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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtatctacacattgctctgaatagatattctcttgtaatacaatacctgaatctgttttgatcttcggtctacatctgtagGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG

Basic information

species Arabidopsis thaliana
transcript AT1G12840.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 8
--gtaggtatctacacattgctctgaat--agatattctcttgtaatacaatacctgaat------ctgttttgatcttcggtctaca-----tctgtagGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG
  || ||  | |     ||||| |   |     |  |  || || |     |   |  ||      | ||| | ||        || |     |||| |||| ||||| ||||||||||| |||||||||||||||   || |  ||||||||| | ||||| ||| | || ||  | ||| ||
ttgttgggttttgtggtttgctttttctttgattcattcctcgtgaacttgtgttttcatggtgctcagttgtaattgcttacataaaactattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATTCTTAGATATGGTCTTCCCCCATCATTCCTG

upper sequence: AT1G12840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G128995_T01 (Zea mays), 3'ss of exon 8
-----gtag--gtatctacacattgctctgaatagatattctcttgtaatacaatacctgaatctgttttgatcttcggtctacatctgt--------agGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG
     || |  ||   || |   |   |||| | | | ||  | |    |    | | |   ||  || |    |  |  ||  | || |        |||| ||||| ||||||||||| |||||||||||||||   || |  ||||||||  | ||||| ||| | |||||  | ||| ||
gctttgttgctgtggttatatggtttgctgagttggtttttgccttctttctctttcgtatgtcatttcttgcttgtgaactgtaactattactgtacagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGCATCCTTAGATATGGTCTCCCTCCATCATTCCTG

upper sequence: AT1G12840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 8
-------gtaggtatctacacattgctctgaatagatattctcttgtaatacaatacctgaatctgttttga----tcttcggtctacatctgt----agGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG
           || | ||    |  |     ||   | |  | || |  || ||| |     ||  | || |    | ||   | || || | |    |||||||||| ||||||||||| || ||||||||||||  ||| |||||||||||| ||||||| ||| | |||||  | ||||||
acttttctcgcgtttttatcactcaccacatattcttgtcttgttatcctaaaatgctatggtccttattcactactttttactttatatttttccaaagGTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCTCCATCCTTCTTG

upper sequence: AT1G12840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA16G05470.1 (Glycine max), 3'ss of exon 8
--------gtaggtatctacac-attgctctgaatagatattctcttgtaatacaatacctgaatctgttt--tgatcttcggtctacatctgt----agGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG
        | |  | |  ||   | |  | |   |   |   || || | |  ||| || |     || |   |  | ||   | || || | |    |||||||||| ||||||||||| || ||||||||||||  ||| |||||||||||| ||||||| ||| | || ||  | ||||||
atttactagcatttgttgaccttaattttatacttttctcaccttttatcactcaacacttattcttgctcactactttttactttatattttttcaaagGTTTTCAGTTCCTGGATGCACTTTTGTGCTGTGCGTTTATTTGCTGAGAGCATTCTGAGATATGGTCTGCCACCATCTTTCTTG

upper sequence: AT1G12840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA02G07260.1 (Glycine max), 3'ss of exon 8
---------gtaggtatctacacattgctctgaataga-tattctcttg--taatacaatac--ctgaat--ctgttttgatcttcggtctacatctgtagGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG
           | || |||      |  ||||  |    | || || |   |  |   |  |  |||| |   | |||| |  |    | |    ||| |||||||||||||||||||||| || ||||| ||||||  |||  ||||||||||| ||||||| ||| | || ||  | ||||||
aaaatgttaacaagt-tctgtgatctcttctgcttgccctgttatcataaatgctgtgactcttctgatttgttatttttacttctttttttttcctgaagGTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACTGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTG

upper sequence: AT1G12840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA16G26220.1 (Glycine max), 3'ss of exon 8
------------gtaggtatctacacattgctctgaatagatattctcttgtaa----tacaatacctg-aatctgttttgatcttcggtctacatctgtagGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG
             || || |||    ||  ||     | |   |  | | ||||    |   |  | |   || |||| |  | |    | |    ||| |||||||||||||||||||||| || ||||| ||||||  |||  | ||||||||| ||||||| ||| | || ||  | ||||||
cataaaatgtgaataagt-tctgtg-atctcttgtgcttgccctgttatcgtaaatgctgtgactcttctgatttgttattttttcttttttttccctgaagGTTTTCAGCTCCTGGATGCACTTTTGTGCAGTGCGTGTATTTACCGAGAGCATTCTGAGATATGGTCTTCCACCATCTTTCTTG

upper sequence: AT1G12840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 8
------------gtaggtatctacacattgctctgaatagatattctcttgtaatacaatacct----gaatctgttttgatctt-cggtctacatctgtagGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG
            || | | |  | | | || |    || | | ||  |||  |||   | |  |     | | | |||| || |   |   | |  ||  ||||||||||||||||||||||||| |||||||| |||   || || ||||| ||  | ||||| || || || ||  | ||||||
tgtgaatgacttgt-gttgttgatagagtg-tggctattgttgtttccttccaatgttaaattttggtaattttatttttatatcatgagtttctccttcagGTTTTCAGCTCCTGGATGCATTTTTGTGCTGTACGTGTCTTTGCAGAGAGTATCCTTAGATATGGCTTGCCACCATCCTTCTTG

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|86077243|gb|DR373000.1|DR373000
EST:     AAAGTTTGAGAAGCTCTCTTTTGCAGT-GTGCTACACCAGTTATGGAGAG                         GTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGC
genomic: AAAGTTTGAGAAGCTCTCTTTTGCAGTGGTGCTACACCAGTTATGGAGAGgtaggtatct ... acatctgtagGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGC
EST: gi|125180499|gb|EL197426.1|EL197426
EST:     AAAGTTTGAGAAGCTCTCTTTTGCAGTGGTGCTACACCAGTTATGGAGAG                         GTTTTCAGCTCCTGGATG
genomic: AAAGTTTGAGAAGCTCTCTTTTGCAGTGGTGCTACACCAGTTATGGAGAGgtaggtatct ... acatctgtagGTTTTCAGCTCCTGGATG
EST: gi|125232451|gb|EL246536.1|EL246536
EST:     TGCTACACCAGTTATGGAGAG                         GTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGC
genomic: TGCTACACCAGTTATGGAGAGgtaggtatct ... acatctgtagGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGC
EST: gi|125183447|gb|EL198401.1|EL198401
EST:     AAAGTTTGAGAAGCTCTCTTTTGCAGTGGTGCTACACCAGTTATGGAGAG                         GTTTTCAGCTCCTGGATGC
genomic: AAAGTTTGAGAAGCTCTCTTTTGCAGTGGTGCTACACCAGTTATGGAGAGgtaggtatct ... acatctgtagGTTTTCAGCTCCTGGATGC
EST: gi|116402070|gb|EG444662.1|EG444662
EST:     AAAGTTTGAGAAGCTCTCTTTTGCAGTGGTGCTACACCAGTTATGGAGAG                         GTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGC
genomic: AAAGTTTGAGAAGCTCTCTTTTGCAGTGGTGCTACACCAGTTATGGAGAGgtaggtatct ... acatctgtagGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGC
EST: gi|125193532|gb|EL208486.1|EL208486
EST:     CTACACCAGTTATGGAGAG                         GTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGC
genomic: CTACACCAGTTATGGAGAGgtaggtatct ... acatctgtagGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGC
EST: gi|125233568|gb|EL247653.1|EL247653
EST:     AGTTATGGAGAG                         G-TTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGC
genomic: AGTTATGGAGAGgtaggtatct ... acatctgtagGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGC
EST: gi|125072573|gb|EL137214.1|EL137214
EST:     AAAGTTTGAGAAGCTCTCTTTTGCAGTGGTGCTACACCAGTTATGGAGAG                         GTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCG
genomic: AAAGTTTGAGAAGCTCTCTTTTGCAGTGGTGCTACACCAGTTATGGAGAGgtaggtatct ... acatctgtagGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctcttgtaatacaatacctgaatctgttttgatcttcggtctacatctgtagGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG
                             ttttgat  putative branch site (score: 4)
         taatacaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtatctacacattgctctgaatagatattctcttgtaatacaatacctgaatctgttttgatcttcggtctacatctgtagGTTTTCAGCTCCTGGATGCATTTCTGTGCTGTGCGTACATTCGCTGAGAGCATTATGAGATACGGTTTACCTCCGGCGTTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA