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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagctgcatagctaagacagaaatagtcagactgtttgttatttagagtcaattcacattttcaaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG

Basic information

species Arabidopsis thaliana
transcript AT5G40760.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 7
--------------gtgagagctgcatagctaagacag-aaatagtcagactgtttgttatttagagtcaattcacattttcaaatgcttt--tcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
               |   |  || |    |   |||| | || | || ||  | ||  ||        |  |   ||||  ||    |    || |||||||||| |||||||| || ||||| ||||| |||||||| |||||||||||  |||||||
aaaaatataggtatatttcatttgtactattttaacagtatattgcca-acaatatggcatgccatagtagctgcaatttataatcaatacaatcctgcagATTGTATTCAGGGAGGACTTTGGGACTGACGGGCGTGGTGGATATTTTGATCAATATGG

upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G130230_T03 (Zea mays), 3'ss of exon 7
----gtgagagctg--catagctaagacagaaatagtcagactgtttgttatttagagtca----attcacattttcaaatgct--tttct----tgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
    || | |  ||   | || |   |  ||   |  | ||   |  | ||  |  |   |    ||  |     |   |||||  || ||    |||||||||| ||||||||||| ||||| |||||||||||||| |||||||||||| |||||||
tattgtaacaattgactacagtttgaaatgagtcaaactgaacctaagataactgaaagtacagtatcaatgacatggcatgctaattactacactgcagATTGTATTCAGGGAAGACTTTGGTACTGAAGGGCGTGGAGGATATTTTGACCAATATGG

upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 7
--------------------------------------------------------------------------------------------------gtgagagctgcata--gctaagacagaaatagtcagactgtttgttatttagagt---caattcacattttcaaatgcttt-------tcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
                                                                                                     |||  |  |||    | |     |||   |     | ||   || |||  ||    ||   |  || |   |||   |       |  ||||||| || || | ||| || |||||||||||||| ||||| |||||||||||  |||||||
gtaagatcctttcctaggtggttacagtattttttttatttctttataaatcatggttggctgttataagttgataacacatcttttgtcagtttgtctgaagaattaaataaaattgatgtcaaaaagctgtattttttcagtaattattgtgcctaacatatgttcttgcatgtaatgaatgaattctgcagATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG

upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 7
---------gtgagagctgcatagctaagacagaaatagtcagactgtttgttatttagag------tcaattcacatttt-caaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
          |        | || ||||  ||   |  |    || || | | || | |        | || |    |||| |      || |||  ||||| |||||||| || |||||||||||||| || ||||| |||||||||||| |||||||
cttaacaatattttgttgccttatctaattcaactactgcattaccgtatttgatatggcacacttttaaacttgagttttgctgtcaattctctgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAATATGG

upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 7
----------gtgaga-gctgcatagctaagacag-aaatagtcagac-tgtttgttatttagagtcaattcacattttcaaatgctttt---cttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
          ||  |    | | ||  | |   |    ||   || || | | | |    ||   | || |    ||||    || ||||    | |||||| |||||||| ||| |||||||||||||||| || || |||||||||||| | |||||
aatttggtctgtctgttattacctaattcatctactgcatgaccaaacatttatatgccatatcttaaacttgagtttttggctgtttttactttggcagATCGTTTTCAGAGAAAATTTTGGAACTGAAGGTCGAGGTGGATATTTTGACCAGTATGG

upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 7
--------------gtgagagctgcatagctaagacagaa-atagtcagactgtttgttatttagagtcaattcacatttt--caaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
              ||  |   |   ||  | |   |    || | |||| |   | |     |   | ||   | | |||  |   |  || | |  ||||| |||||||| || |||||||||||||| || ||||| |||||||||||| | |||||
attaacaatcttttgtt-gccttatctaattcaactactgcattgccagagttgatatggcacaattttaaactagagtttggctgttaattctatgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAGTATGG

upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 7
--------------------gtgagagctgcatagctaagacagaaatagtcagactgtttgttatttagagtcaattcacattttcaaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
                    ||    | |   |  |||   || ||  ||| | |     |    || ||  |      |   |||    |  || | | ||||||||| |||||||| ||||||||||||||||| ||||| ||||||||||| ||||||||
ggttacctcaaaatgttgaagtctctgatcgttttctatttcaaaataagtaatatgccataaacttaagcatgtggctattattt----tttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG

upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S73_244V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------gtgagagctgcatagctaagacagaaatagtcagactgtttgttatttagagtcaattcac-attttcaaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
                |       | |||  |||   || |  | |  |   |||| |    |      |   | |  |||||| | |  |  |||||||||||||||||| ||| || |||||||||||||| || ||||| || || |||||||| ||
gttaaaatagatcaatgcagtctatacatctctatttcatagtttgagaaggtgttcggatgtggttaccctctgattattttctagt-ttcatcttgcagATTGTTTTCAAGGAGGACTTTGGAACTGAAGGACGAGGCGGCTACTTCGACGAATACGG

upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ21593 (Selaginella moellendorffii), 3'ss of exon 6
gtgagagctgcatagctaagacagaaatagtcagactgtttgttatttagagtcaattcacattttc-aaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
                                  |  | |    ||    | |||   |   | ||| ||||    | | |||||||||| |||| |||  ||||||||||||| || || || || || ||||||||||||||
--------------------------------gtatgggtgacaatgacaaatcatcgctagtgttctaaatagcatacatgcagATTGTGTTCAAGGAGAATTTTGGAACTGATGGTCGCGGTGGCTACTTTGACGAATATGG

upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ23968 (Selaginella moellendorffii), 3'ss of exon 6
gtgagagctgcatagctaagacagaaatagtcagactgtttgttatttagagtcaattcacattttc-aaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
                                  |  | |    ||    | |||   |   | ||| ||||    | | |||||||||| ||||||||  ||||||||||||| || || || || || ||||||||||||||
--------------------------------gtatgggtgacaatgacaaatcatcgctagtgttctaaatagcatacatgcagATTGTGTTCAGGGAGAATTTTGGAACTGATGGTCGCGGTGGCTACTTTGACGAATATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcagactgtttgttatttagagtcaattcacattttcaaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
                                         tgcttttctt  CT-rich tract
         tttgttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagagctgcatagctaagacagaaatagtcagactgtttgttatttagagtcaattcacattttcaaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG