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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgggtttgcatgaacatataatgaaactctatagctaatgctgcttctgcggtgctgaatcatagttttacaatgcattgattttctggtacacacagCTTCTGCGGCCGATATACAAGCAAATTGCAGAAAACCGAAATGCTGAGATATTCTCCGCCAATACACTTCTGGTTATTCTTGGGACTAGTTTACTTACAG

Basic information

species Arabidopsis thaliana
transcript AT4G00630.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 9
---------------------------------------------------------------------------------------aatgggtttgcatgaacatataatgaaactctatagctaatgctgctt-ctgcggtgctgaatc-atagttttacaatgc---attgattttctggtacacacagCTTCTGCGGCCGATATACAAGCAAATTGCAGAAAACCGAAATGCTGAGATATTCTCCGCCAATACACTTCTGGTTATTCTTGGGACTAGTTTACTTACAG
                                                                                        ||||| |||  |       |      |   |  || |  | || ||| | || |   | ||||   |  | |  ||||    |||    || ||   || |||| | || ||||| || |||||||||||||| ||||| |  |||||||||||||| || || |||||||| || |||||| |||| || ||| | |||||||
gtgagtttactgttcatttacattattttccctatcctttctgggactttttttgtgtgccatatgtagactctaggctcagctggacatgggcttgtttctttgcttgcatgcatgtttcagttttttctccttgcagctgaatttaatctgcaactatgtaatgagcaatttccattttgtatcaaacagTTGCTTCGGCCTATTTACAAGCAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG

upper sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G093643_T01 (Zea mays), 3'ss of exon 10
------------------------------------------------------------------------------------------aatgggtt---tgcatgaacatataatgaaactctatagctaatgc---tgcttctgcggtgctgaatcatagttttacaatgcattgattt--tctggta-cacacagCTTCTGCGGCCGATATACAAGCAAATTGCAGAAAACCGAAATGCTGAGATATTCTCCGCCAATACACTTCTGGTTATTCTTGGGACTAGTTTACTTACAG
                                                                                            | ||||   |||||  |   ||  |  |  | | |  |   |||   ||| | |       | |   | |  | |  ||||      |||  | | ||| || |||| | || ||||| || ||||| |||||||| ||||| |  |||||||||||||| || || |||||||| || |||||| |||| || ||| | |||||||
gtgagttgactgttcatttacattattttgcttatcctttctggtactttttgtatgccatacgtagactctgggcccagctggacataggtttggttccttgcatacatgcatgtttcagtttttttccccttgcagctgcatgtatctcaattatctacaactatttaatgtgcaattttcgttttgtatcaaacagTTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG

upper sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 9
aatgggtttgcatgaacatataatgaaactctatagctaatgctgcttctgcggtgctgaatcatagt------tttacaatgca-ttgattttctggtacacacagCTTCTGCGGCCGATATACAAGCAAATTGCAGAAAACCGAAATGCTGAGATATTCTCCGCCAATACACTTCTGGTTATTCTTGGGACTAGTTTACTTACAG
       || |      ||||  |   | ||  |||  |    || ||   |  | ||  ||   | |      ||| | ||| | ||       |  |    |||||| || ||||| ||||| ||||| |||||||| || | |||||| || ||||| || |||||||||||  | |||||||||||||||||  | || ||||
-------ttccccctctatatttttggattcattaggaaggcatgttttgacaattcttgattgcactataacttttgctatgtaattttcccatttctctgtacagCTCCTTCGGCCCATATATAAGCAGATTGCAGAGAATCAAAATGCAGAAATATTTTCTGCCAATACACTCTTTGTTATTCTTGGGACTAGCCTTCTCACAG

upper sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 13
aatgggtttgcatgaacatataatgaaactctatagctaatgctgcttctgcggtgctgaatcatagttttacaatgcattgattttctggtacac----acagCTTCTGCGGCCGATATACAAGCAAATTGCAGAAAACCGAAATGCTGAGATATTCTCCGCCAATACACTTCTGGTTATTCTTGGGACTAGTTTACTTACAG
  ||   |    |     |  | |   |    || ||  ||| || | || |  |     ||      | | |  ||   ||| ||||  || |      |||||| || || || |||||||||||  |||||||||| | |||||| || || ||||| ||||||||||| || ||||||||||| || ||| | |||||||
--tgatatcattttggggttcacttggaaggcattgc--atggtggtacttcaattgcagatgtagagtatgctttgtgctgagtttcctgttcttctttacagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATTTTCTCAGCCAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAG

upper sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 17
----aatgggtttgcatgaacatataatgaaactctatagctaatgctgcttctgcggtgctgaatcatagttttacaatgcattgattttctggtacacacagCTTCTGCGGCCGATATACAAGCAAATTGCAGAAAACCGAAATGCTGAGATATTCTCCGCCAATACACTTCTGGTTATTCTTGGGACTAGTTTACTTACAG
    | ||   |    |     |  | |   |    || ||  ||||| |   ||| |   |  |  || | |||    ||  ||  | |  |  |    |||||| || || || |||||||||||  |||||||||| | |||||| || || ||||| || |||||||| || ||||||||||| || ||| | |||||||
gataagtgatatcattttggggttcatttggaaggcattgc--atgcttcaattgcagatgtagagtat-gctttgtgctgagttt-tctgttcttctttacagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATTTTCTCAGCTAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAG

upper sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA03G01600.1 (Glycine max), 3'ss of exon 3
-------aatgggtttgcatgaacatataatgaaactctatagctaatgctgcttctgcggtgctgaatcatag-ttttacaatgcattgattttctggtacacacagCTTCTGCGGCCGATATACAAGCAAATTGCAGAAAACCGAAATGCTGAGATATTCTCCGCCAATACACTTCTGGTTATTCTTGGGACTAGTTTACTTACAG
         |   | |  |||   | || | |||    | |   |||   | |||         || |  |||  |||| | ||| | |  ||  |   |     ||||| || || || ||||| ||||| |||||||| || | |||||| || ||||| || |||||||||||  | |||||||||||||| ||  | || ||||
aggataagctctatatttatgggtacattaggaaggcatgtta-taacaattcttg------attgcactataacttttgctatgtaatt-ttcccacttctttgcagCTCCTTCGACCTATATATAAGCAGATTGCAGAGAATCAAAATGCAGAAATATTTTCTGCCAATACACTCTTTGTTATTCTTGGGACCAGCCTTCTCACAG

upper sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 8
aatgggtttgcatgaacatataatgaaactctatagctaatgctgcttctgcggtgct--gaatcatagttt-tacaatgcattgattttctggtacacac------agCTTCTGCGGCCGATATACAAGCAAATTGCAGAAAACCGAAATGCTGAGATATTCTCCGCCAATACACTTCTGGTTATTCTTGGGACTAGTTTACTTACAG
               || | |  |  | |     |  |  | || |||| |   |  |  |||  | ||  |  ||  |||| | ||||| | | |    |      |||| ||  | || || || ||||||||||| ||||| | |||||| |||||||| || |||||||||||||| |||||  | ||||||||| | |||||||
---------attgagacttgtgttacagcatctgatatgtttctccttcagttattatatgaagtacagcctgcaccttgcacttatttttttgcatctgcttttgcagCTACTTAGACCAATTTATAAGCAAATTGCTGAAAATCAAAATGCAGAGATATTTTCTGCCAATACACTTCTTGTTATCTTGGGGACTAGTCTCCTTACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctgcggtgctgaatcatagttttacaatgcattgattttctggtacacacagCTTCTGCGGCCGATATACAAGCAAATTGCAGAAAACCGAAATGCTGAGATATTCTCCGCCAATACACTTCTGGTTATTCTTGGGACTAGTTTACTTACAG
                                cattgat  putative branch site (score: 4)
                  atagtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgggtttgcatgaacatataatgaaactctatagctaatgctgcttctgcggtgctgaatcatagttttacaatgcattgattttctggtacacacagCTTCTGCGGCCGATATACAAGCAAATTGCAGAAAACCGAAATGCTGAGATATTCTCCGCCAATACACTTCTGGTTATTCTTGGGACTAGTTTACTTACAG

- - ggtttgc
- - - - - - - -acatata
- - - - - - - - - - - atgaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgca