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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcaaagaacatcttcttcaactagcatcttttttacttcttcttgttaacatcctaattctgttaagcctttttccatagAATGCTCCGGAAGGGTCATTCTTCCTTCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGACCCTACAGAGGAACAATGGAGAGAGATATCACAGCTAT

Basic information

species Arabidopsis thaliana
transcript AT2G30970.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G30970.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g14110.1 (Oryza sativa), 3'ss of exon 4
-------gttagcaaagaacatcttcttcaactagcatcttttttactt-----cttcttgttaa-catcctaatt--ctgttaagcctttt-tccatagAATGCTCCGGAAGGGTCATTCTTCCTTCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGACCCTACAGAGGAACAATGGAGAGAGATATCACAGCTAT
        ||||       ||  |||||  |   || |||    |  |       ||| | |    | |  |||||   | ||   ||| |  ||   |||| |||||  | || ||||||||  | |||||||||||||| ||||||||||||||||| || |||||||| ||||||||||||||||||||  | | ||
aggtacacttagtttttctcactttcttataggtgcttctgacctgttgatgggtttcctatagctccttttaatttatttttgttcctctcatctgcagAACGCTCCAAATGGTTCATTCTTTTTGCTTCATGCTTGTGCCCATAATCCTACTGGAGTTGATCCTACAGAAGAACAATGGAGAGAGATATCCTACCAAT

upper sequence: AT2G30970.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g35540.1 (Oryza sativa), 3'ss of exon 4
gttagcaaagaacatcttcttc-----------aactagcatcttttttac---ttcttcttgttaacatcctaattc---tgttaagcctttttccat---agAATGCTCCGGAAGGGTCATTCTTCCTTCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGACCCTACAGAGGAACAATGGAGAGAGATATCACAGCTAT
       || ||| ||   |||              | |   ||| || ||   || || ||||| |||||  | |||   | | |   | |||   ||   |||||||||| || || ||||||||  | |||||||||||||| |||||||| ||||||||||| ||| |||| ||||||||||| |||||||| || |  |
----atgaaaaacttcccattctctggtctggaggtttgtgccttgttgacaggttgtttttgtttacatctaatttcatttatcatttcctttggtatcccagAATGCTCCAGATGGTTCATTCTTTTTGCTTCATGCTTGTGCGCATAATCCCACTGGAGTAGATCCTTCAGAAGAACAATGGAGGGAGATATCTCATCAGT

upper sequence: AT2G30970.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G146677_T01 (Zea mays), 3'ss of exon 4
---gttagcaaagaacatcttcttcaactagcatcttttttacttcttcttgttaac--atcctaa-----ttctgttaagcctttt------tccatagAATGCTCCGGAAGGGTCATTCTTCCTTCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGACCCTACAGAGGAACAATGGAGAGAGATATCACAGCTAT
      |  | |||  || || | |     | ||||  | | ||   |  ||  ||    ||  ||     || |||| |  |||||      ||   |||||||||| || || ||||||||  | |||||||| |||||||||||||| || || ||||| ||||| ||||||||||||||||| ||||| || |  |
ggaaccatgagagattattttgtgctcagtgaatctggtctgctgagtgctgacaatttgtctgaaattccttttgtttatgcttttctgtcatctgcagAATGCTCCAGATGGTTCATTCTTTTTGCTTCATGCATGTGCTCATAATCCCACCGGTGTAGATCCTACGGAGGAACAATGGAGAGAAATATCCCATCAGT

upper sequence: AT2G30970.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 4
---------------------------gttagc---aaagaacatcttcttcaact--agcatcttttttacttctt--cttgttaacatcctaattctgttaagcctttttccata----gAATGCTCCGGAAGGGTCATTCTTCCTTCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGACCCTACAGAGGAACAATGGAGAGAGATATCACAGCTAT
                             | ||   | ||  ||  || | ||  |  ||| |   |  ||||   |    | | | | || ||| |   |||    || || ||||    ||||||||| || || || ||||| || ||||||||||||||||||||||||||||||||||| ||| |||| ||||||||||||||||| ||    |   
gtattttgctctcctaacatttttcagacttgctttataggtcaatttttacagatgaagctttactagtactctatagtctataatcttcttaaattaattattaattattacatatacagAATGCTCCAGATGGTTCCTTCTTTCTGCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGA

upper sequence: AT2G30970.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv12s0028g01820.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------gttagcaaagaacat-cttcttcaactagcatcttttttacttcttcttgttaacatcctaattc-------tgttaagcctttttccatagAATGCTCCGGAAGGGTCATTCTTCCTTCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGACCCTACAGAGGAACAATGGAGAGAGATATCACAGCTAT
                               ||         ||| ||  || ||||    | ||   |  ||| | |  || |  |  | |||        | || |    ||||  | ||||||||||  | || |||||||| || |||||||||||||||||||| ||||||||||| || ||| ||||||||||||||| |||||| ||| | |  |
gtacttaggccggactcattgtgatctgtgatttatttgtctcatactgtttaaacttctgttttccatgtttcctttcctttatttatttatttatttatttatttatttatttttgacagAATGCTCCAAATGGATCATTCTTTCTACTTCATGCTTGTGCTCATAACCCTACTGGAGTGGATCCTTCAGAGGAACAATGGAAAGAGATCTCATACCAGT

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|301502912|gb|HO208452.1|HO208452
EST:     ATCCAGAAACCAAGGGCTTGGATTTCTCAGCATTGATGGATGATGTGAAG                         AATGCTCCGGAAGGGTCATTCTTCCTTCTTCATGCTTGTGCTCATAATCCT
genomic: ATCCAGAAACCAAGGGCTTGGATTTCTCAGCATTGATGGATGATGTGAAGgttagcaaag ... ttttccatagAATGCTCCGGAAGGGTCATTCTTCCTTCTTCATGCTTGTGCTCATAATCCT
EST: gi|86044680|gb|DR340435.1|DR340435
EST:     ATCCAGAAACCAAGGGCTTGGATTTCTCAGCATTGATGGATGATGTGAAG                         AATGCTCCGGAAGGGTCATTCTTCCTTCTTCATGCTTGTGCTCATAATCCT
genomic: ATCCAGAAACCAAGGGCTTGGATTTCTCAGCATTGATGGATGATGTGAAGgttagcaaag ... ttttccatagAATGCTCCGGAAGGGTCATTCTTCCTTCTTCATGCTTGTGCTCATAATCCT
EST: gi|116454920|gb|EG497512.1|EG497512
EST:     ATCCAGAAACCAAGGGCTTGGATTTCTCAGCATTGATGGATGATGTGAAG                         AATGCTCCGGAAGGGTCATTCTTCCTTCTTCATGCTTGTGCTCATAATCCT
genomic: ATCCAGAAACCAAGGGCTTGGATTTCTCAGCATTGATGGATGATGTGAAGgttagcaaag ... ttttccatagAATGCTCCGGAAGGGTCATTCTTCCTTCTTCATGCTTGTGCTCATAATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttttttacttcttcttgttaacatcctaattctgttaagcctttttccatagAATGCTCCGGAAGGGTCATTCTTCCTTCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGACCCTACAGAGGAACAATGGAGAGAGATATCACAGCTAT
                          tcctaat  putative branch site (score: 2)
                                          cctttttccat  putative PPT
     ttttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcaaagaacatcttcttcaactagcatcttttttacttcttcttgttaacatcctaattctgttaagcctttttccatagAATGCTCCGGAAGGGTCATTCTTCCTTCTTCATGCTTGTGCTCATAATCCTACTGGAGTAGACCCTACAGAGGAACAATGGAGAGAGATATCACAGCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA