Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctacaaaccaaataattagtagttttaagattgaagcaatcacaatgtcggtgtggatcaggataaacaaagttctgacttttggtaaatccttttgcagAAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTT

Basic information

species Arabidopsis thaliana
transcript AT5G60920.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G60920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g32110.1 (Oryza sativa), 3'ss of exon 1
-ctacaaaccaaataattagt--agttttaagattgaagcaatcacaatgtcggtgt---ggatcaggataaacaaagttctgacttttggtaaatccttttgcagAAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTT
 |      |  | | ||  |   |  |   |  ||    | ||  |  |  |  |||   |||||  ||||  |||    ||   ||||| |   |||| ||||||| || ||||||||||| |||||| | || ||||| || || |||||||| ||||||   |||||||||||||||||||||
tcatggggcttattcatctgccgaactgctaatttacccccatttcgtttcccttgttcaggatcttgatatgcaa----ctcttttttgttt--tcctcttgcagAGGCTTATGATGCGCTGGATCCAAATGGAAACATCACGATAAAATGGGACGTTATGTCGTGGACTCCTGATGGCTATGTT

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 1
ctacaaaccaaataattagtagttttaagat-tgaagcaatca---caatgtcggtgtggatcaggataaacaaagttctgacttttggtaaatccttttgcagAAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTT
       | || |  ||| ||||| |  | | || | |  | |   |    ||||  || | |   ||    ||        || |   |   |  | |||||||||| |||||| |||| |||||| | || ||||| ||||| |||||||| ||||||   |||||||||||||| || |||
----ccgcgaatttcttattagttgtgtggtgtgtaccttttaaatcggaatcgggatgtaacttaatgcttaattcatattctctctcttttttttcttgcagAAGCTTATGATTCGCTGGATCCAAATGGGAACATCACAATAAAATGGGACGTTATGCAATGGACTCCTGATGGTTACGTT

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os10g35460.1 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------------------------------------------ctacaaaccaaataatta--gtagttttaag----attgaagcaatcacaatgtc--ggtgtggatcaggataaacaaagttctgacttttggtaaatccttttgcagAAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTT
                                                                                     ||| |   |   | |   ||     |||         |||| ||     | ||  | | |||||     |    |    | | ||||||| |   | || ||||||| || |||||| | || |||||| | |||||||| || || ||||||||||| |||   ||||||||||||||||||| |
gtaagcacgcccatcttcttcttcttctttttttctttctttgtttttttttggaaatgagccgcagctgacaaaaagatcactcacacatggatacactgtcgtgacactaaccaatgcctaagccattttgttttcttgttttggatttttctttttatgtgtatcacttttgcttgttgctcttgcagATGCTTATGATTCCCTGGATCCAAACGGCAACATCACGATAAAATGGGATGTGATGCAATGGACTCCTGATGGCTATGCT

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G32130.1 (Glycine max), 3'ss of exon 1
--ctacaaaccaaataattagtagttttaagattgaagcaatcacaatgtcggtgtggatcaggataaacaaagttctgacttttggtaaatccttttgcagAAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTT
  | |   |   |  ||     || | | |  |||    ||     |  ||  |   ||| |    |||     |    | ||||      | | ||||||||||| |||||| |||||||||||   || || || ||||| ||||||||||| || |||||||| || ||||||||||||
agcaattgagtgagaaaaatagagctctgat-ttgttataagttttac-tccataaagattaattcaaaattcatcaatatttttttcttgttcatttgcagAAGCCTATGATCCGCTTGATCCAACCGGAAATATAACAATCAAATGGGATGTCATTAGCTGGACCCCAGATGGCTATGTT

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 1
ctacaaaccaaataattagtagttttaagattgaagcaatcacaatgtcggtgtggatcaggataaacaaagttctgacttttggtaaatccttttgcagAAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTT
                                   | |  | |     |  |    ||     |||    | || | | ||||  |   |   ||| ||||||| |||||| | ||||||||| | || || || ||||| ||||||||| |||| |||||||| |||||||||||||||
-----------------------------------gtatccccctctccccttcatat---attaattttaattttaagtttttctgtttatcttt-cagaagCTTATGATCCACTTGATCCAAATGGAAATATCACAATCAAATGGGATATTATAAGCTGGACACCTGATGGCTATGTT

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G22410.1 (Glycine max), 3'ss of exon 1
ctacaaaccaaataatta-gtagttttaagattgaagcaatcacaatgtcggtgtggatcaggataaacaaagttctgacttttggtaaatccttttgcagAAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTT
  | ||   |   |  ||  |||   |  ||||     ||  |     ||  |   ||| |   ||||     |    | || | |    | | ||||||||||| |||||| | ||||||||    || || || ||||| || |||||||| || ||||||||||| ||||||||||||
-aagaattgagggagatatatagagctctgatttgttgaaaaatttactctatagagattaatttaaaattgatcaatatttcttgcttgttcatttgcagAAGCCTATGATCCACTTGATCCTACCGGAAATATAACAATCAAGTGGGATGTCATTAGCTGGACTCCAGATGGCTATGTT

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 1
ctacaaaccaaataattagtagttttaagattgaagcaatcacaatgtcggtgtggatcaggataaacaaagttctgactttt----ggtaaatccttttgcagAAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTT
   ||||  ||  ||  | |    |     || | | |||   ||||||  || | |||   | ||   | ||  | |  |||    |||  ||  || ||||||||| || ||| ||||||||||||| || || || || || || |||||||| |||||||||||||| ||||| ||||||
--ccaaaaaaagaaaagattgaactctccctttatgaaatt-taatgtca-tgagaatcttaagaattgaggtattcatctttctttggtggatgtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT

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|152035431|gb|BP853321.2|BP853321
EST:     GGCCTTATGGATCGTCTTCTTGATTTCTTCATCTTCTTTTACTTCGACAG                         AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATG
genomic: GGCCTTATGGATCGTCTTCTTGATTTCTTCATCTTCTTTTACTTCGACAGgttactttct ... ccttttgcagAAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcggtgtggatcaggataaacaaagttctgacttttggtaaatccttttgcagAAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTT
                           ttctgac  putative branch site (score: 2)
                                            tccttttgc  putative PPT
                 ataaacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctacaaaccaaataattagtagttttaagattgaagcaatcacaatgtcggtgtggatcaggataaacaaagttctgacttttggtaaatccttttgcagAAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- -caaacca
- - - - - - - - - - - - - - - - - - -aatcaca
- - - - - - - - - - - - - - - - - - - - - - - - -ggtgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaaa