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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagcttatagaaacccaaaactcagatcttcatatagattcaaattcagattcttgagctgacaatctttctgcaatgcagGCTTCTGATATCTGGAATATGATCTCTCAAGGAGCTTATTTATATGTTTGTGGTGACGCCAAAGGCATGGCAAGAGATGTTCACAGATCTCTCCACACAA

Basic information

species Arabidopsis thaliana
transcript AT4G30210.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os08g14570.1 (Oryza sativa), 3'ss of exon 15
gta--tgagcttatagaaacccaaaactcagatcttcatatagattcaaattcagattcttga--------gctgacaat-----ctttctgcaatgcagGCTTCTGATATCTGGAATATGATCTCTCAAGGAGCTTATTTATATGTTTGTGGTGACGCCAAAGGCATGGCAAGAGATGTTCACAGATCTCTCCACACAA
|||  ||| ||  | || |     |    | || ||  |  |  | ||||||||  || |||         ||| | | |     | ||   |  | |||||||| || |||||| | |||||||| || || | |||  | || || |||||||| |||||||||||||| |||||||| || |||  ||||||||| |
gtaattgaactacttgacattttca---tacatgtttgttgatctgcaaattcatgtttttgttcagcgttgctcatatttcctacctttgtctgtccagGCTTCCGAAATCTGGGACATGATCTCCCAGGGTGGTTACATTTACGTCTGTGGTGATGCCAAAGGCATGGCCAGAGATGTACATAGAGTTCTCCACACCA

upper sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G144407_T01 (Zea mays), 3'ss of exon 16
gtatga--gcttatagaaacccaa--aactcagatcttcatatagattcaaattcagattcttgagctgacaatctttctgcaatgcagGCTTCTGATATCTGGAATATGATCTCTCAAGGAGCTTATTTATATGTTTGTGGTGACGCCAAAGGCATGGCAAGAGATGTTCACAGATCTCTCCACACAA
|||  |  |||  | |    |  |  ||||        | |  | |  ||    |  | |  |    || |  | ||  |    | ||||| ||||| |||||| | |||||||| ||||| |||||  | ||||| |||||||| |||||||||||||| |||||||| || |||  ||||||||| |
gtaacacagctgctcgttttctgatcaacttctgctgccctccaaacccagtggctcactgctc--ttgcctttgttcattttttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGATGCCAAAGGCATGGCCAGAGATGTACATAGAGTTCTCCACACCA

upper sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: AC217947.4_FGT002 (Zea mays), 3'ss of exon 15
-----gtatgagcttatagaaacccaaaactcagatcttcatatagattcaaattcagattcttgagctgacaatctttctgcaatgc-agGCTTCTGATATCTGGAATATGATCTCTCAAGGAGCTTATTTATATGTTTGTGGTGACGCCAAAGGCATGGCAAGAGATGTTCACAGATCTCTCCACACAA
       |   ||| ||       ||||  || | |   | |  |      ||  |||   ||     |      |||| | || | | |||| ||||| |||||| | |||||||| ||||| |||||  | ||||| ||||||||||||||||||||||| ||||| || || |||  |||||| || |
gtaatcaagctgctcatcttgtgacaaacttctgttaccc-tccaacccgtaacccagtggctcacagttcttgcctttgtccatttccagGCATCTGAAATCTGGGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGACGCCAAAGGCATGGCCAGAGACGTACATAGAGTTCTCCATACCA

upper sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA13G00990.1 (Glycine max), 3'ss of exon 16
gtatgagcttatagaaacccaaaactcagatctt-catatagattcaaattcagattcttgagctgacaatctttctgcaatgcagGCTTCTGATATCTGGAATATGATCTCTCAAGGAGCTTATTTATATGTTTGTGGTGACGCCAAAGGCATGGCAAGAGATGTTCACAGATCTCTCCACACAA
|||    ||| |    |   |  | | |  | || |  ||  |  |    |   || | | |  ||||  |   | |||  |||||||||| || || ||||  ||||| ||||||||||||||  | ||||| |||||||| ||||| |||||||| || ||||| ||| |  | || |||||||
gtacttactttttcccagatacgatttatttattaccaatcaacgcggtatgccatgccttaattgacggttcatgtgcc-tgcagGCTTCAGAAATTTGGAGCATGATATCTCAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGTGCCCTGCACACAA

upper sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA17G07050.2 (Glycine max), 3'ss of exon 16
gtatgagcttatagaaacccaaaactcagatcttcatatagattcaaattcagattcttgagctgacaatctttctgcaatgcagGCTTCTGATATCTGGAATATGATCTCTCAAGGAGCTTATTTATATGTTTGTGGTGACGCCAAAGGCATGGCAAGAGATGTTCACAGATCTCTCCACACAA
|||     |    || ||  ||       ||  ||| ||  || |    |    |   | |    ||  |   | |||  |||||||||| || || ||||  ||||| || |||||||||||  | ||||| |||||||| ||||| |||||||| || ||||| ||| |  | || |||||||
gtacttattctcggatac--aatttattaattatca-atcaatgcggtatgccttatcttaatcaacggttcatgtgcc-tgcagGCTTCAGAAATTTGGAGCATGATATCACAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGCGCCCTGCACACAA

upper sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv11s0052g00880.t01 (Vitis vinifera), 3'ss of exon 16
---------------------------------gtatgagcttatagaaacccaaaactcagatcttcatatagattcaaattcagattcttgagctgacaa-------tctttctgcaatgcagGCTTCTGATATCTGGAATATGATCTCTCAAGGAGCTTATTTATATGTTTGTGGTGACGCCAAAGGCATGGCAAGAGATGTTCACAGATCTCTCCACACAA
                                  | |||  || | |         |   | || |  ||||  |||    | ||  |  ||||| ||  ||       | |   |   ||  |||| || ||||| |||||| | || ||||| ||||  ||  | ||||| |||||||| ||||||||||||||||| ||||| |||||| |||| || || |
gtacgggactctcatttctcagaagggccattcatctgaagtttttg---tttttgatatatatatatatatgtattattgtccatttgtttgagatgctaagtgcatgtttgctttatatctagGCGTCGGATATTTGGAATGTAATTTCTCAGGGAGGCTACATTTATGTCTGTGGTGATGCCAAAGGCATGGCAAGGGATGTCCACAGAACTCTTCATACCA

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|124708728|gb|EH800130.1|EH800130
EST:     CTCGTGAAGGACCCACCAAAGAATACGTACAGCACAAGATGATGGACAAG                         GCTTCTGATATCTGGAATATGATCTCTCAAGGAG
genomic: CTCGTGAAGGACCCACCAAAGAATACGTACAGCACAAGATGATGGACAAGgtatgagctt ... tgcaatgcagGCTTCTGATATCTGGAATATGATCTCTCAAGGAG
EST: gi|124841774|gb|EH926211.1|EH926211
EST:     AGATGATGGACAAG                         GCTTCTGATATCTGGAATATGATCTCTCAAGGAGCTTATTTATATGTTTGT
genomic: AGATGATGGACAAGgtatgagctt ... tgcaatgcagGCTTCTGATATCTGGAATATGATCTCTCAAGGAGCTTATTTATATGTTTGT
EST: gi|116436419|gb|EG479011.1|EG479011
EST:     CTCGTGAAGGACCCACCAAAGAATACGTACAGCACAAGATGATGGACAAG                         GCTTCTGATATCTGGAATATGATCTCTCAAGGAGCTTATTTATATGTTTGT
genomic: CTCGTGAAGGACCCACCAAAGAATACGTACAGCACAAGATGATGGACAAGgtatgagctt ... tgcaatgcagGCTTCTGATATCTGGAATATGATCTCTCAAGGAGCTTATTTATATGTTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcatatagattcaaattcagattcttgagctgacaatctttctgcaatgcagGCTTCTGATATCTGGAATATGATCTCTCAAGGAGCTTATTTATATGTTTGTGGTGACGCCAAAGGCATGGCAAGAGATGTTCACAGATCTCTCCACACAA
                              agctgac  putative branch site (score: 3)
                                       tctttctgc  putative PPT
     atatagattcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgagcttatagaaacccaaaactcagatcttcatatagattcaaattcagattcttgagctgacaatctttctgcaatgcagGCTTCTGATATCTGGAATATGATCTCTCAAGGAGCTTATTTATATGTTTGTGGTGACGCCAAAGGCATGGCAAGAGATGTTCACAGATCTCTCCACACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG