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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaagatttttagatttctctcttgtaaacctgcttaaatctgatacgtgaactctgaacttttttctttgttaaaatgcttagGTAATAAATCTTCGATCAATCCGTCCGCTTGACCGAGCCACCATCAATGCTTCAGTGAGGAAAACGAGTAGATTGGTAACAGTTGAAGAAGGTTTCCCAC

Basic information

species Arabidopsis thaliana
transcript AT5G50850.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G043198_T02 (Zea mays), 3'ss of exon 10
---------gtatgaagatttttagatttctctcttgt------aaacctgcttaaatctgatacgtgaactctgaacttttttctttgttaa---aatgcttagGTAATAAATCTTCGATCAATCCGTCCGCTTGACCGAGCCACCATCAATGCTTCAGTGAGGAAAACGAGTAGATTGGTAACAGTTGAAGAAGGTTTCCCAC
          | | |    || || | | |   |||||      | | ||  ||    |||  | ||  | ||      || ||||||  |||     || | ||||||| |||||||| |||||  | ||||| ||  |||| || || ||||| || ||||||||||| | |||||||||||| || |||||||| ||||| |
gtaatttgttttttatttcttctaaactacagccttgtgctgtcagatctcattttccctggga-gtccagtcgttgtcttattctttagtaattctctgttcagGTAATCAATCTTCGCTCAATTAGACCGCTGGATAGAGCTACTATTAATGCATCTGTGAGGAAAACCAATAGATTGGTAACCGTAGAAGAAGGCTTCCCTC

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 11
---gtatgaagatttttagatttctctcttgtaaacctgcttaaatctgatacgtgaactctgaacttttttctttgttaaaat--gcttagGTAATAAATCTTCGATCAATCCGTCCGCTTGACCGAGCCACCATCAATGCTTCAGTGAGGAAAACGAGTAGATTGGTAACAGTTGAAGAAGGTTTCCCAC
     |      ||| ||     || ||         |||  |||  | ||  | |   ||  ||   |      ||||   ||  || ||||| || ||| | || |||||||| |||||||| ||| |||| ||||||||||| || |||||||| |  ||  |||| |||||||||||||| || || |
gtaaaactttagtttataatgaactttccccctcttttgcaaaaacttcatttgggttatcataatggtgagtgatgttcttatccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTC

upper sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 11
-----------------------------------------gtatgaagatttttagatttctctcttgtaaacctgcttaaatctgatacgtgaactctgaacttttttctttgttaaaatgcttagGTAATAAATCTTCGATCAATCCGTCCGCTTGACCGAGCCACCATCAATGCTTCAGTGAGGAAAACGAGTAGATTGGTAACAGTTGAAGAAGGTTTCCCAC
                                          |  ||  | |  ||| |||     ||   ||     ||  ||    |   | |     | | || ||  | ||||  |      |||| ||||||||||| ||||||||||| |||||| || |  | |||||||||||||| |||||||| || ||| |||| || |||||||| || ||||| |
gtaactcaaaagaagtttgaaattattttctttgtattggattcagacaactagtagttttggaagttcagaaaggtattccattcagtttttaaggaaagcaattgttgttctgtttga---tacagGTTATAAATCTTCGCTCAATCCGTCCCCTTGACAGATCGGCAATCAATGCTTCAGTCAGGAAAACTAGCAGACTGGTGACTGTTGAAGAGGGGTTCCCTC

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|124946833|gb|EL022718.1|EL022718
EST:     GCAGCTGAGAAGCTCGCAGAAGAGGGAACAAGTGCTGAG                         GTAATAAATCTTCGATCAATCCG
genomic: GCAGCTGAGAAGCTCGCAGAAGAGGGAATAAGTGCTGAGgtatgaagat ... aaatgcttagGTAATAAATCTTCGATCAATCCG
EST: gi|125284365|gb|EL298450.1|EL298450
EST:     AGGGAATAAGTGCTGAG                         GTAATAAATCTTCGATCAATCCGTCCGCTTGACCGAGCCACCATCAATGCT
genomic: AGGGAATAAGTGCTGAGgtatgaagat ... aaatgcttagGTAATAAATCTTCGATCAATCCGTCCGCTTGACCGAGCCACCATCAATGCT
EST: gi|164095204|gb|ES182773.1|ES182773
EST:     GCCCTCAAGGCAGCTGAGAAGCTCGCAGAAGAGGGAATAAGTGCTGAG                         GTAATAAATCTTCGATCAATCCG
genomic: GCCCTCAAGGCAGCTGAGAAGCTCGCAGAAGAGGGAATAAGTGCTGAGgtatgaagat ... aaatgcttagGTAATAAATCTTCGATCAATCCG
EST: gi|125154964|gb|EL185324.1|EL185324
EST:     GCTCGCAGAAGAGGGAATAAGTGCTGAG                         GTAATAAATCTTCGATCAATCCGTCCGCTTGACCGAGCCACCATCAATGCT
genomic: GCTCGCAGAAGAGGGAATAAGTGCTGAGgtatgaagat ... aaatgcttagGTAATAAATCTTCGATCAATCCGTCCGCTTGACCGAGCCACCATCAATGCT
EST: gi|164161339|gb|ES094743.1|ES094743
EST:     GAAGCTCGCAGAAGAGGGAATAAGTGCTGAG                         GTAATAAATCTTCGATCAATCCGTCCGCTTGACCGAGACCACCATCAATGC
genomic: GAAGCTCGCAGAAGAGGGAATAAGTGCTGAGgtatgaagat ... aaatgcttagGTAATAAATCTTCGATCAATCCGTCCGCTTGACCGAG-CCACCATCAATGC
EST: gi|116376968|gb|EG419560.1|EG419560
EST:     GCAGCTGAGAAGCTCGCAGAAGAGGGAATAAGTGCTGAG                         GTAATAAATCTTCGATCAATCCGTCCGCTTGACCGAGCCACCATCAATGCT
genomic: GCAGCTGAGAAGCTCGCAGAAGAGGGAATAAGTGCTGAGgtatgaagat ... aaatgcttagGTAATAAATCTTCGATCAATCCGTCCGCTTGACCGAGCCACCATCAATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgcttaaatctgatacgtgaactctgaacttttttctttgttaaaatgcttagGTAATAAATCTTCGATCAATCCGTCCGCTTGACCGAGCCACCATCAATGCTTCAGTGAGGAAAACGAGTAGATTGGTAACAGTTGAAGAAGGTTTCCCAC
         atctgat  putative branch site (score: 4)
                            aacttttttctttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaagatttttagatttctctcttgtaaacctgcttaaatctgatacgtgaactctgaacttttttctttgttaaaatgcttagGTAATAAATCTTCGATCAATCCGTCCGCTTGACCGAGCCACCATCAATGCTTCAGTGAGGAAAACGAGTAGATTGGTAACAGTTGAAGAAGGTTTCCCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG