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

gtattgaatcagttctatacttttgttttcccaatatttgattctgtgtgtatggtttcttaaagacttaatgtttttgtcatgctagCTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG

Basic information

species Arabidopsis thaliana
transcript AT5G39740.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 4
--gtattgaatcagttctatacttttgttttcccaatatttgattctgtgtgtatggtttcttaaagacttaatgtttttgtcatgctagCTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG
   |||| |         | | | |   ||  | | | ||          | |||  | | ||    |||   ||      || | ||||| ||||| ||||| ||||||||||||||||||||||| || || |  ||  ||||| | ||||| ||||| || || |||
gtatatttatgtctgcaaagaatgtaaattgtctattgttactaagcacatatattttgtattgctaactccttgcccacatctt-ctagCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S371_31V6.3 (Physcomitrella patens), 3'ss of exon 3
-------------------gtattgaatcagttctatacttttgttttcccaatatttgattctgtgtgtatggtttcttaaagacttaatgtttttgtcatgc-tagCTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG
                   ||  |   | | | |    ||||||||||    |    |  | || |  || || ||  || | | |      || |  |  |||  ||||||||| ||||| ||||||||||||||||||  | | || |   | ||  ||||  | |||||||  || || |    |
gtacgtattcacttgtctagtgattttttactcccgaccttttgtttttgacaacggtcttcctttccgtttgtttgtttgatgtcaatggtttgtattggtgcgcagCTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGTTGGACCAGGAGTACGTAGGCAATGAGACG
















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|163989936|gb|ES084236.1|ES084236
EST:     CTCACTGTTTGGTCTTACCAACTATGCTGCAG                         CTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAA
genomic: CTCACTG-TTGGTCTTACCAACTATGCTGCAGgtattgaatc ... gtcatgctagCTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAA
EST: gi|125030521|gb|EL102790.1|EL102790
EST:     AGCTTCCTCAGTATGGACTCACTGTTGGTCTTACCAACTATGCTGCAG                         CTTACTGTACTGGCCTTCTTTTAGGCTCGTCGTGTTCTGAAAATGCTGGAA
genomic: AGCTTCCTCAGTATGGACTCACTGTTGGTCTTACCAACTATGCTGCAGgtattgaatc ... gtcatgctagCTTACTGTACTGGCCTTCTTTT-GGCTCGTCGTGTTCTGAAAATGCTGGAA
EST: gi|164171723|gb|ES204694.1|ES204694
EST:     CCAACTATGCTGCAG                         CTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCGTGAAAATGCTGGAA
genomic: CCAACTATGCTGCAGgtattgaatc ... gtcatgctagCTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTC-TGAAAATGCTGGAA
EST: gi|116398433|gb|EG441025.1|EG441025
EST:     TGAGCTTCCTCAGTATGGACTCACTGTTGGTCTTACCAACTATGCTGCAG                         CTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAA
genomic: TGAGCTTCCTCAGTATGGACTCACTGTTGGTCTTACCAACTATGCTGCAGgtattgaatc ... gtcatgctagCTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAA
EST: gi|164235519|gb|ES002528.1|ES002528
EST:     CACTGTTGGTCTTACCAACTATGCTGCAG                         CTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAA
genomic: CACTGTTGGTCTTACCAACTATGCTGCAGgtattgaatc ... gtcatgctagCTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAA
EST: gi|125201477|gb|EL216431.1|EL216431
EST:     AGCTTCCTCAGTATGGACTCACTGTTGGTCTTACCAACTATGCTGCAG                         CTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAA
genomic: AGCTTCCTCAGTATGGACTCACTGTTGGTCTTACCAACTATGCTGCAGgtattgaatc ... gtcatgctagCTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAA
EST: gi|164059358|gb|ES112609.1|ES112609
EST:     TGAGCTTCCTCAGTATGGACTCACTGTTGGTCTTACCAACTATGCTGCAG                         CTTACTGTACTGGCCTTC
genomic: TGAGCTTCCTCAGTATGGACTCACTGTTGGTCTTACCAACTATGCTGCAGgtattgaatc ... gtcatgctagCTTACTGTACTGGCCTTC
EST: gi|116398349|gb|EG440941.1|EG440941
EST:     TGAGCTTCCTCAGTATGGACTCACTGTTGGTCTTACCAACTATGCTGCAG                         CTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAA
genomic: TGAGCTTCCTCAGTATGGACTCACTGTTGGTCTTACCAACTATGCTGCAGgtattgaatc ... gtcatgctagCTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttgattctgtgtgtatggtttcttaaagacttaatgtttttgtcatgctagCTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG
                                acttaat  putative branch site (score: 4)
                                        tttttgtc  CT-rich tract
                                  ttaatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgaatcagttctatacttttgttttcccaatatttgattctgtgtgtatggtttcttaaagacttaatgtttttgtcatgctagCTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA