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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGTTTGGCATTTCAATCATATCTGCCGTGAGGGTCGGTCTTCTTCTGGCTCCAGGTGGAGAATTCGCGTTTGTTGCTTTTGGAGAAGCTGTCAATCAGgttattatatatatgatgatttctgttttttgcttttttacgatgggtttagtaactgcagtgtttcttggagagtatatgggttgtttttgatgcttcc...

Basic information

species Arabidopsis thaliana
transcript AT4G00630.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G00630.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 5'ss of exon 13
ATTGTTTGGCATTTCAATCATATCTGCCGTGAGGGTCGGTCTTCTTCTGGCTCCAGGTGGAGAATTCGCGTTTGTTGCTTTTGGAGAAGCTGTCAATCAGgttattatatatatgatgatttctgtttttt---gctttttta--cgatgggtttagtaactgcagtgtttcttggagagtatatgggttgtttttgatgcttcc----
| | ||||| ||||| | |||| |||| ||  |||| |||||  | || || || ||||| || || || |||||||| || |||||||||||||||||||||    |     || |  ||||||||||||     | |||||   |||  | |   ||  |        |||  |  |  | |    |  |     ||  ||      
AGTATTTGGAATTTCCACCATAGCTGCTGTTCGGGTTGGTCTGTTGCTTGCACCTGGTGGGGAGTTTGCTTTTGTTGCCTTCGGAGAAGCTGTCAATCAGgtt----tggccctggttctttctgtttttttgtattgttttaggtgataagatgtatatgtcacacacatctgagttaagaca-aactcatggacaatatttttgcag

upper sequence: AT4G00630.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA07G08030.1 (Glycine max), 5'ss of exon 12
ATTGTTTGGCATTTCAATCATATCTGCCGTGAGGGTCGGTCTTCTTCTGGCTCCAGGTGGAGAATTCGCGTTTGTTGCTTTTGGAGAAGCTGTCAATCAGgttattatatatatgatgatttctgttttttgcttttttacgatgggtttagtaactgcagtgtttcttggagagtatatgggttgt-ttttgatgcttcc-----
| | ||||| |||||  |||| |||||| | || || ||||||||||| |||||||| |||||||| || ||||| |||||||| |||||||| ||||||||| |  | | |   |      |||||||    |  || |     || |||  || |    | ||| ||  | | || ||   |  | ||||  || ||       
AGTTTTTGGTATTTCTCTCATTTCTGCCATCAGAGTGGGTCTTCTTCTTGCTCCAGGGGGAGAATTTGCATTTGTGGCTTTTGGTGAAGCTGTTAATCAGgttttcgtctttgaaaa-----ctgttttgctttccttcagttctggattataaattattatatttatttaaaa-tacatcattcttcttttcttgtttttgacaa

upper sequence: AT4G00630.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA03G01600.1 (Glycine max), 5'ss of exon 5
ATTGTTTGGCATTTCAATCATATCTGCCGTGAGGGTCGGTCTTCTTCTGGCTCCAGGTGGAGAATTCGCGTTTGTTGCTTTTGGAGAAGCTGTCAATCAGgttattatatatatgatgatttctgttttttgcttttttacgatgggtttagtaactgcagtgtttcttggagagtatatgggttgtttttgatgcttcc
|   ||||| |||||  |||| |||||  | || || ||||||||||| ||||| || |||||||| || ||||| |||||||| |||||||| ||||||||| || |   |   |    || || |||       ||  |       | | ||| |    | ||| ||  | |  |   |  ||| ||||| || ||  
AGCTTTTGGTATTTCTCTCATTTCTGCTATCAGAGTGGGTCTTCTTCTTGCTCCGGGAGGAGAATTTGCATTTGTGGCTTTTGGTGAAGCTGTTAATCAGgtttttgtccttgaaaactgttttgctttcctagagttctctggattataaataattattatatttatttaaaataaatagttttgcttttgttgttttt

upper sequence: AT4G00630.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA18G46420.1 (Glycine max), 5'ss of exon 20
ATTGTTTGGCATTTCAATCATATCTGCCGTGAGGGTCGGTCTTCTTCTGGCTCCAGGTGGAGAATTCGCGTTTGTTGCTTTTGGAGAAGCTGTCAATCAGgttattatatatatgatgatttctgtttt------ttgcttttttacgatgggtttagtaactgcagtgtttcttggagagtatatgggttgtttttgatgcttcc
  ||||||| |||||  |||| |||||| | || || ||||||||||| ||||| ||||| || || || ||||| |||||||| |||||||| ||||||||| || |   ||  |   ||| |  |        |||  |||     || || ||  ||      || ||| | | | | ||  |   ||  |||||  | ||  
-ATGTTTGGGATTTCTCTCATTTCTGCCATCAGAGTTGGTCTTCTTCTTGCTCCTGGTGGGGAGTTTGCATTTGTGGCTTTTGGTGAAGCTGTTAATCAGGtttttgtccttaaaactgttttttctgccaatagttgtctttcattaatagggttt-tactctaggtctttatagtaaaataagtcactt--ttttggagttt--

upper sequence: AT4G00630.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 5'ss of exon 11
ATTGTTTGGCATTTCAATCATATCTGCCGTGAGGGTCGGTCTTCTTCTGGCTCCAGGTGGAGAATTCGCGTTTGTTGCTTTTGGAGAAGCTGTCAATCAGgttattatatatatga---tgat-ttctgttttttgcttttttacgatgggtttagtaactgcagtgtttcttggagagtatatgggttgtttttgatgcttcc
| | |||||||||||||||||||||||  | || || ||||||||||| ||||| || |||||||| || ||||| |||||||| ||||| || ||||||||| |  | | | |||   | ||  | ||||  |    |||    | |    ||| |   |  |     |  |  |   | |    ||   | |||  |     
ACTTTTTGGCATTTCAATCATATCTGCAATAAGAGTTGGTCTTCTTCTTGCTCCGGGGGGAGAATTTGCTTTTGTGGCTTTTGGTGAAGCCGTTAATCAGgttttcctttctgtgaacttaatactttgttcatgagatttactggttaacattattgtttatacaaccttatcaactttttggaagtcactcttgtaga----

upper sequence: AT4G00630.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: PP1S2_217V6.1 (Physcomitrella patens), 5'ss of exon 15
ATTGTTTGGCATTTCAATCATATCTGCCGTGAGGGTCGGTCTTCTTCTGGCTCCAGGTGGAGAATTCGCGTTTGTTGCTTTTGGAGAAGCTGTCAATCAGgttatta-tatatatgat--------gatttctgttttttgcttttttacgatgggtttag--taactgcagtgtttcttggagagtatatgggttgtttttgatgcttcc------------------------------
      |||| ||||||   |  |||| ||  | | ||| ||  | |||||||| ||||||||||| |||||||| |||||||| ||||| || |||||||  |    || || ||||         ||   | || ||  | |   |     || || |   || |||||  || |       |  |     |||| ||| |||   | |                              
------TGGCCTTTCAACTGTTGCTGCTGTACGTGCCGGGCTCTTCCTGGCTCCTGGTGGAGAATTTGCGTTTGTCGCTTTTGGTGAAGCGGTGAATCAGGCAAGCgctaaatctgatttaaaaacaatgaatcttgttaacataactttcggggattaaaaatagctgcacagtcttcaaacaaagaaccatgttgctttagatttgttctcatgttgggtgatgttcacacatacacag

upper sequence: AT4G00630.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: PP1S31_202V6.1 (Physcomitrella patens), 5'ss of exon 14
ATTGTTTGGCATTTCAATCATATCTGCCGTGAGGGTCGGTCTTCTTCTGGCTCCAGGTGGAGAATTCGCGTTTGTTGCTTTTGGAGAAGCTGTCAATCAGgttattatatatatgatg-atttctgttttttgcttttttacgatgggtttagta-actgcagtgtttcttggagagtatatgggttgtttttgatgcttcc-----------------------------
                               ||||  ||  | ||||| ||||||||||| ||||| |||||||| || |||||||||||||| |||||||  | | | |  |   || | ||   | || |  |  |  | ||    | | ||| |    | |   | ||| |||   ||| | | ||||||  | || |                              
------------------------------AAGGGCTGGGTTGCTTCTTGCTCCAGGTGGTGAATTTGCGTTTGTAGCATTTGGAGAAGCTGTGAATCAGGCAAGTTTGTGCAATCTGGAATTAAATCTTgtattcataaatgaattttcttgtacaacctacttcgttttgaagatagtatcgttcgttttttct-ctgcagttatccgcatcctgttctacaagtgttt

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|86068174|gb|DR363931.1|DR363931
EST:     CTCCAGGTGGAGAATTCGCGTTTGTTGCTTTTGGAGAAGCTGTCAATCAG                         GGTATAATGACTCCGCAGCTATCTTCATTACTGTTTCTCGTCGTGGGAATA
genomic: CTCCAGGTGGAGAATTCGCGTTTGTTGCTTTTGGAGAAGCTGTCAATCAGgttattatat ... tttcttccagGGTATAATGACTCCGCAGCTATCTTCATTACTGTTTCTCGTCGTGGGAATA
EST: gi|86068176|gb|DR363933.1|DR363933
EST:     CTCCAGGTGGAGAATTCGCGTTTGTTGCTTTTGGAGAAGCTGTCAATCAG                         GGTATAATGACTCCGCAGCTATCTTCATTACTGTTTCTCGTCGTGGGAATA
genomic: CTCCAGGTGGAGAATTCGCGTTTGTTGCTTTTGGAGAAGCTGTCAATCAGgttattatat ... tttcttccagGGTATAATGACTCCGCAGCTATCTTCATTACTGTTTCTCGTCGTGGGAATA
EST: gi|86068175|gb|DR363932.1|DR363932
EST:     CTCCAGGTGGAGAATTCGCGTTTGTTGCTTTTGGAGAAGCTGTCAATCAG                         GGTATAATGACTCCGCAGCTATCTTCATTACTGTTTCTCGTCGTGGGAATA
genomic: CTCCAGGTGGAGAATTCGCGTTTGTTGCTTTTGGAGAAGCTGTCAATCAGgttattatat ... tttcttccagGGTATAATGACTCCGCAGCTATCTTCATTACTGTTTCTCGTCGTGGGAATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGTTTGGCATTTCAATCATATCTGCCGTGAGGGTCGGTCTTCTTCTGGCTCCAGGTGGAGAATTCGCGTTTGTTGCTTTTGGAGAAGCTGTCAATCAGgttattatatatatgatgatttctgttttttgcttttttacgatgggtttagtaactgcagtgtttcttggagagtatatgggttgtttttgatgcttcc

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG