Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcacatttctcaatctctttctctctacgaagaagaaaacctggaacttttctcattttgggttttgattgattaatggtttgaattctcctgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCTTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG

Basic information

species Arabidopsis thaliana
transcript AT5G55280.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 1
gtcacatttctcaatctctttctctctacgaagaagaaaacctggaacttttctcattttgggttttgattgattaatggtttgaattctcct----gtgt----tccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCTTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG
              |||  |  | | |  | |  |     | || || | ||| | | || | || | |  ||||| |  | | |||  | ||    || |    | ||| |||||||||||||||| ||||| || || || |||||||| ||||| ||| | |||  |||||| || ||||||||||||||||| |||||||| || |
---------taggctctggtgttttttctgtatgattgttcgtgaaattattcccttcttagcttct-acagattactaatgttaatgttgcttgccgtttgatattcagGGTGTTGATTTCTATGCAATAAATACAGACTCTCAAGCTCTATTACACTCTGCGGCTTCGAACCCTCTCCAAATTGGAGAACTTTTGACTCGTGGACTAG
















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|86039268|gb|DR335023.1|DR335023
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|86039263|gb|DR335018.1|DR335018
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         --TGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|86039248|gb|DR335003.1|DR335003
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATRATTYCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACACGG
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGG
EST: gi|86039251|gb|DR335006.1|DR335006
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|86039267|gb|DR335022.1|DR335022
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACAAGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|86039259|gb|DR335014.1|DR335014
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTC
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTC
EST: gi|86039253|gb|DR335008.1|DR335008
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         --TGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|86039264|gb|DR335019.1|DR335019
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|86039254|gb|DR335009.1|DR335009
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|86039257|gb|DR335012.1|DR335012
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         --TGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|86039261|gb|DR335016.1|DR335016
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|86039272|gb|DR335027.1|DR335027
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|86039256|gb|DR335011.1|DR335011
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|86039271|gb|DR335026.1|DR335026
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|86039249|gb|DR335004.1|DR335004
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|301501112|gb|HO206652.1|HO206652
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|86039260|gb|DR335015.1|DR335015
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|86039250|gb|DR335005.1|DR335005
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|86039269|gb|DR335024.1|DR335024
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|86039262|gb|DR335017.1|DR335017
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
EST: gi|86039270|gb|DR335025.1|DR335025
EST:     GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAG                         AGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT
genomic: GTGGTGGTGGTAACAATGCCGTTAACCGGATGATTTCAAGCGGTTTACAGgtcacatttc ... tgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttctcattttgggttttgattgattaatggtttgaattctcctgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCTTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG
                        gattaat  putative branch site (score: 3)
                                       ttctcctgtgttcc  putative PPT
                ttttgattgattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcacatttctcaatctctttctctctacgaagaagaaaacctggaacttttctcattttgggttttgattgattaatggtttgaattctcctgtgttccagAGTGTTGATTTCTATGCGATAAACACGGATTCGCAAGCTCTGTTACAGTCTTCTGCTGAGAACCCACTTCAAATTGGAGAACTTTTAACTCGTGGGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA