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

ACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAGgtgtgactcgtcttttccaaactccaaatattctcattcagtaaaataaaaataatgcttatgattactccgtttaccaaaaaaaaaaagaagaaaaaaa...

Basic information

species Arabidopsis thaliana
transcript AT4G29100.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G29100.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA07G09180.3 (Glycine max), 5'ss of exon 4
ACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAGgtgtgactcgtcttttccaaactccaaatattctcattcagtaaaataaaaataatgcttatgattactccgtttaccaaaaaaaaaaagaagaaaaaaa------
|||||||| ||||||||| ||| ||||||||||| || || ||||||||||||||||||||||||||| | || | | | ||| | | || | | | | ||| || || | ||| ||| || | | | | | | | | |
ACTGACACGGCCTCTGTCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtgatgtttctcctcctccacgagcaagtgatggaatgctgcacgctgt---taaagcctaa---tggtccatttcacacagagagattggatctatatacatttt

upper sequence: AT4G29100.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA05G35610.1 (Glycine max), 5'ss of exon 5
ACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAGgtgtgactcgtcttttccaaactccaaatattctcattcagt----aaaataa--aaataatgcttatgattactccgtttaccaaaaaaaaaaagaagaaaaaaa------------------------------------------------------------------------
|||||||| || |||||| | | ||||||||||| || || |||||||||||||||||||||||||| || | ||| || ||| || || || | | | | |||| | || ||| || | | |||| | |
ACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGCTATATCAGATTCCTTCAGAGTCAAATTGAGgtaattaatgtttattctcctctgtcaatttttgcaaacaaccacgagagtcagtgaatagtactcatggc-acgctagatgttaaaagtccattatttcacgttgttctaatccttctgcttccactttattagtttttgaagttctaaaaatattctcttttccccgtggatgcag

upper sequence: AT4G29100.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA08G04110.2 (Glycine max), 5'ss of exon 5
ACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAGgt--gtgactcgtcttttccaaactccaaatattctcattcagtaaaataaaaat-aatgctta-tgattactccgtttaccaaaaaaaaaaagaagaaaaaaa--------------------------------------------------------------------------
|||||||| || |||||| | | ||||||||||| || || |||||||||||||||||||||||||| | | | || ||| ||| ||| | | | | | | | | || || |||| | | | | | || | | |
ACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGgtcattaatgtttattctcctcgctctgtcgatttttgcaaacgaccacgagagtcagtgaatagtgatggcacgctagatgttagaagtccattatttcacgttgttctaatctttctgcttccactttagtttttgaagttctaaaaatattctcttttccccgtggatgatgcag

upper sequence: AT4G29100.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv11s0016g03560.t01 (Vitis vinifera), 5'ss of exon 5
ACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAGgtg-tgactcgtcttttcca---aactccaaatattctcattcagtaa-aataa-aaataatgcttatgattactccgtttaccaaaaaaaaaaagaagaaaaaaa-----------------------------
||||||||||| |||||| ||| ||||||||||| || || |||||||| |||||||||||||||||| || || || |||| | | | | | ||| | || | | | | | || | | || | ||| || | || ||| | |
ACTGACACAGCTTCTGTCTTGTTAGAAGCTATTGGTTATATCAGATTCCTCCAGAGTCAAATTGAGgtgatgtttcttcccttccttttatttttacaaacaaccatgaactagtagtgacgggcacaggtttttaaagcttcattt-tcagttattgaagttctaaatatattcccttctcttatccccctaaaatgcag

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|47831794|gb|CK121478.1|CK121478
EST:     TCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAG                         GCTCTGAGTCATCCATACTTTGGTACGACTGCCTCGGGGAATATGAGGCAC
genomic: TCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAGgtgtgactcg ... actgttgcagGCTCTGAGTCATCCATACTTTGGTACGACTGCCTCGGGGAATATGAGGCAC
EST: gi|47832050|gb|CK121734.1|CK121734
EST:     TCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAG                         GCTCTGAGTCATCCATACTTTGGTACGACTGCCTCGGGGAATATGAGGCAC
genomic: TCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAGgtgtgactcg ... actgttgcagGCTCTGAGTCATCCATACTTTGGTACGACTGCCTCGGGGAATATGAGGCAC
EST: gi|164056426|gb|EL974424.1|EL974424
EST:     TTGGATACATTAGATTCCTTCAGAGTCAAATTGAG                         GCTCTGAGTCATCCATACTTTGGTACGACTGCCTCGGGGAATATGAGGCAC
genomic: TTGGATACATTAGATTCCTTCAGAGTCAAATTGAGgtgtgactcg ... actgttgcagGCTCTGAGTCATCCATACTTTGGTACGACTGCCTCGGGGAATATGAGGCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAGgtgtgactcgtcttttccaaactccaaatattctcattcagtaaaataaaaataatgcttatgattactccgtttaccaaaaaaaaaaagaagaaaaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcttttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctcattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taccaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa