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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccttatgttgtgaatgaaaaaatagtcatgaagctgaaaaggataactctgtgttactctgaatttcgcagacaaagttgttaattctcttaaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGGCCTGGAAGGATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG

Basic information

species Arabidopsis thaliana
transcript AT5G20000.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 6
gtatgccttatgttgtgaatgaaaaaatagtcatgaagctgaaaaggataactctgtgttactctgaatttcgcagacaaagttgttaattctc-ttaaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGGCCTGGAAGGATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
                             | ||      || | | | ||  | ||||    | | |    ||   |  |  || ||    | | |||||||     |||||||| ||||||| |||||| | || || ||  ||||||| || |||||  |||||||  | || || ||||||||||||||||||||||||||||| || 
-------------------------gtgtgccactgctttgcatatgtta--tatgtgccgat-taataaccgtgaaggagtttattgtgacacgttaaatgttccatgcagGTTCTGATGGCAACAAATAGGATAGACATCTTGGATCAGGCCCTTCTGAGGCCTGGTCGCATAGACAGGAAAATTGAATTTCCTAATCCTAATGAGGAT

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 6
gtatgccttatgttgtgaatgaaaaaatagtcatgaagctgaaaaggataactctgtgttactctgaatttcgcagacaaagttgttaattctcttaaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGGCCTGGAAGGATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
                     | | |  | |  ||   |||     | |   |  ||| |  | | |||   | | | | |||| | |  | | || |||   |  |||||||||||||||| || ||  | || || ||| |||||||||| |||||  |||||||  | || || ||||| ||||||||||| |||||||| || || 
-------------------gtacacatcacttgtgctcctgtgt--gctggattagtgat-ttgtaaat---gtata-acagttatga--tgttttgaatatttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 6
--------------------------------------------------gtatgccttatgttgtgaatgaaaa-----aatagtc--atgaagctgaaaaggataactctgtgttactc---tgaatttcgcagacaaa--gttgttaattctcttaa-atgact-----gttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGGCCTGGAAGGATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
                                                   |||| |   |||| ||||   |||     || |||   |   | | || |    | ||||||| | ||||   |||  |  |    |||    ||||  |   ||| || || | |      ||| ||||||||||||| |||||||| |||||||| ||||||||||| || ||  | |||||| |||||||  |||| ||||||||||| || ||||||||||||
gtaaaggagctatactgttatgtgtattaaggggaattttaaagctagtcttatgtccactgttctgaaaagaaatctgtaacagttgaacttaacagatattatttactctgtctgactcatttgagatgagttctcaattctttgtggaggttctgaagataaattttcaattgtagGTTTTGATGGCCACAAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCTGGACGGATTGACCGGAAGATTGAATTTCCAAACCCTAATGAAGAG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 6
---------------------------gtatgccttatgttgtgaatgaaaaaatagtcatgaagctgaaaaggataactctgtgttactctgaatttcgcagacaa-agttgttaattctcttaaatga------ctgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGGCCTGGAAGGATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
                            || |    || ||     |      ||   ||     || |||||   || | |||   | | |||| ||  |||| |  | ||      ||  || |   |      |  ||| ||||||||||||| || ||||| |||||||| ||||||||||| || ||  | || ||| |||| ||  |||||||||||||||| || ||||||||||||
gtaaaggagctatactgtaatagtgtattaaggggaattttaaagctagtctgatgtccactgttctaaaaag---aaatatgtaacagt-tgaacttaacagatattatttaccctctcatttgagaaaaattttcaattgtagGTTTTGATGGCCACCAATCGGATTGATATCCTGGATCAAGCCCTCCTTAGACCAGGACGGATAGACCGGAAAATTGAATTTCCAAACCCTAATGAAGAG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 6
gtatgccttatgttgtgaatgaaaaaatagtcatgaagctgaaaaggataactctgtgttactctgaatttcgcagacaaagttgttaattctcttaaatgac----tgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGGCCTGGAAGGATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
                           || || | ||  | |      |   |  ||  ||   | ||||| |       |  |    ||| | | | |||||    | || ||||||||||||||||||||||| ||||||||| |||||||||| || ||  |||||||| | ||||| ||||| ||||| || || ||||| || ||||||
--------------------------gtactcctcaa--taatttctcttcgttggtagtaagttaaattttgtctctgtaaataactattgtatgagatgaccatttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGGCCTGGACGAATTGACAGGAAGATTGAGTTCCCAAATCCCAACGAAGAG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------------------------------------------------gtatgcct-tatgttgtgaatgaaaaaatagtcatgaagctgaaaaggataactctgtgttactc--tgaatttcgcagacaaagttgttaattctcttaaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGGCCTGGAAGGATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
                                                                     ||||   | | | || ||  ||    | | || ||  ||  |||   |  || |   ||  | |   || | |  | |    |  |   | |    | | |   |   || |||||||| |||||||||||||| ||||||||||| || ||||| || ||| |||| ||| ||||||| ||||| ||||| ||||| ||||| ||||  |||
gtactattaataattgctaccctttttgcttctgctgtagttgtgtgtgcccacttgtattatatttgtgtatttatatgtattatgtgtgtggtatttgttatctagtagaatcagcaaaatggttggaaattggtggaatctgtatgtcatatctgtgacaa-catgatcaatattttcagGTTTTAATGGCTACAAATCGAATTGATATTCTTGACCAAGCCCTCCTCAGGCCAGGACGGATTGACAGGAAGATTGAGTTTCCAAATCCCAATGGGGAG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S7016_1V6.1 (Physcomitrella patens), 3'ss of exon 1
gtatgccttatgttgtgaatgaaaaaatagtcatgaagctgaaaaggataactctgtgttact--ctgaatttcgcagacaaagttgttaattctcttaaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGGCCTGGAAGGATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
          |   |||| | || ||| | |||  | | |   ||   |  ||  ||||| ||   ||| ||||        |     ||  | ||||    ||||  ||||||| ||||||||||| ||||| ||||||||||| |||||||||||  | || || ||| | |||||  |||||||||| || || ||||| |  ||||||
----------ttgggtgagtaaataaacaatcac-atgttctgaaaattgccttcgtgttgctggttgactttcaactgattatcaactacctatcttgg--gacttatgcagGTGTTGATGGCTACGAATCGAATTGATATTCTAGATCAAGCTCTCTTGCGACCCGGACGAATTGACCGGAAAATTGAGTTCCCCAATCCAACCGAAGAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|116400365|gb|EG442957.1|EG442957
EST:     TTGAGCTTCTCAATCAACTTGACGGATTCGAGGCGTCAAACAAAATCAAG                         GTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGG
genomic: TTGAGCTTCTCAATCAACTTGACGGATTCGAGGCGTCAAACAAAATCAAGgtatgcctta ... actgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGG
EST: gi|124837625|gb|EH922064.1|EH922064
EST:     TGAGCTTCTCAATCAACTTGACGGATTCGAGGCGTCAAACAAAATCAAAG                         GTTTTGATGGCTACAAATCGTATTGAT
genomic: TGAGCTTCTCAATCAACTTGACGGATTCGAGGCGTCAAACAAAATCAA-Ggtatgcctta ... actgttgcagGTTTTGATGGCTACAAATCGTATTGAT
EST: gi|86079899|gb|DR375656.1|DR375656
EST:     TTGAGCTTCTCAATCAACTTGACGGATTCGAGGCGTCAAACAAAATCAAG                         GTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGG
genomic: TTGAGCTTCTCAATCAACTTGACGGATTCGAGGCGTCAAACAAAATCAAGgtatgcctta ... actgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGG
EST: gi|125264896|gb|EL278981.1|EL278981
EST:     TCAACTTGACGGATTCGAGGCGTCAAACAAAATCAAG                         GTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGG
genomic: TCAACTTGACGGATTCGAGGCGTCAAACAAAATCAAGgtatgcctta ... actgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttactctgaatttcgcagacaaagttgttaattctcttaaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGGCCTGGAAGGATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG
                           tgttaat  putative branch site (score: 3)
                             ttaattctcttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccttatgttgtgaatgaaaaaatagtcatgaagctgaaaaggataactctgtgttactctgaatttcgcagacaaagttgttaattctcttaaatgactgttgcagGTTTTGATGGCTACAAATCGTATTGATATTCTGGATCAAGCTCTTCTCCGGCCTGGAAGGATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA