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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaacaaataatgaattttagttgtaattcagatcttatgttgtagaataatggattttagttgtgtccttaacttattgtgttgaattcgatgtagATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAACAGGGCAGACACTCTAGATCCTGCTCTCTTACGTCCTGGAAGACTTGATC

Basic information

species Arabidopsis thaliana
transcript AT5G58290.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 3
----gtgagaacaaataatgaattttagttgtaattcagatcttatg-ttgtagaataatggattt-tagttgtgtccttaacttattgtgttgaattcgatgtagATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAACAGGGCAGACACTCTAGATCCTGCTCTCTTACGTCCTGGAAGACTTGATC
     |    ||| ||| ||      |  | | ||  |  || |||| ||| ||  | | | |||| |     |||  ||   |||   ||| ||||     | |||||||||||||||| || || |||||||| ||||| |||||||| || |||||||| || || ||||| |||||||| |||||||| || ||| | ||  
agggatttacacagatattgtcgagaatattttatgaaattcctatgcttgaaggttgaagtatttctcaccatgtgtttt-tttaaaatgtcgaat-----gcagATGGATGGATTTGATCAAACAGTGAATGTGAAGGTTATAATGGCGACCAACAGGGCGGATACCCTAGACCCTGCTCTGTTACGTCCAGGTAGATTGGACA

upper sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 3
---gtgagaacaaataat--gaattttagttgtaattcagatcttatgttgtagaataatggattttagttgtgtcct-taacttattgtgttgaattcgatgtagATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAACAGGGCAGACACTCTAGATCCTGCTCTCTTACGTCCTGGAAGACTTGATC
    | | | ||||   |  || ||  |   ||  |  ||||  || |||      || | | | ||  |||| || | | | | ||  ||||   |  | |  |||||||||| ||||| || || |||||||| ||||| ||||||||||| ||  ||||||||||||||||||||||||| || |||||||| ||||||||  
tctctaaaagcaaacttttggagttccaacagttttctagattata-gttcc----tactagctcttt-ttgtttcttattagtaatgttgttatctatgttacagATGGATGGGTTTGATCAAACAGTGAATGTGAAGGTTATAATGGCAACTAATCGGGCAGACACTCTAGATCCTGCTCTGTTGCGTCCTGGTAGACTTGACA

upper sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 3
---gtgagaacaaataatgaattttagttgtaattcagatcttatgttgtagaata-atggattttagttgtgtccttaacttattgtgttgaatt-cgatgtagATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAACAGGGCAGACACTCTAGATCCTGCTCTCTTACGTCCTGGAAGACTTGATC
    | | | | ||   ||    ||   | || ||    || ||  || ||      |    ||||  || | || |     || |||| | | ||  | || |||||||||| ||||| || || || ||||| ||||| ||||||||||| ||  ||||||||||||||||||||||| | || |||||||| ||||||||  
tctctaaaagctaactttgggaattc-ctatagtt----tcctagattataattcctactagttttttttatttcttattagtaatgtggttatttatgttgcagATGGATGGGTTTGATCAAACAGTCAATGTGAAGGTTATAATGGCAACTAATCGGGCAGACACTCTAGATCCTGCTTTGTTGCGTCCTGGTAGACTTGACA

upper sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------gtgaga-acaaataatgaattttagttgtaattcagatct---tatgttgtagaataatg---------gattttagttgtgtccttaa--------cttattgtgttgaattcgatgtagATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAACAGGGCAGACACTCTAGATCCTGCTCTCTTACGTCCTGGAAGACTTGATC
                                                                          || |   |    ||| | |||| |||    || |  |||   ||| | || |    |           |||||||| | | | || ||         | |||   |    ||   |  |||||||||| |||||||| || || ||||| || || || |||||||| ||||| ||||||||| | || |||||||| || ||||||||||| |||||||
gtatctatgaaatgatatttatgttaggtgctgtgagtaggttgttactactattagtagttactaatttctgatgggctgctgtgaattagtttttgtttctcttaacctctagctatttggttgggctacacttccctatgattttagatattttctgaagtgttggtttaattacctgttcttttcttcagATGGATGGTTTTGACCAAACAGTTAATGTTAAAGTTATTATGGCAACTAACAGAGCAGACACTTTGGACCCTGCTCTGTTGCGTCCTGGAAGGCTTGATC

upper sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------------------------------------gtgagaacaaataatgaattt---tagttgtaattcagatcttatgttgtagaataatggatt-ttagttgtg--tccttaacttattgtgttgaattcgatgt--------agATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAACAGGGCAGACACTCTAGATCCTGCTCTCTTACGTCCTGGAAGACTTGATC
                                                                                 ||  || ||| || |  |||   || ||    |   |||   |   ||||      |  ||| |||| |     |  ||||||| |||  ||    || |  |        |||||||||| ||||||||||| |||||||| ||||||||||||||||| ||  | ||||||||||| || ||||| ||  | |||||||||||||| || |
gtaggtttaaaaggatatggatcttatagagatatggatttaattaaaaaaaaggcctgaaaatcagttgttaactggggatgccaaaaaaaaagggctttgattaatttgtctgttgattacagcatgtacttgcttctattgttagctaaaaatgtttaactttttggatttgggtctaaattcttctccagATGGATGGGTTTGACCAGACTGTGAATGTTAAGGTCATAATGGCAACTAATCGAGCAGACACTCTGGACCCTGCACTTCTTCGTCCTGGAAGACTCGACC

upper sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 3
gtgagaacaaataatgaattttagttgtaattcagatcttatgttgtagaataatggattttagttgtgtccttaacttattgtgttgaattcgatgtagATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAACAGGGCAGACACTCTAGATCCTGCTCTCTTACGTCCTGGAAGACTTGATC
                                             ||| ||    |||    ||| | ||      || |     |||   |      |||||||||| || || || ||||||||||| ||||| || ||||| |||||| | || |||||| | ||||| || ||||| ||||| |||||||||||  
---------------------------------------------gtaaaa----ggaaccgagtagagtaagccgctgacgtccttgtgctt--ctcagATGGATGGTTTCGATCAAACCGTGAATGTGAAGGTTATCATGGCTACAAACCGTGCGGACACTTTGGATCCCGCGCTCTTGCGTCCGGGAAGACTTGACA

upper sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ04233 (Selaginella moellendorffii), 3'ss of exon 3
gtgagaacaaataatgaattttagttgtaattcagatcttatgttgtagaataatggattttagttgtgtccttaacttattgtgttgaattcgatgtagATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAACAGGGCAGACACTCTAGATCCTGCTCTCTTACGTCCTGGAAGACTTGATC
                                             ||| ||    |||    ||| | ||      || |     |||   |      |||||||||| || || || ||||||||||| ||||| || ||||| |||||| | || |||||| | ||||| || ||||| ||||| |||||||||||  
---------------------------------------------gtaaaa----ggaaccaagtagagtaagccgctgacgtccttgtgctt--ctcagATGGATGGTTTCGATCAAACCGTGAATGTGAAGGTTATCATGGCTACAAACCGTGCGGACACTTTGGATCCCGCGCTCTTGCGTCCGGGAAGACTTGACA

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|125218194|gb|EL232277.1|EL232277
EST:     CGTATTCTCATGGAGCTTCTTAATCAG                         ATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAAC
genomic: CGTATTCTCATGGAGCTTCTTAATCAGgtgagaacaa ... ttcgatgtagATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAAC
EST: gi|164145427|gb|ES040431.1|ES040431
EST:     AGGGAAGTTCAGCGTATTCTCATGGAGCTTCTTAATCAG                         ATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAAC
genomic: AGGGAAGTTCAGCGTATTCTCATGGAGCTTCTTAATCAGgtgagaacaa ... ttcgatgtagATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAAC
EST: gi|116455275|gb|EG497867.1|EG497867
EST:     CAGGAGCCGATAGGGAAGTTCAGCGTATTCTCATGGAGCTTCTTAATCAG                         ATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAAC
genomic: CAGGAGCCGATAGGGAAGTTCAGCGTATTCTCATGGAGCTTCTTAATCAGgtgagaacaa ... ttcgatgtagATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAAC
EST: gi|164007736|gb|ES207362.1|ES207362
EST:     CAGGAGCCGATAGGGAAGTTCAGCGTATTCTCATGGAGCTTCTTAATCAG                         ATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGC
genomic: CAGGAGCCGATAGGGAAGTTCAGCGTATTCTCATGGAGCTTCTTAATCAGgtgagaacaa ... ttcgatgtagATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGC
EST: gi|86084279|gb|DR380038.1|DR380038
EST:     CTCATGGAGCTTCTTAATCAG                         ATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAAC
genomic: CTCATGGAGCTTCTTAATCAGgtgagaacaa ... ttcgatgtagATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagaataatggattttagttgtgtccttaacttattgtgttgaattcgatgtagATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAACAGGGCAGACACTCTAGATCCTGCTCTCTTACGTCCTGGAAGACTTGATC
                         ccttaac  putative branch site (score: 3)
                           ttaacttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaacaaataatgaattttagttgtaattcagatcttatgttgtagaataatggattttagttgtgtccttaacttattgtgttgaattcgatgtagATGGATGGATTTGACCAGACCGTGAATGTCAAGGTCATAATGGCAACAAACAGGGCAGACACTCTAGATCCTGCTCTCTTACGTCCTGGAAGACTTGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA