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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctttaagttagatgtcttgcttacttgatcttacacaagcaacattgttattctatactttttttgaatctcaaaactttttttgttttattaccctttacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAA

Basic information

species Arabidopsis thaliana
transcript AT5G17770.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g59930.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------------------------------------------------------------gtacctttaag-ttagatgtcttgcttacttgatcttacacaagcaacattgttattctatactttttttgaatctcaaaactttttttgttttattaccctttacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAA
                                                                                                | |  | |  | ||| || | ||| |||  |||  || |||||   |  | | |  ||   | || | ||   | |   |  ||    || ||| ||  |  ||       ||||| | ||||  || |||   || ||  | || || ||||||||||| ||||| || ||||||||||||||||||||||||
gttgttttctttctgttccaagcaacttgtgttaagtctataatgggtgtttattgactctgaaagagttttgtgttatctattatgctttagccagcatttatgtgcttacatttattgattaggtgacatt-cacaattgaattgggtgctc---atttgtctttggtttatgagtttaacatggtttcttctctgtt-----ctagGGTCGTTTCAGATACCAAGTTGGGCAAGTGAGAGCTTTTGGAATGCTAGCTGGTGGATCAGGCATCACTCCCATGTTCCAA

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G133213_T01 (Zea mays), 3'ss of exon 4
gtacctttaagttagatgtcttgcttacttgatcttacacaa-gcaacattgttattctatac-tttttttgaatctcaaaactttttttgttttattaccctttacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAA
         |  | ||| |    |  |||  ||    | |    |||  |   ||   |  || |||   |  |  |   |  ||  | ||| || ||  |   ||      ||||  | |||||||| ||    || ||  | ||||||||||||||||| ||||| || |||||||| ||||| ||||| |||
---------aaatggattttcctcaaactctatgaatcgcctcacaatttctgtaccatgcacatttgccttcagttaggaggttaatatgtattcttctctgatat-----agGGCCGATTCAAGTACCACGTTGGCCAAGTGAGGGCATTTGGAATGCTGGCTGGTGGATCAGGCATTACTCCAATGTTTCAA

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G29720.1 (Glycine max), 3'ss of exon 4
gtacctttaagttagatgtcttgcttacttgatcttacacaagcaacat-tgttattctatactttttttgaatctcaaaactttttttgttttattaccctttacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAA
        | | ||       |   ||     |  |  |    |||  | || ||    ||       |||    | | |  |  ||  | ||||  |   ||  |||  |||||  | |||||||| ||||| ||  || ||||||||||||| |||||||||||||| || || ||||| || ||||| |||
--------aggatattcacagt-tatatgcatttctgtattcacaatgtctgataccaaatgaaagacttgttatttaga--tagttgggctttaacataatt-gctt-ccagGGACGTTTCAAGTACCAACCTGGCGAGGTTAGGGCATTTGGGATGCTTGCTGGAGGCTCTGGAATCACCCCAATGTTTCAA

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 4
gtacctttaagttagatgtcttgcttacttgatcttacacaagcaacat-tgttattctatactttttttgaatctcaaaactttttttgttttattaccctttacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAA
         ||   | |  |     ||     |  |  |    |||  | || ||    ||   |   |||    | | |  |  ||  | ||||  |   ||  |||  |||||  | |||||||| ||||| ||  || ||||||| ||||| |||||||||||||| || || ||||| || |||||||||
---------agggtgttcacagttatatgcatttctgtattcacaatgtctgataccaaatgaatgacttgttatttaga--taattgggctttaacataatt-gctt-ccagGGACGTTTCAAGTACCAACCTGGCGAGGTTAGGGCTTTTGGGATGCTTGCTGGAGGGTCTGGAATCACCCCAATGTTCCAA

upper sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 4
gtacctttaagttagatgtcttgcttacttgatcttacacaagcaacattgttattctatactttttttgaatctcaaaactttttttgttttattaccctttactt--gtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAA
               || || | | | | | ||  || | ||   |  | |   |     |     |  |  ||| |  | |  | ||| | |||||    ||| ||   ||||||  | |||| |||||||   || ||  ||||||||||||| ||||||||||||||||| || || || || |||||||||
------------ggaatatcattcatgcataat--taaataaaacagttagaactgaagaaaaaaatgaggctcttatcaatactgttggtgtattaaatgttaattctatcagGGGCGTTTCAGGTATCAAGTTGGCCAAGTTAGGGCATTTGGGATGCTTGCTGGAGGTTCTGGAATTACACCAATGTTCCAA

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|47828476|gb|CK118160.1|CK118160
EST:     ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAG                         GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
genomic: ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAGgtacctttaa ... tacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
EST: gi|164131967|gb|ES199452.1|ES199452
EST:     AGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAG                         GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
genomic: AGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAGgtacctttaa ... tacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
EST: gi|164016546|gb|ES206430.1|ES206430
EST:     ATTTCAGGGAGGTGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAG                         GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTT
genomic: ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAGgtacctttaa ... tacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTT
EST: gi|86066440|gb|DR362197.1|DR362197
EST:     ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAG                         GGTAGGTTCAAGTATCAACCAGGGTCAGTTTAGGGCA
genomic: ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAGgtacctttaa ... tacttgtcagGGTAGGTTCAAGTATCAACCAGG-TCAGTTTAGGGCA
EST: gi|86066414|gb|DR362171.1|DR362171
EST:     ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAG                         GGTAGGTTCAAGTATCAA
genomic: ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAGgtacctttaa ... tacttgtcagGGTAGGTTCAAGTATCAA
EST: gi|163978699|gb|ES179419.1|ES179419
EST:     TTTCAGGGTAGGTGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAG                         GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTT
genomic: TTTCAGGG-AGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAGgtacctttaa ... tacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTT
EST: gi|86066411|gb|DR362168.1|DR362168
EST:     ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTNNNGGGACCAAAG                         GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
genomic: ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAGgtacctttaa ... tacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
EST: gi|86066408|gb|DR362165.1|DR362165
EST:     ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAG                         GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
genomic: ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAGgtacctttaa ... tacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
EST: gi|86066428|gb|DR362185.1|DR362185
EST:     ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAG                         GGTAGGTTCAAGTATCAACCAGGTCAGTTT
genomic: ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAGgtacctttaa ... tacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTT
EST: gi|164075208|gb|ES124978.1|ES124978
EST:     CATCTTGCCGTAAAGGGACCAAAG                         GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
genomic: CATCTTGCCGTAAAGGGACCAAAGgtacctttaa ... tacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
EST: gi|86066425|gb|DR362182.1|DR362182
EST:     ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAG                         GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
genomic: ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAGgtacctttaa ... tacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
EST: gi|86066436|gb|DR362193.1|DR362193
EST:     ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAG                         GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
genomic: ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAGgtacctttaa ... tacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
EST: gi|86066448|gb|DR362205.1|DR362205
EST:     ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAG                         GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
genomic: ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAGgtacctttaa ... tacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
EST: gi|86082753|gb|DR378512.1|DR378512
EST:     TTTCAGGGAGATGCGTGTTGGNAG-CCATCTTGCCGTAAAGGGACCAAAG                         GGTAGGTTCAAG-ATCAACCAGG-CAGTTTAGGGCATTTGGAATGCTTGCT
genomic: TTTCAGGGAGATGCGTGTTGG-AGACCATCTTGCCGTAAAGGGACCAAAGgtacctttaa ... tacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
EST: gi|86066444|gb|DR362201.1|DR362201
EST:     ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAG                         GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGC
genomic: ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAGgtacctttaa ... tacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGC
EST: gi|86066429|gb|DR362186.1|DR362186
EST:     ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAG                         GGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT
genomic: ATTTCAGGGAGATGCGTGTTGGAGACCATCTTGCCGTAAAGGGACCAAAGgtacctttaa ... tacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatactttttttgaatctcaaaactttttttgttttattaccctttacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAA
                       ctttttttgttttatt  CT-rich tract
     tttttttgaatctcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctttaagttagatgtcttgcttacttgatcttacacaagcaacattgttattctatactttttttgaatctcaaaactttttttgttttattaccctttacttgtcagGGTAGGTTCAAGTATCAACCAGGTCAGTTTAGGGCATTTGGAATGCTTGCTGGAGGTTCAGGCATCACTCCCATGTTCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG