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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTGTCACAGGAAAGATCTACCACTTGAAGTATTCGCCTCCAGAGACAGAAGAGATTGCTGTTAGACTCACCCAACGTTTTGATGATACCGAAGAGAAGgcaaatcaatacttcttatatatctcttgaaagtttctcattcgataattatttctacacatgagattgactcttagtcaaattatgtctctgaagtttttctctttcgctgtag

Basic information

species Arabidopsis thaliana
transcript AT5G47840.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G47840.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA09G36900.4 (Glycine max), 5'ss of exon 4
TCCTGTCACAGGAAAGATCTACCACTTGAAGTATTCGCCTCCAGAGACAGAAGAGATTGCTGTTAGACTCACCCAACGTTTTGATGATACCGAAGAGAAGgcaaatcaatacttcttatatatctcttgaaagtttctcattcgataattatttctacacatgagattgactcttagtcaaattatgtctctgaagtttttctctttcgctgtag
|||||| || || ||||| || |||||||||||||| |||||||||||| |||| || || |  || || |||||||| ||||||||||| ||||| ||||||  |||  |      ||||||| ||  |       | |  | | |||   ||||   ||  |   |  |||        |||   | ||    ||| ||  |||| |   |||
TCCTGTTACCGGCAAGATATATCACTTGAAGTATTCTCCTCCAGAGACACAAGAAATAGCCGCAAGGCTTACCCAACGCTTTGATGATACAGAAGAAAAGgcat-tcatca------atatatccctata-------tgaaactacaatcccttctttccactaagatatctc--------atttcttttcctttgttgtttgcttttgacttag

upper sequence: AT5G47840.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv18s0041g01280.t01 (Vitis vinifera), 5'ss of exon 6
TCCTGTCACAGGAAAGATCTACCACTTGAAGTATTCGCCTCCAGAGACAGAAGAGATTGCTGTTAGACTCACCCAACGTTTTGATGATACCGAAGAGAAGgcaaatcaatacttcttatatatctcttgaa---agtttctcat-----tcgataattatttctacacatgagattgactcttagtcaaattatgtctctgaagtttttctctttcgctgtag-----------------------------------------------------
||||||||| || | ||| ||||||||||||||||| || || ||||  ||||| ||||||| ||| || || ||||| ||||||||||| || || ||||||  |    | |  || |   |   || ||   | |  ||  |     | | | ||||| |       |   ||||  ||||   |    | |   ||| |  || | ||  ||  | |                                                        
TCCTGTCACTGGGAGGATATACCACTTGAAGTATTCTCCCCCTGAGAATGAAGAAATTGCTGCTAGGCTTACTCAACGCTTTGATGATACTGAGGAAAAGgcatgttctaaatcattgtgattgctttaaattcattgccttgtggtccttggttattatatgctgctttcttattgtttcttgtcctgcatcttgatcttattttgtgcttgttttcagccattttggtctttaattgatagccttcattcactttctcttctgatcatgtttag
















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|47832013|gb|CK121697.1|CK121697
EST:     AAGAGATTGCTGTTAGACTCACCCAACGTTTTGATGATACCGAAGAGAAG                         GCAAAACTGCGGCTGAAGACTCATAACCAAAATGTGAGTGATGTGCTTTCT
genomic: AAGAGATTGCTGTTAGACTCACCCAACGTTTTGATGATACCGAAGAGAAGgcaaatcaat ... ttcgctgtagGCAAAACTGCGGCTGAAGACTCATAACCAAAATGTGAGTGATGTGCTTTCT
EST: gi|125323323|gb|EL337405.1|EL337405
EST:     GAGATTGCTGTTAGACTCACCCAACGTTTTGATGATACCGAAGAAGAAAG                         GCAAAACTGCGGCTGAAGACTCATAAC
genomic: GAGATTGCTGTTAGACTCACCCAACGTTTTGATGATACCGAAGA-GAA-Ggcaaatcaat ... ttcgctgtagGCAAAACTGCGGCTGAAGACTCATAAC
EST: gi|164177631|gb|EL983303.1|EL983303
EST:     AAGAGATTGCTGCTAGACTCACCCAACGTTTTGATGATACCGAAGAGAAG                         GCAAAACTGCGGCTGAAGACTCATAACCAAAATG
genomic: AAGAGATTGCTGTTAGACTCACCCAACGTTTTGATGATACCGAAGAGAAGgcaaatcaat ... ttcgctgtagGCAAAACTGCGGCTGAAGACTCATAACCAAAATG
EST: gi|164010048|gb|ES119910.1|ES119910
EST:     AAGAGATTGCTGTTAGACTCACCCAACGTTTTGATGATACCGAAGAGAAG                         GCAAAACTGCGGCTGAAGACTCATAACCAAAA
genomic: AAGAGATTGCTGTTAGACTCACCCAACGTTTTGATGATACCGAAGAGAAGgcaaatcaat ... ttcgctgtagGCAAAACTGCGGCTGAAGACTCATAACCAAAA
EST: gi|125064077|gb|EL131830.1|EL131830
EST:     TTGCTGTTAGACTCACCCAACGTTTTGATGATACCGAAGAGAAG                         GCAAAACTGCGGCTGAAGACTCATAACCAAAATGTGAGTGATGTGCTTTCT
genomic: TTGCTGTTAGACTCACCCAACGTTTTGATGATACCGAAGAGAAGgcaaatcaat ... ttcgctgtagGCAAAACTGCGGCTGAAGACTCATAACCAAAATGTGAGTGATGTGCTTTCT
EST: gi|124825906|gb|EH910772.1|EH910772
EST:     TGATACCGAAGAGAAG                         GCAAAACTGCGGCTGAAGACTCATAACCAAAATGTGAGTGATGTGCTTTCT
genomic: TGATACCGAAGAGAAGgcaaatcaat ... ttcgctgtagGCAAAACTGCGGCTGAAGACTCATAACCAAAATGTGAGTGATGTGCTTTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTGTCACAGGAAAGATCTACCACTTGAAGTATTCGCCTCCAGAGACAGAAGAGATTGCTGTTAGACTCACCCAACGTTTTGATGATACCGAAGAGAAGgcaaatcaatacttcttatatatctcttgaaagtttctcattcgataattatttctacacatgagattgactcttagtcaaattatgtctctgaagtttttctctttcgctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA