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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggttcctgcaccacgtattaggttgaattaagacatcataacggcagtcatgttgtatatttttgacggaatcttgtcattattatcctctgtagAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG

Basic information

species Arabidopsis thaliana
transcript AT3G11130.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 5
gtagggttcctgcaccacgtattaggttgaattaagacatcataacggca-gtcatgttgtatat--ttttgacggaatcttgtcattattatcctctgt-agAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG
 || | | |    |    | |  || |    |||| |  | || |||  | |   |||| |||||  |  | ||       ||   |  || ||  |  | |||| |||||| ||||||| ||||||||||| ||||| ||||||||||| || || || ||||| |||||||| ||||| ||||| |||||    ||||||
atatgctacacctatgctggagcagttc---ttaaaagtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctttttcacccatcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 5
gtagggttcctgcaccacgtattaggttgaattaagacatcataacggca-gtcatgttgtatat--ttttgacggaatcttgtcattattatcctctgt-agAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG
 || | | |    |    | |  || ||   |||| |  | || |||  | |   |||| |||||  |  | ||       ||   |  || ||  |  | |||| |||||| ||||||| ||||||||||| ||||| ||||||||||| || || || ||||| |||||||| ||||| ||||| |||||    ||||||
atatgctacacctatgctggaacagttt---ttaaaagtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctttttcacccatcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 4
gtagggttcctgcaccacgtattaggttgaattaagacatcataacggcagtcatgttgtatatttttgacggaatcttgt----cattattatcctctgtagAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG-
   |  |    | |     | | ||   | | | ||  || | | |   | |  |||||||| |  ||  |  | |  | |       | ||  |      ||||||||||| ||||||| ||||||||||| ||||| ||||| ||||||||||| |||||||| |||||||| ||||| |||||||||||    |||||| 
-cggactaaaagaaatttctgtaagtcagtaattagtaattaca-caatactt-tgttgtatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAGG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
gtagggttcctgcaccacgtattaggttgaattaagacatcataacggcagtcatgttgtatatttttgacggaatcttgt----cattattatcctctgtagAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG
   |  |    | |     | | ||   | | | ||  || | | |   | |  |||||||| |  ||  |  | |  | |       | ||  |      ||||||||||| ||||||| ||||||||||| ||||| ||||| ||||||||||| |||||||| |||||||| ||||| |||||||||||    ||||||
-cggactaaaagaaatttctgtaagtcagtaattagtaattaca-caatactt-tgttgtatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 5
gtagggttcctgcaccacg-----tattaggttgaattaagacatcataacggcagtcatgttgtatatttttgacggaatcttgtcattattatcctctgtagAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG
 | || ||  ||  ||  |      || | | |   ||     || |   |  ||    || | ||  |||||          |||  |     |  ||| ||||| ||||||||||| |||||||| ||||| || ||||||||||||||||||||||||||||| |||||||||||||| ||||| |||||||| || || 
ttgggattgttgatccttgaaaacaatcatggtcttttttactataactcctacaagtctgatctaggttttttttttgggtatgttgt----gttgtctatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGATCAACAGCGGAGCCAGGCTCTTGAAGCACATGCGGCATCATTTGCTCAATTCAAA

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 5
-gtagggttcctgcaccacgtattaggt--tgaattaagacatcataacggcagtca---tgttgtatatttttgacggaatcttgtcattattatcctctgtagAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG
  | || ||  ||  ||  | |     |  ||   |     |  |||||  |  | |   || | ||  || ||    | || ||||  || |    || | ||||| ||||||||||| |||||||| ||||| || ||||||||||| ||||||||||||||||| |||||||||||||||||||| |||||||| || || 
attgggattgttggtccttgaaaacaatcatggtcttttttactataactcctataagtctgatctagtttcttttttgtatgttgt-gttgt----ctatatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGAACAACAGCGGAGCCAGGCTCTTGAAGCACATGCTGCATCATTTGCTCAATTCAAA

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 5
gtagggttcctgcaccac-gtattagg-ttg-aattaagacatcataacggcagtcatgttg-tatatttttgacggaatcttgtcattattatcctctgtagAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG
      |   || |  |  |||| ||  |||  ||     || | | |    |   |   || | |||||| |      | |    |||||| | |  |||||||  |||||||||| || ||||| ||||| |||||||| ||||||||||| || || ||||| |||||||| ||||||||||| ||||| || ||||| 
---ttatctgtgtataattgtataagaattgtgatcttttcaccgtgattttaacaaacctgatctattttggtttatttttccatattattttgcattgtagAGGGCACAATTGGTAAAGGGAAACATGCAACTTTTCTCAGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCTGCATCATTTGCCCAATTTAAA

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 5
gtagggttcctgcaccac-gtattagg-ttg-aattaagacatcataacggcagtcatgttg-tatatttttgacggaatcttgtcattattatcctctgtagAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG
      |   || |  |  |||  ||  |||  ||      | ||| |    |   |   || | |||||| |      |||    |||||| | |  ||||||| || |||||||| || ||||| ||||| |||||||||||||||||||| || || ||||| |||||||| ||||| ||||| ||||| || ||||| 
---ttatctgtgtataattgtacaagaattgtgatctttttaccatgaatttaacaagcctgatctattttggtttatttctccatattattttgcattgtagAGGCCGCAATTGGTAAAGGGAAACATGCAACTTTTCTCTGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCCGCATCATTTGCCCAATTTAAA

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 5
gtagggttcctgcaccacgtattaggttgaattaagacatca-taacggcagtcatgttgtatatttttgacgg-aatcttgtcat--tattatcctctgtagAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG
     |||  |  ||   ||  | ||   |  |    | ||| |     |||  || |  |    || |||    ||| |   |||  ||||      |  |||| |||||  | || ||||| |||||||||||||||||||| || || || || || || || |||||||| ||||||||||| || ||   |||||| 
---ttgttgttttacttggttgttgggaaatctttctcctcagttttttcagagatttcctggtgttctgattttaatttccacatcctatttatgcttacagAGGCCACAGCTTGTCAAAGGGAATATGCAGCTTTTCTCTGTTGAACAGCATCGTAGTCAAGCTCTTGAAGCTCATGCTGCATCATTCGCCACGTTTAAA

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 3'ss of exon 5
gtagggttcctgcaccacgtattagg--ttgaattaagacatcataacggcagtcatgttgtatatttttg-acggaatcttgtcattattatcctctgtagAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG
  |    ||||   | || | ||     || |||||     |      ||      | |  | ||    || |  ||   || | |||  | |  | |  || | || ||| | ||||||||||| |||||| | || || ||||| || ||| |||| ||||| |||||||| |||||||| || ||||||       ||
--atctctcctcagcaacctcttgaaattttaattatcgtttagagttggttcctttctcatttaacactgcattgacagttcttatttctctggttttcagCGGCCCCAACTTGTGAAAGGAAACATGCAGTTGTTTTCAGTGGACCAGCAGAGGAGTCAGGCGCTTGAAGCTCATGCTGCGTCATTTGCTTCCCACCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acggcagtcatgttgtatatttttgacggaatcttgtcattattatcctctgtagAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG
                                          ttatcctct  CT-rich tract
         atgttgtatattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagggttcctgcaccacgtattaggttgaattaagacatcataacggcagtcatgttgtatatttttgacggaatcttgtcattattatcctctgtagAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC