctata-tgtttagttatgattgtcgtgctagtgtgagcattttttatttcctgttcagatttttgtttgaa---

upper sequence: AT3G04500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA20G36570.1 (Glycine max), 5'ss of exon 3
ATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAGgtaactgtgtatatc-tctcctccttttcggctttagtgattattcatatctggtttccta-tgaacatatatttgagaacattagtcatgtgattgtagtc
|||| ||||| || |||||||| |||||||| ||||| ||||||||||||||||| || ||||||||| |  | || ||  |||| ||  ||||    |||| ||  |   || |||    |   |   ||||| || ||| | ||   || | | ||| ||     || ||| |   |  |  |||  |  ||||    
ATGATTATCGGCTCTTCTGTGGGGATCTTGGTAACGAGGTGAATGATGATGTTCTCTCAAAAGCATTTTCACGGTTTCCTTCCTTTAACTTGGCACGAgtaagtggattcctcatctaactcgagttctcttta-tgtttagttatgattgttgtgctagtgtgagcattttttatttc-ctgttcagatttttgtttga

upper sequence: AT3G04500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA11G01300.1 (Glycine max), 5'ss of exon 3
ATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAGgtaactgtgtatatctctcctccttttcggctttagtgattattcata--tctggt-ttcctatgaacatatatttgagaacatt--agtcatgtgattgtagtc---------------------------------------------------------------------------
|||| ||||| || || || || |||||||| || ||||||||||||||||||||||| |||| |||| |  |||||||  |||| ||  ||||   ||||| ||  |   ||      |      |  |||  || |||   ||   | ||||  | || ||| ||| | | |     |  |  ||   | || ||| ||                                                                             
ATGATTATCGGCTCTTTTGCGGCGATCTTGGTAATGAAGTGAATGATGATGTTCTTTCAAAAGTATTTTCACGATTCCCTTCCTTTAACTTGGCACGGgtaagtggattactcatctagctcaaatgatttttatgtttaggaatgattgtggtgcttctgtgagcatttttctatttcctcttcagatttttgtttgaagggacagagttgttaatatttgtgtatcttaacgtaggtcttgcttaatgacctgaagttatgtttgatcttgtctag

upper sequence: AT3G04500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv09s0018g01710.t01 (Vitis vinifera), 5'ss of exon 3
ATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAGgtaactgtgtatatctctcctccttttcggctttagtgattattcatatctggtttcctatgaacatatatttga-gaacattagtcatgtgattgtagtc-
|||| |||||| | || |||||||||||||| || || ||||| |||||||||||||| ||||||||| |  |||| ||  |||||||||||||||  |||| | | ||| || |||    |||     |||  | ||||   |  |||  | |   || |   | |  |||  | |   | ||  | ||  | |  || 
ATGATTATCGTTTATTTTGTGGTGATCTTGGCAATGAGGTGAACGATGATGTTCTTTCAAAAGCATTTTCACGATTTCCTTCCTTCAATATGGCCAGAgtaagtttatatttccctcaagttttatacttttttttattaggaac-tctaatattagat-attgtttgcttggtgtattgttgttttttgcatatcctct

upper sequence: AT3G04500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv14s0036g00630.t01 (Vitis vinifera), 5'ss of exon 3
ATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAGgtaactgtgtatatctctcctccttttcggctttagtgattattcatatctggtttcctatgaa-catatatttgag--aacattagtcatgtgattgtagtc
|||| |||||| | || |||||||||||||| || || |||||||||||||||||||| ||||||||| |  |||| ||  ||||||||||||| || |||| | | ||| ||  ||    | ||   ||||  |  |||||   |  |   ||  ||   | ||| |  |||    |   | ||   | ||    |  | 
ATGATTATCGTTTATTTTGTGGTGATCTTGGCAATGAGGTGAATGATGATGTTCTTTCAAAAGCATTTTCACGATTTCCTTCCTTCAATATGGCTAAAgtaagtttctatttcattcaagttctttaccttttct--ttattaggaattctattattagatatcatttgcttggtgcatggtgagctttttgcccattct-

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|116430691|gb|EG473283.1|EG473283
EST:     ATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAG                         GTCATTAGAGATAAGCGGACTGGTAAAACCAAGGGTTATGGGTTTGTGAGT
genomic: ATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAGgtaactgtgt ... accatgacagGTCATTAGAGATAAGCGGACTGGTAAAACCAAGGGTTATGGGTTTGTGAGT
EST: gi|19878344|gb|AU239175.1|AU239175
EST:     ATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAG                         GTCATTAGAGATAAGCGGACTGGTNAAACCAAGGGTTATGGGTTTGNGAGT
genomic: ATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAGgtaactgtgt ... accatgacagGTCATTAGAGATAAGCGGACTGGTAAAACCAAGGGTTATGGGTTTGTGAGT
EST: gi|86088425|gb|DR384184.1|DR384184
EST:     ATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAG                         GTCATTAGAGATAAGCGGACTGGTAAAACCAAGGGTTATGGGTTTGTGAGT
genomic: ATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAGgtaactgtgt ... accatgacagGTCATTAGAGATAAGCGGACTGGTAAAACCAAGGGTTATGGGTTTGTGAGT
EST: gi|164140703|gb|ES206885.1|ES206885
EST:     ATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAG                         GTCATTAGAGATAAGCGGACTGGTAAAACCAAGGGTTATGGGTTTGTGAGT
genomic: ATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAGgtaactgtgt ... accatgacagGTCATTAGAGATAAGCGGACTGGTAAAACCAAGGGTTATGGGTTTGTGAGT
EST: gi|47828762|gb|CK118446.1|CK118446
EST:     ATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAG                         GTCATTAGAGATAAGCGGACTGGTAAAACCAAGGGTTATGGGTTTGTGAGT
genomic: ATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAGgtaactgtgt ... accatgacagGTCATTAGAGATAAGCGGACTGGTAAAACCAAGGGTTATGGGTTTGTGAGT
EST: gi|124722739|gb|EH814141.1|EH814141
EST:     CTTCAATATGGCCAAG                         GTCATTAGAGATAAGCGGACTGGTAAAACCAAGGGTTATGGGTTTGTGAGT
genomic: CTTCAATATGGCCAAGgtaactgtgt ... accatgacagGTCATTAGAGATAAGCGGACTGGTAAAACCAAGGGTTATGGGTTTGTGAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAGgtaactgtgtatatctctcctccttttcggctttagtgattattcatatctggtttcctatgaacatatatttgagaacattagtcatgtgattgtagtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccttttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagaacat