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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacaaaaataagaagaaaaatatataaagcagttgatgaaaaatatagttatctctatatgaatatgttagatttttcttttggactcatattatatggtcatatactatgaattgtgcagTACATGGTGTTTGCTTGTTCGGACTCACGAGTGTGCCCATCACACGTACTAGACTTCCATCCTGGAGATGCCTTCGTGGTTCGTAATATCGCCAATATGG

Basic information

species Arabidopsis thaliana
transcript AT5G14740.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G14740.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G121878_T01 (Zea mays), 3'ss of exon 10
gtaaaacaaaaataagaagaaaaatatataaagcagttgatgaaaaatatagttatctctatatgaatatgttagatttttcttttggactcatattatatggtcata----tactatgaattgtgcagTACATGGTGTTTGCTTGTTCGGACTCACGAGTGTGCCCATCACACGTACTAGACTTCCATCCTGGAGATGCCTTCGTGGTTCGTAATATCGCCAATATGG
                            |       | | | | ||     |  | |      ||| | | |  | |  ||||||| | || |  | | |||    |     | |||||     |||||||||||||||| ||||| || ||||| || |||||||||||       || | | | || || || || ||||||   ||||| || || |||   ||||
---------------------------gtcgctgcatagctaacaaccgcgggaaccg--gcctgattttttgtgctccttctttttgcctgacctgacatgacagtgattttgctatgctgcatgcagTACATGGTGTTCGCTTGCTCCGACTCCCGTGTGTGCCCATCGGTGACCCTGGGCCTGCAGCCCGGCGAGGCCTTCACCGTTCGCAACATAGCCGCCATGG

upper sequence: AT5G14740.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G08590.2 (Glycine max), 3'ss of exon 4
gtaaaacaaaaataagaagaaaaatatataaagcagttgatgaaaaatatagttatctctatatgaatatgttagatttttcttttggactcatattatatggtcatatactatgaattgtgcagTACATGGTGTTTGCTTGTTCGGACTCACGAGTGTGCCCATCACACGTACTAGACTTCCATCCTGGAGATGCCTTCGTGGTTCGTAATATCGCCAATATGG
                |  |   || ||||||| || |     | || ||   | ||   || | || |    |  || || | ||  ||| || || | | ||  | |    |   || | |||| ||||||||||||||| || |||||| | ||||||||||| || || ||||| ||||| || ||||| ||||| |||||  | ||| | ||||| || |
--------------gaattatttatttataaagtagct-----agaacatccctttcgg-atttaaaaagaaaattttgttttattaaactaattttgtctcgtt-tgt----ttgttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTAGATTTCCAACCAGGAGAGGCCTTTGTGGTCAGAAATGTTGCCAACATTG

upper sequence: AT5G14740.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G01050.2 (Glycine max), 3'ss of exon 4
gtaaaacaaaaataagaagaaaaatatataaagcagttgatgaaaaatatagttatctctatatgaatatgttagatttttcttttggactcatattatatggtcatatactatgaattgtgcagTACATGGTGTTTGCTTGTTCGGACTCACGAGTGTGCCCATCACACGTACTAGACTTCCATCCTGGAGATGCCTTCGTGGTTCGTAATATCGCCAATATGG
                           || ||  | ||  | | | |       ||| || |  || |  |   ||  ||| | ||  |   |  | || | ||| | |    |   || | ||||  |||||||||||||| || |||||| | ||||||||||| || || ||||| ||||| || ||||| ||||| |||||  | ||| | || || || |
-------------------------tcatgaattatttatttatagagtagaaaatccctttcggatttagaacgaaatttttgttctataaaactaattttgtcttgtttgtttgttttttcagTTTATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTAGATTTCCAACCAGGAGAGGCCTTTGTGGTCAGAAATGTTGCTAACATTG

upper sequence: AT5G14740.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0066g01210.t01 (Vitis vinifera), 3'ss of exon 4
gtaaaacaaaaataagaagaaaaatatataaagcagttgatgaaaaatatagttatctctatatgaatatgttagatttttcttttggactcatattatatggtcatatacta-tgaattgtgcagTACATGGTGTTTGCTTGTTCGGACTCACGAGTGTGCCCATCACACGTACTAGACTTCCATCCTGGAGATGCCTTCGTGGTTCGTAATATCGCCAATATGG
                         | | | | |  |   |   | || ||    | ||   |||| || |  | ||||      ||       | ||  |  | |  ||| | |  ||  |||||| ||||||||| || || |||||||| || || ||||||||||| || || |||||||| || || ||||| || ||||| || ||  | ||||| ||||
-------------------------aaacagacccttaatttctacatttacgcgtttcaggatgagta-gaaaaatttacaaaatgacagttgactagttaattaactacaaatttatgttgcagTTCATGGTGTTCGCATGCTCGGACTCTCGGGTTTGCCCATCACATGTGCTGGACTTCCAACCAGGGGATGCTTTTGTGGTCCGGAACGTTGCCAACATGG

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|125257260|gb|EL271345.1|EL271345
EST:     TTGTATGGTGAGCTCGCCAAAGGTCAAAGCCCAAAG                         TACATGGTGTTTGCTTGTTCGGACTCACGAGTGTGCCCATCACACGTACTA
genomic: TTGTATGGTGAGCTCGCCAAAGGTCAAAGCCCAAAGgtaaaacaaa ... aattgtgcagTACATGGTGTTTGCTTGTTCGGACTCACGAGTGTGCCCATCACACGTACTA
EST: gi|152035330|gb|BP850738.2|BP850738
EST:     GACCAATCCTGCTTTGTATGGTGAGCTCGGCAAAGGTCAAAGCCCAAAG                         TACATGGTGTT
genomic: GACCAATCCTGCTTTGTATGGTGAGCTCGCCAAAGGTCAAAGCCCAAAGgtaaaacaaa ... aattgtgcagTACATGGTGTT
EST: gi|124744941|gb|EH836103.1|EH836103
EST:     AGACCAATCCTGCTTTGTATGGTGAGCTCGCCAAAGGTCAAAGCCCAAAG                         TACATGGTGTTTGCTTGTTCGG
genomic: AGACCAATCCTGCTTTGTATGGTGAGCTCGCCAAAGGTCAAAGCCCAAAGgtaaaacaaa ... aattgtgcagTACATGGTGTTTGCTTGTTCGG
EST: gi|47828530|gb|CK118214.1|CK118214
EST:     GACCAATCCTGCTTTGTATGGTGAGCTCGCCAAAGGTCAAAGCCCAAAG                         TACATGGTGTTTGCTTGTTCGGACTCACGAGTGTGCCCATCACACGTACTA
genomic: GACCAATCCTGCTTTGTATGGTGAGCTCGCCAAAGGTCAAAGCCCAAAGgtaaaacaaa ... aattgtgcagTACATGGTGTTTGCTTGTTCGGACTCACGAGTGTGCCCATCACACGTACTA
EST: gi|124705878|gb|EH797280.1|EH797280
EST:     GACCAATCCTGCTTTGTATGGTGAGCTCGCCAAAGGTCAAAGCCCAAAG                         TACATGGTGTTTGCTTGTTCGGACTCACGAGTGTG
genomic: GACCAATCCTGCTTTGTATGGTGAGCTCGCCAAAGGTCAAAGCCCAAAGgtaaaacaaa ... aattgtgcagTACATGGTGTTTGCTTGTTCGGACTCACGAGTGTG
EST: gi|125061463|gb|EL130102.1|EL130102
EST:     TCCTGCTTTGTATGGTGAGCTCGCCAAAGGTCAAAGCCCAAAG                         TACATGGTGTTTGCTTGTTCGGACTCACGAGTGTGCCCATCACACGTACTA
genomic: TCCTGCTTTGTATGGTGAGCTCGCCAAAGGTCAAAGCCCAAAGgtaaaacaaa ... aattgtgcagTACATGGTGTTTGCTTGTTCGGACTCACGAGTGTGCCCATCACACGTACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttagatttttcttttggactcatattatatggtcatatactatgaattgtgcagTACATGGTGTTTGCTTGTTCGGACTCACGAGTGTGCCCATCACACGTACTAGACTTCCATCCTGGAGATGCCTTCGTGGTTCGTAATATCGCCAATATGG
                                   atatactatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaacaaaaataagaagaaaaatatataaagcagttgatgaaaaatatagttatctctatatgaatatgttagatttttcttttggactcatattatatggtcatatactatgaattgtgcagTACATGGTGTTTGCTTGTTCGGACTCACGAGTGTGCCCATCACACGTACTAGACTTCCATCCTGGAGATGCCTTCGTGGTTCGTAATATCGCCAATATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG