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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattgacattggtttgattgaacttacattttcttttttttttccgattctaatgcagaattgttaactatgaatgtttcttatatttttgcagACGTCTGACATATTGTATTATGAAGTTTTGGATATTCCTCTTCCAGAATTGCAAGGTCTTAAGACTCTAAAAGTAGCTTTCCATAGTGCCACAAAGGATG

Basic information

species Arabidopsis thaliana
transcript AT3G11910.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11910.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 19
gtgattgacattggtttgattgaacttacattttcttttttttttccgattctaatgcagaattgttaactatgaatgtttcttatatttt-tgcagACGTCTGACATATTGTATTATGAAGTTTTGGATATTCCTCTTCCAGAATTGCAAGGTCTTAAGACTCTAAAAGTAGCTTTCCATAGTGCCACAAAGGATG
  | |   | ||    |  ||    ||   |||   |   ||       || |  |||| |  |   |   |      ||| |  ||| |  ||||||| || ||||||||||||||||| || ||||||||||| || ||||||||||| || || || || || ||||| || |||||   ||| ||||||||||
--gttaacctttcacctctttttgtttttttttgggtcagttagcatagtttttctgcataggtaaaatacaaagggatttatactatctggtgcagACATCAGACATATTGTATTATGAGGTGTTGGATATTCCACTGCCAGAATTGCAGGGCCTGAAAACCCTGAAAGTTGCATTCCACCATGCTACAAAGGATG

upper sequence: AT3G11910.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 23
gtgattgacattggtttgattgaacttacattttcttttttttttccgattctaa---tgcagaattgttaactatgaatgtttcttatat-------ttttgcagACGTCTGACATATTGTATTATGAAGTTTTGGATATTCCTCTTCCAGAATTGCAAGGTCTTAAGACTCTAAAAGTAGCTTTCCATAGTGCCACAAAGGATG
                             || ||||| ||| ||| |||    |    | ||  |   ||     |  || ||  ||  |        |||||||||| |||||||| |||||||| || ||| |||| ||||| || |||||||||||  || | || ||||| ||||| || |||||   ||| || || ||||
---------------------------gtatattcttctttatttgcgacataagcactacatgaccattgggcttatattttattttcacgcctggcttttgcagACTTCTGACATCTTGTATTACGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACTCTTAAAGTTGCATTCCACCATGCAACTAAAGATG

upper sequence: AT3G11910.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GRMZM2G418232_T01 (Zea mays), 3'ss of exon 2
gtgattgacattggtttgattgaacttacattttcttttttttttccgattctaatgcagaattgttaactatgaatgtttcttatatttttgcagACGTCTGACATATTGTATTATGAAGTTTTGGATATTCCTCTTCCAGAATTGCAAGGTCTTAAGACTCTAAAAGTAGCTTTCCATAGTGCCACAAAGGATG
|| |      || ||||| |  ||  |     |  ||| | | |  | | |    ||  | | |    ||||        |||  ||      |||||||||||||| |||||||||||||| |||||||| || || |||||||||||    || || || || ||||| || || ||   | | || |||||||
gttaaccttttttgtttggtc-aatatgagcatgatttctgtgtaacaaat---gtgttggacttcctactaaagcgccatctggta------cagACGTCTGACATCTTGTATTATGAAGTGTTGGATATACCACTGCCAGAATTGCAGTTCCTAAAAACCCTGAAAGTTGCATTTCACCATCCTACGAAGGATG

upper sequence: AT3G11910.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 23
------------------------------gtgattgacat--tggtttgattgaacttacattttcttttttttttccg-attctaatgcagaattgttaactatgaatgtttcttatattttt-------------gcagACGTCTGACATATTGTATTATGAAGTTTTGGATATTCCTCTTCCAGAATTGCAAGGTCTTAAGACTCTAAAAGTAGCTTTCCATAGTGCCACAAAGGATG
                               || |||| ||  | ||||| ||    ||   |||  |||||| | |    ||  |  |  | || | |||   |   |   |||||   | ||               ||||  ||||| || || |||||||||||| | || || ||||||||||||||||||||||| || | ||| ||||| ||||| |||  ||| ||||||||||
gttgctttcacaaatactgagacaaatttgatgcttgatatgatcgtttgttttttattttttttatttttttatatatatatatttttatataacttttagtaacagaaacttcttccttcttctttggcctttggaacagAGTTCTGATATTTTATATTATGAAGTTCTAGACATCCCTCTTCCAGAATTGCAAGGTCTGAAAAATCTGAAAGTTGCTTTTCATCATGCTACAAAGGATG

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|124911675|gb|EH985755.1|EH985755
EST:     GATATGTTAGTTCACTATAATCAG                         ACGTCTGACATATTGTATTATGAAGTTTTGGATATTCCTCTTCCAGAATTG
genomic: GATATGTTAGTTCACTATAATCAGgtgattgaca ... atttttgcagACGTCTGACATATTGTATTATGAAGTTTTGGATATTCCTCTTCCAGAATTG
EST: gi|124717098|gb|EH808500.1|EH808500
EST:     TTCAGATATGTTAGTTCACTATAATCAG                         ACGTCTGACATATTGTATTATGAAGTTTTGGATATTCCTCTTCCAG
genomic: TTCAGATATGTTAGTTCACTATAATCAGgtgattgaca ... atttttgcagACGTCTGACATATTGTATTATGAAGTTTTGGATATTCCTCTTCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccgattctaatgcagaattgttaactatgaatgtttcttatatttttgcagACGTCTGACATATTGTATTATGAAGTTTTGGATATTCCTCTTCCAGAATTGCAAGGTCTTAAGACTCTAAAAGTAGCTTTCCATAGTGCCACAAAGGATG
                      tgttaac  putative branch site (score: 2)
                                     tttcttatattttt  putative PPT
                        ttaactatgaatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattgacattggtttgattgaacttacattttcttttttttttccgattctaatgcagaattgttaactatgaatgtttcttatatttttgcagACGTCTGACATATTGTATTATGAAGTTTTGGATATTCCTCTTCCAGAATTGCAAGGTCTTAAGACTCTAAAAGTAGCTTTCCATAGTGCCACAAAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG