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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatattttcatgattagatttagttagtacaccattagttgtttcttggatgtgttttctttgaggtggaaacttgataatctaaatcatttttcccgctgttatatctcttacttgttaaattaagttagattttctatgtactgcagTGAGTTTGAGGAATTGGAAGCTAAGCCTACAATGGCAGTTATGGATGGTCCTCTTGAACCATCATCAACTGCTAGGGATGCCCCTGATGATCCTGCTTTT

Basic information

species Arabidopsis thaliana
transcript AT1G08370.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g06020.1 (Oryza sativa), 3'ss of exon 5
gtaatattttcatgattagatttagttagtacaccattagttgtttcttggatgtgttttctttgaggtgga--aacttgataatctaaatcatttttcccgctgttatatctcttacttgttaaattaagttagattttctatgtactgcagTGAGTTTGAGGAATTGGAAGCTAAGCCTACAATGGCAGTTATGGATGGTCCTCTTGAACCATCATCAACTGCTAGGGAT---GCCCCTGATGATCCTGCTTTT
                                                    |     |  |||||| || |  |   |   | |||||     ||| |     | ||||| |   | || |   | | | ||    | |   ||||||||||||||||||||||||||||||||   ||||||   || | ||| ||||| || |||||||| || ||  |  | |  | |   |   || |||  |||| |   
---------------------------------------------------gttcccatcttttgagttgaactacacttgcattctaagc---tttacatttagctatatattggaattat---actgattt---ctgttggtgtactgcagTGAGTTTGAGGAATTGGAAGCTGTTCCTACATCCGCTGCTATAGATGGCCCCCTTGAACCTTCTTCGTCGTCCACTGTTCTAGTTTCTAATGCCCCTGAT---

upper sequence: AT1G08370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G39120.1 (Glycine max), 3'ss of exon 5
gtaatattttcatgattagatttagttagtacaccattagttgtttcttggatgtgttttctttgaggtggaaacttgataatctaaatcatttttcccgctgttatatctcttacttgttaaattaagttagattttctatgtactgcagTGAGTTTGAGGAATTGGAAGCTAAGCCTACAATGGCAGTTATGGATGGTCCTCTTGAACCATCATCAACTGCTAG---GGATGCCCCTGATGATCCTGCTTTT
                                                   |  ||    ||| |       | |||    ||        | |||   |   || |||   ||   | | |   || | |     ||  |  || |||||||||||||||||| | |||||    || || |||||||| ||||||||||||||||| ||||||||| || |||      |||   |||||| ||||| |   
---------------------------------------------------agttgacagcttagctagcataccttagacattacccatttatttttggacattgtatactttgaatttgagtatatggttctgcttacacatattgcagTGAGTTTGAGGAACTAGAAGCAGTACCAACTATGGCAGTAATGGATGGTCCTCTTGAGCCATCATCATCTACTACTTCCAATGTGGCTGATGTTCCTGAT---

upper sequence: AT1G08370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0080g00860.t01 (Vitis vinifera), 3'ss of exon 5
gtaatattttcatgattagatttagttagtacaccattagttgtttcttggatgtgttttctttgaggtggaaacttgataatctaaatcatttttcccgctgttatatctcttacttgttaaattaagttagattttctatgtactgcagTGAGTTTGAGGAATTGGAAGCTAAGCCTACAATGGCAGTTATGGATGGTCCTCTTGAACC---ATCATCAACTGCTAGGGATGCCCCTGATGATCCTGCTTTT
                                             | ||| || |   ||  |||  ||   |  |    ||  |||   ||| ||     ||  | ||   || |     ||||||      ||| | | | |||||||| ||||||||||||||||||||    || || |||||||| |||||||||||||| || ||   |||||||||  |     |||   | |||| ||||| |   
--------------------------------------------attttgaatat---ttggttggtgttacatttcaggaaattaa--tattattattattgaaaaatgcatttcacaa-aaattatcactaattatgttt-tactgcagCGAGTTTGAGGAATTGGAAGCAGTTCCAACTATGGCAGTGATGGATGGTCCTCTAGAGCCCTCATCATCAACCTCCTCAAATGTTGCAGATGTTCCTGAT---

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|125281547|gb|EL295632.1|EL295632
EST:     AGTGCATATTCCAAGGTTAACCAGAAGCCAAAGGCCTCATCTTCAAAGAG                         TGAGTTTGAGGAA
genomic: AGTGCATATTCCAAGGTTAACCAGAAGCCAAAGGCCTCATCTTCAAAGAGgtaatatttt ... tgtactgcagTGAGTTTGAGGAA
EST: gi|152036002|gb|AU237449.2|AU237449
EST:     AGTGCATATTCCAAGGGTAACCAGAAGCCAAAGGCCTCATCTTCAAAGAG                         TGAGTTTGAGGAATTGGAAGCTAAGCCTACAATGGCAG
genomic: AGTGCATATTCCAAGGTTAACCAGAAGCCAAAGGCCTCATCTTCAAAGAGgtaatatttt ... tgtactgcagTGAGTTTGAGGAATTGGAAGCTAAGCCTACAATGGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccgctgttatatctcttacttgttaaattaagttagattttctatgtactgcagTGAGTTTGAGGAATTGGAAGCTAAGCCTACAATGGCAGTTATGGATGGTCCTCTTGAACCATCATCAACTGCTAGGGATGCCCCTGATGATCCTGCTTTT
             ctcttac  putative branch site (score: 3)
                                      ttttctat  putative PPT
                       ttaaattaagttagat  TA-rich tract