Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctttatttgcttctagtacttttgccaaatattttattctggacagacttctggtgactcattgtttatcttaacaaattctagTTTGAATTTGAACATTGTACCTCTCTTTGAGAAAACTCTTAGTGCCAGTGATGCTGGTCGCATTGGTCGTCTAGTTCTTCCAAAAGCCTGTGCAGAG

Basic information

species Arabidopsis thaliana
transcript AT2G30470.1
intron # 4
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G30470.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G05840.1 (Glycine max), 3'ss of exon 6
gtatcctttatttgcttc---tagtacttttgc-caaatattttattctg-gacagacttctggtgactcatt-----gtttatcttaacaaattctagTTTGAATTTGAACATTGTACCTCTCTTTGAGAAAACTCTTAGTGCCAGTGATGCTGGTCGCATTGGTCGTCTAGTTCTTCCAAAAGCCTGTGCAGAG
||||||||||| |  ||    | ||  | |||  || ||||  ||  ||  || ||  |   | ||  | |||     ||||  |||||   ||  ||||||||| |  |   | || ||  | ||||||||     | |||||||||||||| ||||| ||||| ||||| ||||| |||||||||||||| |||
gtatcctttatattttttatttggttgtcttgaacatatataatagactctgatagtataaagttggtttattcagtagtttcccttaatgtatgatagTTTGAAATCCACTGTAGTGCCATTATTTGAGAAGGTGTTGAGTGCCAGTGATGCAGGTCGAATTGGCCGTCTTGTTCTCCCAAAAGCCTGTGCTGAG

upper sequence: AT2G30470.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G38490.1 (Glycine max), 3'ss of exon 1
gtatcctttatttgcttctagtacttttgccaaatattttattctggacagacttctggtgactcattgtttatcttaacaaattctagTTTGAATTTGAACATTGTACCTCTCTTTGAGAAAACTCTTAGTGCCAGTGATGCTGGTCGCATTGGTCGTCTAGTTCTTCCAAAAGCCTGTGCAGAG
| ||   ||  |||| | |   || |   | |  | || |||        || |  |    | |     || || ||| ||  ||  |||||||| |  |  || || ||  | ||||||||     | |||||||||||||| ||||| |||||||| || ||||| |||||| | ||||| |||
gcataggtt--ttgcctgttacacatcgtcta--tgttatatataaatttgattcatcaccagtttcccttgatgttatca--ttacagtttgaagtctactatagTGCCATTGTTTGAGAAGGTATTGAGTGCCAGTGATGCAGGTCGAATTGGTCGACTTGTTCTCCCAAAATCTTGTGCTGAG

upper sequence: AT2G30470.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv06s0004g08100.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------gtatcctt-tatttgcttctagtacttttgccaaatattttattctggacagacttctggt--gactcattgtttatcttaa------caaattctagTTTGAATTTGAACATTGTACCTCTCTTTGAGAAAACTCTTAGTGCCAGTGATGCTGGTCGCATTGGTCGTCTAGTTCTTCCAAAAGCCTGTGCAGAG
                                       |||| |  || | |  | |  |  || ||  | ||    | |  |||   |     || |   | | | |||||| ||||        |  ||| ||||||||||  | |||||| ||  | || |||||   ||| ||||| |||||||||||||| ||||||||| | || || |||||||| ||||| || 
gtatccataaatatttcatactttaatttttaagttgattatcatcataatagaatgtgat-tttatgtaacattcaatgtgttggtttgttcattgattcaattaagtgtttaccttacatatgttatcttcaagTTTGAATTCCACCATTGTGCCATTATTCGAGAAGGTTCTGAGTGCTAGTGATGCTGGTCGAATTGGTCGTTTGGTCCTCCCAAAAGCATGTGCTGAA

upper sequence: AT2G30470.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S31_242V6.1 (Physcomitrella patens), 3'ss of exon 5
gtatccttt----atttgcttctagtacttttgccaaatattttattctggacagact---tctggtgactcattg----------------tttatcttaacaa---attctagTTTGAATTTGAACATTGTACCTCTCTTTGAGAAAACTCTTAGTGCCAGTGATGCTGGTCGCATTGGTCGTCTAGTTCTTCCAAAAGCCTGTGCAGAG
|||||||||     |||| || |   | |||    |||||     | | |||   | |   | | | |  |||||                 |||  ||| ||||   |||  ||     |    | |||    ||||| || |||||||  || |||||||||||||| ||||| ||||||||| | || ||||||||||| || || |||
gtatcctttctaagtttgtttattcaaatttgtgtaaataggggttacgggattcagtgagtttcgagtatcattacaatctaatcttcagttttcacttgacaatgcattacagCACACAAACTACCATCACTCCTCTGTTCGAGAAAATGCTGAGTGCCAGTGATGCCGGTCGGATTGGTCGTTTGGTGCTTCCAAAAGCATGCGCCGAG

upper sequence: AT2G30470.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S42_132V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------gtatcctttatttgcttct--------agtacttttgccaaatattttatt--ctggacagacttctggtgactcattgtttatcttaacaaattctagTTTGAATTTGAACATTGTACCTCTCTTTGAGAAAACTCTTAGTGCCAGTGATGCTGGTCGCATTGGTCGTCTAGTTCTTCCAAAAGCCTGTGCAGAG
                   | || |  | | || ||          ||   |||||  |  | | | |||  ||  | ||  | | | | |     |||   |   ||   ||| |||| || |    | |||    ||  | || |||||||  || |||||||| ||||||||||| ||||||||| | || ||||||||||| ||||| |||
gtatcctttcagatttcatgcattcaatttctgatttcgtgggatgagggtttttgggatttttatgattttcttaaaagggtacagtttaaattgtgtacttgacaatgtattttagTATGCAAACCACCATCACTCCCTTGTTCGAGAAAATGCTGAGTGCCAGCGATGCTGGTCGGATTGGTCGTTTGGTGCTTCCAAAAGCATGTGCTGAG

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|164136734|gb|EL983102.1|EL983102
EST:     TATACGGATAAAGAGGTTCAGCAGATCTCTGGAAA                         TTTGAATTTGAACATTGTACCTCTCTTTGAGAAAACTCTTAGTGCCAGTGA
genomic: TATACGGATAAAGAGGTTCAGCAGATCTCTGGAAAgtatccttta ... caaattctagTTTGAATTTGAACATTGTACCTCTCTTTGAGAAAACTCTTAGTGCCAGTGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttattctggacagacttctggtgactcattgtttatcttaacaaattctagTTTGAATTTGAACATTGTACCTCTCTTTGAGAAAACTCTTAGTGCCAGTGATGCTGGTCGCATTGGTCGTCTAGTTCTTCCAAAAGCCTGTGCAGAG
 tatcttaac  putative branch site 
                                   tttatcttaacaaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctttatttgcttctagtacttttgccaaatattttattctggacagacttctggtgactcattgtttatcttaacaaattctagTTTGAATTTGAACATTGTACCTCTCTTTGAGAAAACTCTTAGTGCCAGTGATGCTGGTCGCATTGGTCGTCTAGTTCTTCCAAAAGCCTGTGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG