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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttctattccaaactctcctcttttctgaaatatctctttttgtctagtatcatcatcactcataacaaaacacttgttacttggtgaaaaaatagGTTGACAAGATTTATCTAAGCACGCCAACAAAGATTGCTATTTTGGATCACGAGAAAAAGAGGACTTTCGTTATTCGCAAGGACGGGCTTGCTGATGCTG

Basic information

species Arabidopsis thaliana
transcript AT5G57330.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G57330.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G06380.1 (Glycine max), 3'ss of exon 6
gtaagttttctattccaaactc-tcctcttttctgaaatatctctttttgtctagtatcatcatcactcataacaaaacacttgttactt-ggtgaaaaaatagGTTGACAAGATTTATCTAAGCACGCCAACAAAGATTGCTATTTTGGATCACGAGAAAAAGAGGACTTTCGTTATTCGCAAGGACGGGCTTGCTGATGCTG
  |    |||||  |  | | | |   |  ||| || | |    | |||   |||  ||    |     ||||       ||| ||  ||   ||| |  ||||||||||||||| ||||| ||||| || ||||||||||| ||| | ||||| || |||||||| || || ||| | || || || || ||| |||||||||
-gactcattctagccacatcacgtagccaattccgatagactgatgttt-catagattc--tgttgactataaactgttgcttattcttttattgatatgatagGTTGACAAGATATATCTTAGCACTCCCACAAAGATTGCAATTATTGATCATGAAAAAAAGAGAACATTTGTTGTGCGTAAAGATGGCCTTCCTGATGCTG

upper sequence: AT5G57330.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G17630.1 (Glycine max), 3'ss of exon 6
gtaagttttctattccaaactctcctcttttctgaaatatctctttttgtctagtatcatcatcact-cataacaaaacacttgttacttggtgaaaaaatagGTTGACAAGATTTATCTAAGCACGCCAACAAAGATTGCTATTTTGGATCACGAGAAAAAGAGGACTTTCGTTATTCGCAAGGACGGGCTTGCTGATGCTG
   | |  |     ||| |   |         |  ||||      | | ||  | |   |  | ||| || |  ||  || ||| |  ||  ||| |  ||||||||||||||| ||||| ||||| || ||||||||||| ||| | ||||| || |||||||| || || ||| | || || || || ||| |||||||||
--gactcattctagccatatcatgtagccgattccaatagactgatgtttcatggactctgttgactacaaactaatgcatttgct-tttattgatatgatagGTTGACAAGATATATCTTAGCACTCCCACAAAGATTGCAATTATTGATCATGAAAAAAAGAGAACATTTGTTGTGCGTAAAGATGGCCTTCCTGATGCTG

upper sequence: AT5G57330.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G00780.1 (Glycine max), 3'ss of exon 6
-gtaagttttctattccaaactctcctcttttctgaaatatctctttttgtctagtatcatcatcactcataacaaaacacttgttacttggtgaaaaaatagGTTGACAAGATTTATCTAAGCACGCCAACAAAGATTGCTATTTTGGATCACGAGAAAAAGAGGACTTTCGTTATTCGCAAGGACGGGCTTGCTGATGCTG
 || |    ||||  |  |  | |      |      || |       | ||   |    | || | |   |||  |   |   ||| ||  | | |  |||| |||||| ||| ||||||||||| || ||||||||||| ||| | ||||| ||||| ||||| ||  | ||  | || || || || ||| |||||||||
tgtgacacatctaggcacatgtatgtaacctgtcctgatgtacaggcatttcatatgctttgatgagttgaaactgacttcac-ttattt--ttatatgatagTTTGACAGGATATATCTAAGCACTCCTACAAAGATTGCAATTCTTGATCATGAGAAGAAGAGAACAATTGTATTACGTAAAGATGGTCTTCCTGATGCTG

upper sequence: AT5G57330.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G06880.1 (Glycine max), 3'ss of exon 6
gtaagttttctattccaaactctcctcttttctgaaatatctctttttgtctagtatcatcatcactcataacaaaacacttgttacttggtgaaaaaatagGTTGACAAGATTTATCTAAGCACGCCAACAAAGATTGCTATTTTGGATCACGAGAAAAAGAGGACTTTCGTTATTCGCAAGGACGGGCTTGCTGATGCTG
|  |  | |     |     | |   || | ||||  ||      |||  |   |    | || | |   |||       |   |  ||  |  ||  |||| |||||| ||| ||||| ||||| || ||||||||||| ||| | ||||| ||||||||||| ||  | ||  | || || || || ||| |||||||||
gacacatctaggcacatgtgtgtaacctgtcctgatgtactggcattt--catatgctttgatgagttgaaactggcacttcactttttctttgaatgatagTTTGACAGGATATATCTCAGCACTCCTACAAAGATTGCAATTCTTGATCATGAGAAAAAGAGAACAATTGTATTGCGTAAAGATGGTCTTCCTGATGCTG

upper sequence: AT5G57330.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G06880.2 (Glycine max), 3'ss of exon 6
gtaagttttctattccaaactctcctcttttctgaaatatctctttttgtctagtatcatcatcactcataacaaaacacttgttacttggtgaaaaaatagGTTGACAAGATTTATCTAAGCACGCCAACAAAGATTGCTATTTTGGATCACGAGAAAAAGAGGACTTTCGTTATTCGCAAGGACGGGCTTGCTGATGCTG
        |     |     | |   || | ||||  ||      |||  |   |    | || | |   |||       |   |  ||  |  ||  |||| |||||| ||| ||||| ||||| || ||||||||||| ||| | ||||| ||||||||||| ||  | ||  | || || || || ||| |||||||||
--------taggcacatgtgtgtaacctgtcctgatgtactggcattt--catatgctttgatgagttgaaactggcacttcactttttctttgaatgatagtttgacagGATATATCTCAGCACTCCTACAAAGATTGCAATTCTTGATCATGAGAAAAAGAGAACAATTGTATTGCGTAAAGATGGTCTTCCTGATGCTG

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|125166546|gb|EL192292.1|EL192292
EST:     GATGCGATAACTTTTGAATCCGAA                         GTTGACAAGATTTATCTAAGCACGCCAACAAAGATTGCTATTTTGGATCAC
genomic: GATGCGATAACTTTTGAATCCGAAgtaagttttc ... gaaaaaatagGTTGACAAGATTTATCTAAGCACGCCAACAAAGATTGCTATTTTGGATCAC
EST: gi|125267008|gb|EL281093.1|EL281093
EST:     CGTTTTACCGAACAAGGCGATGCGATAACTTTTGAATCCGAA                         GTTGACAAGATTTATCTAAGCACGCCAACAGAGATTGCTATTTTGGATCAC
genomic: CGTTTTACCGAACAAGGCGATGCGATAACTTTTGAATCCGAAgtaagttttc ... gaaaaaatagGTTGACAAGATTTATCTAAGCACGCCAACAAAGATTGCTATTTTGGATCAC
EST: gi|164034416|gb|ES197180.1|ES197180
EST:     ACAGGGAACGTTTTACCGAACAAGGCGATGCGATAACTTTTGAATCCGAA                         GTTGACAAGATTTATCTAAG
genomic: ACAGAGAACGTTTTACCGAACAAGGCGATGCGATAACTTTTGAATCCGAAgtaagttttc ... gaaaaaatagGTTGACAAGATTTATCTAAG
EST: gi|86081208|gb|DR376965.1|DR376965
EST:     ACAGAGAACGTTTTACCGAACAAGGCGATGCGATAACTTTTGAATCCGAA                         GTTGACAAGATTTATCTAAGCACGCCAACAAAGATTGCTATTTTGGATCAC
genomic: ACAGAGAACGTTTTACCGAACAAGGCGATGCGATAACTTTTGAATCCGAAgtaagttttc ... gaaaaaatagGTTGACAAGATTTATCTAAGCACGCCAACAAAGATTGCTATTTTGGATCAC
EST: gi|125026164|gb|EL098433.1|EL098433
EST:     ACAGAGAACGTTTTACCGAACAAGGCGATGCGATAACTTTTGAATCCGAA                         GTTGACAAGATTTATC
genomic: ACAGAGAACGTTTTACCGAACAAGGCGATGCGATAACTTTTGAATCCGAAgtaagttttc ... gaaaaaatagGTTGACAAGATTTATC
EST: gi|125283732|gb|EL297817.1|EL297817
EST:     CAGAGAACGTTTTACCGAACAAGGCGATGACGATAACTTTTGAATCCGAA                         GTTGACAAGATT
genomic: CAGAGAACGTTTTACCGAACAAGGCGATG-CGATAACTTTTGAATCCGAAgtaagttttc ... gaaaaaatagGTTGACAAGATT
EST: gi|164230957|gb|ES014405.1|ES014405
EST:     ACAGAGAACGTTTTACCGAACAAGGCGATGCGATAACTTTTGAATCCGAA                         GTTGACAAGATTTATCTAAGC
genomic: ACAGAGAACGTTTTACCGAACAAGGCGATGCGATAACTTTTGAATCCGAAgtaagttttc ... gaaaaaatagGTTGACAAGATTTATCTAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctagtatcatcatcactcataacaaaacacttgttacttggtgaaaaaatagGTTGACAAGATTTATCTAAGCACGCCAACAAAGATTGCTATTTTGGATCACGAGAAAAAGAGGACTTTCGTTATTCGCAAGGACGGGCTTGCTGATGCTG
                   tcataac  putative branch site (score: 2)
                                            tgaaaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttctattccaaactctcctcttttctgaaatatctctttttgtctagtatcatcatcactcataacaaaacacttgttacttggtgaaaaaatagGTTGACAAGATTTATCTAAGCACGCCAACAAAGATTGCTATTTTGGATCACGAGAAAAAGAGGACTTTCGTTATTCGCAAGGACGGGCTTGCTGATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG