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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGATGTCTTCATACCTATGCGGTGCATACAGATTCTGTTTGGGCGCTTGCATGCAACCCATCATTTAGTCATGTTTATAGCGGTGGAAGAGACCAATGTgtgagtagacaccaaacttgtttctttctttggttttcttccagcgtataacctccttttttaatttcatttatctgttatgtttccgtcag

Basic information

species Arabidopsis thaliana
transcript AT3G05090.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os12g06810.2 (Oryza sativa), 5'ss of exon 9
GCGATGTCTTCATACCTATGCGGTGCATACAGATTCTGTTTGGGCGCTTGCATGCAACCCATCATTTAGTCATGTTTATAGCGGTGGAAGAGACCAATGTgtgagt-agacaccaaacttgtttctttctttggttttcttccagcgtataacctccttttttaatttcatttatctgttatgtttccgtcag
||||||| ||||| | ||||| |||||||| ||||| || |||||||||||| |||  || || ||||||||||||||||| ||||||||||| || |  |||||| |     ||||  |||| | |  ||   | || |   |      ||||| | | |||  | |    |  | |               
GCGATGTATTCATTCTTATGCTGTGCATACTGATTCAGTCTGGGCGCTTGCAAGCACTCCTTCGTTTAGTCATGTTTATAGTGGTGGAAGAGATCAGTCGgtgagtcaagtttcaaa--tgttgcataattgcttcttttctgaattctgaaccttcctgttt--tcttggatggcag---------------

upper sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G167999_T02 (Zea mays), 5'ss of exon 9
GCGATGTCTTCATACCTATGCGGTGCATACAGATTCTGTTTGGGCGCTTGCATGCAACCCATCATTTAGTCATGTTTATAGCGGTGGAAGAGACCAATGTgtgagtagacaccaaacttgtttctttctttggttttcttccagcgtataacctccttttttaatttcatttatctgttatgtttccgtcag
||| ||| ||||| | ||||| |||||||| |||||||||||||| |||||| |||  ||  ||||| ||||||| || || ||||||||||| |||| |||||||  |     | ||||| | | |  |||  |      ||  |||   | || ||||  | ||| || |||    | |||| | |    
GCGTTGTGTTCATTCTTATGCTGTGCATACTGATTCTGTTTGGGCACTTGCAAGCACTCCTGCATTTGGTCATGTCTACAGTGGTGGAAGAGATCAATCTgtgagttaaatt--atcttgtgtatattattgaatagt---cactgtacttcgtcgttttgaacttttatgtattccctgtgttccag----

upper sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA19G42990.1 (Glycine max), 5'ss of exon 9
GCGATGTCTTCATACCTATGCGGTGCATACAGATTCTGTTTGGGCGCTTGCATGCAACCCATCATTTAGTCATGTTTATAGCGGTGGAAGAGACCAATGTgtgagtaga------caccaaacttgtt-tctttctttggttttcttccagcgtataacctccttttttaatttcatttatctgttatgtttccgtcag-----------------------------------------
  ||||| | ||| | ||||| || |||||||||||||||||||| |||||  ||| |||| ||||||||||||||||||| || || ||||||   |  ||||||  |       |  ||| ||    ||   ||    |||| |  || |  ||       || |   ||| ||| |   | |  |||||     ||                                         
AAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTTGCCAGCACCCCAACATTTAGTCATGTTTATAGTGGAGGGAGAGACTTTTCAgtgagtgcaaccttctattaaatttaacatcaaactaattttttttatcatcacatcttgaatttgtcacattacatctccttttcttgttta-actagtgaacctcgtattctaatgttgtattcttttataccctaag

upper sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA19G43070.1 (Glycine max), 5'ss of exon 9
GCGATGTCTTCATACCTATGCGGTGCATACAGATTCTGTTTGGGCGCTTGCATGCAACCCATCATTTAGTCATGTTTATAGCGGTGGAAGAGAC----CAATGTgtga--------------gtagacaccaaacttgtttctttctttggtttt---cttccagcgtata---------acctccttttttaatttcatttatctgttatgtttcc----gtcag------------------
| ||||| | ||| | ||||| || |||||||||||||||||||| |||||  ||| |||| ||||||||||||||||||| || || ||||||    || || ||||               |  ||| ||||||  ||| | |  ||  | ||     |  ||  |||          | ||||||||    ||| | || |       || | |    ||||                   
GAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTTGCCAGCACCCCAACATTTAGTCATGTTTATAGTGGAGGGAGAGACTTTTCAgtgagtgaaaccttctactgaaattaacatcaaactattttttattattattattacatcttgagtttatgtgaaatcacatctccttttcctgtttaacttgtgaacctcgtcttctaatgtcatattcttttatgccttaag

upper sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA03G40360.1 (Glycine max), 5'ss of exon 9
GCGATGTCTTCATACCTATGCGGTGCATACAGATTCTGTTTGGGCGCTTGCATGCAACCCATCATTTAGTCATGTTTATAGCGGTGGAAGAGACCAATGTgtgagta------------------gacaccaaac--ttgtttctttctttggtttt---cttccagcgtataac--ctccttttttaatttcatttatctgttatgtttccgtcag----------------------
| ||||| | ||| | ||||| || |||||||||||||||||||| |||||  ||| |||| ||||||||||||||||||| || || ||||||   |  ||||||                    ||| |||||  || |||  || ||   | ||    ||    |  |||||  |||||||| |  ||| | || |        | | |    |                      
GAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTTGCCAGCACCCCAACATTTAGTCATGTTTATAGTGGAGGGAGAGACTTTTCAgtgagtgcgaccttctattaaatttaacatcaaactatttttttgttattacatcttgaatttatgtcacataacatctccttttcttgtttaacttgtgaacctcatcttctaatgttgtattcttttataccctaag

upper sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA03G40440.4 (Glycine max), 5'ss of exon 9
GCGATGTCTTCATACCTATGCGGTGCATACAGATTCTGTTTGGGCGCTTGCATGCAACCCATCATTTAGTCATGTTTATAGCGGTGGAAGAGACCAATGTgtgagtagacacc-------aaacttgtttctttctttggttttcttccagcgtataacctc---cttttttaatttcatttatctgttatgtttccgtcag------------------------------------------
| ||||| | ||| | ||||| || |||||||||||||||||||| || ||  ||| |||| ||||||||||||||||||| || || ||||||   |  ||||||  |  |        ||| |    ||   || |  |||| |   |       | ||    ||| | | |  |||| | ||  ||   | |    |                                            
GAGATGTGTGCATTCTTATGCAGTTCATACAGATTCTGTTTGGGCACTCGCCAGCACCCCAGCATTTAGTCATGTTTATAGTGGCGGGAGAGACTTTTCAgtgagtgaaaccttctattaaaattaacatcaaactatatttttttattattactacatcttgaacttatgtgacatcatatctccttttcctgtttaacttgtgaacctcatcttctaatgccgtattcttttataccttaag

upper sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA10G30050.1 (Glycine max), 5'ss of exon 8
GCGATGTCTTCATACCTATGCGGTGCATACAGATTCTGTTTGGGCGCTTGCATGCAACCCATCATTTAGTCATGTTTATAGCGGTGGAAGAGACCAATGTgtgagta-gacaccaaacttgtttctttctttggttttcttccagcgtataacctccttttttaatttcatttatctgttatgtttccgtcag---------------------------
 || ||| | ||| | ||||| || |||||||||||| ||||||| |||||| |||   || ||||||||||||||||||| ||||| ||||||   | |||||||            |   || ||  ||    |  |||  |   ||||   |   |  ||  |||  || ||  || | | ||  || |                            
ACGCTGTGTGCATTCTTATGCAGTTCATACAGATTCTATTTGGGCTCTTGCAAGCACTTCAACATTTAGTCATGTTTATAGTGGTGGTAGAGACTCTTCTgtgagtgcagtttttcgataaatttttaattatcatgactttgaatttatatgatgtctccttgttttgcttaattagtgaagcttgtgttactgattcgtaattcttttatttttgtag

upper sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv14s0030g01350.t01 (Vitis vinifera), 5'ss of exon 9
GCGATGTCTTCATACCTATGCGGTGCATACAGATTCTGTTTGGGCGCTTGCATGCAACCCATCATTTAGTCATGTTTATAGCGGTGGAAGAGACCAATGTgtgagtaga-------caccaaacttgttt--------ctttctttggttttcttccagcgtataacctccttttttaatttcatttatctgttatgtttccgtcag------------------------------------------------------------------------------------------
| ||||  | ||| ||||||| ||||||||||||||||| ||||| |||||| ||| |||| ||||||| ||||||||||| ||||| || ||||  |  ||||||| |       | |  ||||               |||    |  |  |||    || |  ||    |||||  || | ||    | | |||||| |  |                                                                                            
GAGATGCGTGCATTCCTATGCCGTGCATACAGATTCTGTCTGGGCACTTGCAAGCACCCCAACATTTAGCCATGTTTATAGTGGTGGGAGGGACCTTTCCgtgagtacagttttctcccagaactcaaccaatgcaaatattcccctgcctctttcttatgttttgccattattttt--ttcctttagcatatgatgttttctcccttttttctttctctatctctctctctctctcttttctgatctttttctgcaatactcatcctttgatgcccaattctgtttatactctcag

upper sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S84_75V6.1 (Physcomitrella patens), 5'ss of exon 2
GCGATGTCTTCATACCTATGCGGTGCATACAGATTCTGTTTGGGCGCTTGCATGCAACCCATCATTTAGTCATGTTTATAGCGGTGGAAGAGACCAATGTgtgagtagacaccaa--acttgtttctttctttggttttcttccag------cgtataacctc-----cttttttaatttcatttatc-tgttatgtttccgtcag---------------------------------------------------
 || ||  ||||| |||| ||||| || || ||||||||||||||  ||||| |||  |||||||| |||||||| |||||||| ||  | |||   |  || |||     | ||  || |  | |    |  ||   |   |||       | ||||| ||       | |  |    | ||   |  | |||  ||| | |  |                                                   
ACGTTGCATTCATTCCTACGCGGTTCACACGGATTCTGTTTGGGCTTTTGCAAGCACGCCATCATTCAGTCATGTGTATAGCGGCGGTCGTGACTCCTCAgtaagtttttgcaaaggacctcctacaggatagggcagttggccattatgttcatataaactagcaagttctggtgggcttatacgttgttttaaattttcttttgtattctttaaccattgtcacttgattcttgattctatcttcgttgaatcag

upper sequence: AT3G05090.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S28_153V6.1 (Physcomitrella patens), 5'ss of exon 7
---GCGATGTCTTCATACCTATGCGGTGCATACAGATTCTGTTTGGGCGCTTGCATGCAACCCATCATTTAGTCATGTTTATAGCGGTGGAAGAGACCAATGTgtgagtagacaccaaacttgtttctttctttggttttcttccagcgtataacctccttttttaatttcatttatctgttatgtttccgtcag---------
    || ||  ||||| | |||||||| || |  |||||||||||||| |||||| |||  |||||||| |||||||| ||||| ||| |    |||   | ||| |||       |    |  ||  | |||| |  |  |  |||  | |   | | ||  | |     ||||| |  |  |||     |  |         
ACAACGTTGCATTCATTCTTATGCGGTTCACATTGATTCTGTTTGGGCCCTTGCAAGCACGCCATCATTCAGTCATGTGTATAGTGGTCG---CGACTTCTCTgtaagttctttaaaggactacttaatgcttttggctgttggcagt-tctgttcacgttaatcatcacaatttacccatcttgtaaatatttgataattaca

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGATGTCTTCATACCTATGCGGTGCATACAGATTCTGTTTGGGCGCTTGCATGCAACCCATCATTTAGTCATGTTTATAGCGGTGGAAGAGACCAATGTgtgagtagacaccaaacttgtttctttctttggttttcttccagcgtataacctccttttttaatttcatttatctgttatgtttccgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA