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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttggctttcctcaataattcttctctcctaaaatttggtagttaacgttatgcattggtggcttcttaatcagtccgctcttgttcgtctttatgcagCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT

Basic information

species Arabidopsis thaliana
transcript AT4G24860.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 21
atttggctttcctcaataattcttctctcctaaaatttggtagttaacgttatgcattggtggctt-cttaatcagtccgctcttgttcgtct-tta--tgcagCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT
        ||     |    |    | |  ||   || | ||  |||  || |  |||   | | |   | |  | |   |||| ||   ||| |||  |||||||||| || |||||  |  | |||||||||||||| ||||| || ||||||||||| || ||||| ||||  ||||| | ||| |||||||| ||||| |
---ctatattttgggacggatggagtattatatg-ttggctacctaattttctctatttaagtcctatcttaaaaattgcctctggtaaatctgttacttgcagCCTTGCAAGGGAATATTGCTGTTTGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATAT

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 6
---atttggctttcctcaa----taattcttctctcctaaaatttggtagttaacgttatgcattggtggcttcttaatcagtccgctcttgttcgtctttatgcagCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT
   || |    |   || |    |||  ||||     || | |||     || || |  |  | |   |   |  |||     || |     ||| |  || |||||||||| || || ||  |  | || ||||||||||| |||||||| || |||||||| |||||||| ||||  ||||| |  || || |||||||| || |
gtaatcttagatatgtcgagttttaaaacttcatctgtagattttc----ttgacctactatagtcaagatcttataactg--cctccgcaattcattctt-tgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G435582_T01 (Zea mays), 3'ss of exon 1
--atttggctttcctcaataattcttctctcctaaaatttggtagttaacgttatgcattggtggcttcttaatcagtccgctcttgttcgtctttatgcagCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT
  || |    |   |||   | | ||    | | |  | | |   ||   |   | |  ||||       | || | | |   ||   |    | | |||||||||| || || ||  |  | || ||||||||||| |||||||| || |||||||| |||||||| ||||  ||||| |  || || |||||||| || |
taatcttagatatgtcag--agttttaaaacttcatctgtagattttcttgacctactatggtcaagatcttataactgcctcctcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
atttggctttcctcaataattcttctctcctaaaatt-tggtagttaacgttatgca-ttggtggcttcttaa-tcagtccgctcttgttcgtctttatgc-agCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT
   | ||  |  ||  | ||| ||   | ||||  |     | |   ||    |  |  ||   |     ||| | |    | |  | |||   | ||| | |||| |||||||||||| |  | ||||| || ||||| ||||||||||| |||||||| || || |||||||  || |||| ||| || ||||| ||||| |
--atagcaatattc--ttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 17
-atttggctttcctca-ataattcttctctcc-taaaatttggtagttaacgttatgcattggtggcttcttaatcagtccgctcttgttcgtcttt-atgcagCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT
 | ||       || | |||||| |  |  || |  || ||| |  ||| |   ||  |||      |   | |||  ||  || |   |   ||||  ||||||| || |||||||| || |||||||| || ||||||||||| || || ||||| ||||| ||| | || |  ||||||| ||| |||||||||||||| |
caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaat--attatccattctgttatc--tcaactttgaattaccttttgtgcagCCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTT

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 19
-atttggctttcctca-ataattcttctctcc-taaaatttggtagttaacgttatgcattggtggcttcttaatcagtccgctcttgttcgtcttt-atgcagCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT
 | ||       || | |||||| |  |  || |  || ||| |  ||| |   ||  |||      |   | |||  ||  ||||   |   ||||  ||||||| || ||||| || || |||||||| || ||||||||||| || || ||||||||||| ||| | || |  ||||||| ||| |||||||||||||| |
caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaat--attatccattctgttatc--tcgactctgaattaccttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTT

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 21
atttggctttcctcaataattcttctctcctaaaatttggtagttaacgttatgcattggtggc--ttcttaatcagtccgctcttgttcgtctttatgcagCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT
   |     ||   || | |       |   ||  | | |    |  | |     |||  |     || ||| |   |         ||    |  |||||||| || || || || || |||||||| || |||||||| || ||||| ||||||||||| ||||| || |  ||||||| ||| || ||||||||||| |
--gtaaaaatcacaaacattaaaataatgtgaagttgtagcccatctcttgtcaaattattaatcatttttattttatgattgtgaattaccttccatgcagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 4
atttggctttcctcaataattcttctctcctaaaatttggtagttaacgttatgcattggtggcttcttaatcagtccgctcttgttcgtcttt-atgcagCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT
   |     ||   || | |       |   ||  | | |   ||  | |     |||  |  | | || ||        | |   | | |||  |||||||| || || || || || |||||||| || |||||||| || ||||| ||||||||||| ||||| || |  ||||||| ||| || ||||||||||| |
-agtaaaaatcacaaacattaaagtaatgtgaagttgtaggccttctcttgtcaaattattatcatttttatattgtgattgtgaattgccttccatgcagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
atttggctttcctcaataattcttctctcctaaaatttggtagttaacgttatgcattggtggcttcttaatcagtccgctcttgttcgtctttatg-cagCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT
                                                  | ||  || ||   ||  |  |        |||      | | |||| ||||||||||  ||  | || |||||||| ||||| |||||||| |||||||||||||| || || || || |  || |||| ||| || |||||||| || |
-----------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtctaacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

upper sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: EFJ34631 (Selaginella moellendorffii), 3'ss of exon 10
atttggctttcctcaataattcttctctcctaaaatttggtagttaacgttatgcattggtggcttcttaatcagtccgctcttgttcgtctttatg-cagCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT
                                                  | ||  || ||   ||  |  |        |||      ||| |||| ||||||||||  ||  | || |||||||| ||||| |||||||| |||||||||||||| || || || || |  || |||| ||| || |||||||| || |
-----------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtctaacgaatctatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacgttatgcattggtggcttcttaatcagtccgctcttgttcgtctttatgcagCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT
                    tcttaat  putative branch site (score: 3)
                                  ctcttgttcgtcttt  putative PPT
                   ttcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttggctttcctcaataattcttctctcctaaaatttggtagttaacgttatgcattggtggcttcttaatcagtccgctcttgttcgtctttatgcagCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - -tcctcaa
- - - - - - - - - - -cttctct
- - - - - - - - - - - - - - cctaaaa