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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagccacaatttggttggattaaataaatttgttagacataagtctctgttgcaacttttttctagacataacattgttcaagtacttcataactgcaaagttccttgagatttcacccctaatagtaaatagagttgttcacttgtatttttgtgatgaaatactttataattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT

Basic information

species Arabidopsis thaliana
transcript AT1G04140.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 11
gttagccacaatttggttggattaaataaatttgttagacataagtctctgttgcaacttttttctagacataacattgttcaagtacttcataactgcaaagttccttgagatttcacccctaatagtaaatagagttgttcacttgtatttttgtgatgaaatactttataattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT
                                                                                 | |   |||  |   || | | |||  |     |   |   ||||  |  |  ||  ||   |  || | | | ||  || |  |   |||  |||     |||  ||||||| ||||| || || |||||||| || || ||||||||||||||||||   || ||| ||| | ||||| | |  |||||  | || |||   | | | |
---------------------------------------------------------------------------------ctaaccctt--ttggtggacaattctgtagttctgatcatttaattttggactgatgtg---atatgaaatct-gttctgcatgatgatattttta-----ttcgctgcagTTTTCACCTACATCAGAGCACATACTACTGGCATATGGTCGTCGTCATAACTCACTTCTGAGGGGCATTTTCATGGATGGCAAGACCACAATCCCTGTGT

upper sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g18820.2 (Oryza sativa), 3'ss of exon 12
gttagccacaatttggttggattaaataaatttgttagacataagtctctgttgcaacttttttctagacataacattgttcaagtacttcataactgcaaagttccttgagatttcacccctaatagtaaatagagttgttcacttgtatttttgtgatgaaatacttta-taattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT
                                                                                         |      ||||   ||     | | || |    || |  ||  |  | ||   ||     | |||  | || |  || |||  | |  |    |||   ||||||||||||| || || |||||||| ||  | ||||||||||||||||||   ||| |  | | |||||||||||  ||||| |||||   |   | | | |
--------------------------------------------------------------------------------------gactggcttttgcatttttgacctaaacttgagaaatattgata--tgaaattcaaca-----actttcttcatcagttaatttggtgagcacttgtttttctgcagTTCTCACCCACTTCAGAGCACATACTATTGGCATATGGTCGTCGTCATAACTCTATGCTTAGGAGCATTGTGATGGATGGGGAAACTGGAATTCCTGTAT

upper sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G007229_T01 (Zea mays), 3'ss of exon 11
gttagccacaatttggttggattaaataaatttgttagacataagtctctgttgcaacttttttctagacataacattgttcaagtacttcataactgcaaagttccttgagatttcacccctaatagtaaatagag-ttgttcacttgta-tttttgtgatgaaat---actttataattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT
                                                                                                   |||     ||  ||  | |  | | ||   | || ||  ||      ||| | ||||  | ||  |||   |   | |   |     |||   ||||||||||||| || ||||| ||||| ||  | |||||||||||||||||| | || ||  | | |||||| ||    || || ||||        |   | |
------------------------------------------------------------------------------------------------caaaaaagcatttaggacctgagtc-tgatgacagatggatcttacatttttgcagttttcatcattgaattggatcctgtttgtctctcttttgatgcagTTCTCACCTACATCCGAACACATACTTTTGGCATATGGTCGTCGTCATAGCTCGCTCCTTAGGAGCATAGTTGTGGAAGGCGAAAATGGGGTTCCCGTAT

upper sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 11
gttagccacaatttggttggattaaataaatttgttagacataagtctctgttgcaacttttttctagacataacattgttcaagtacttcataactgcaaagttc-cttgagatttcacccctaatagtaaatagagttgttcacttgtatttttgtgatgaaatactttataattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT----
                                                                                     |  | || ||   ||||   | |||  ||  | |  | | ||   ||| | | ||     |||  |||| ||   |      | ||  |  |     ||| | ||||||||||||| || ||||| ||||| ||  | |||||||||||||||||| | || ||  | | ||||||    |||  |||||  | || ||   |||  |    
-----------------------------------------------------------------------------------tttgttgcaaaaagccaaaaaccacttaggaccttagtc-tgat--caaagataatt-----cttacatttctgcagttctcatcgttgaacctctc--ttttcatgcagTTCTCACCTACATCCGAACACATACTTTTGGCATATGGTCGTCGTCATAGCTCGCTGCTTAGGAGCAT----AGTCGTGGAGGGAGAAAATGGGATTCCTGTAT

upper sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 10
gttagccacaatttggttggattaaataaatttgttagacataagtctctgttgcaacttttttctagacataacattgttcaagtacttcataactgcaaagttccttgagatttcacccctaatagtaaatagagttgttcacttgtatttttgtgatgaaatactttataattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT
                                                                                      |  |  ||   || |||||   | | |||      | |||| ||| | ||  ||  |  ||    ||    ||   |||  | |  || |     ||    ||||||||||||| || || |||||||| || ||||| |||||||| || |||||||||||| | || || ||||| | ||||||||||||||||| || | | |
------------------------------------------------------------------------------------tcaacttttaggggctaagttttattaaattgg---tcaaata-taatttgaaatggcctttt---cttagaggactgaat-ttgtgcaactgctgtttgatatgcagTTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGGTTCTCTTCTTAAAAGTATTGTCATTGATGGAGAAACAACATTACCTATAT

upper sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA03G32620.4 (Glycine max), 3'ss of exon 10
gttagccacaatttggttggattaaataaatttgttagacataagtctctgttgcaacttttttctagacataacattgttcaagtacttcataactgcaaagttccttgagatttcacccctaatagtaaatagagttgttcacttgtatttttgtgatgaaatactttataattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT
                                                                                | |   |  |   ||||   | |  ||   |  ||| |           ||||| | || |  | | |  || |  |   | | |   ||    ||  | ||        ||||||| || || || |||||||| || ||||| |||||||| ||||||||||||||| | || || ||||| |  ||||||||||||||||  | | | |
--------------------------------------------------------------------------------taactcatgttgcaacttttaggggcc---aagttttattaaattggtcaaatataatt-tgaaatggccttctcttagaggattgaattgctgtttgatat--------agTTCTCGCCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGTCATGGTTCTCTTCTTAAAAGTATTGTTATCGATGGAGAAACAACATTGCCTATAT

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|125108137|gb|EL161182.1|EL161182
EST:     TGTCCCGGGCAATTAGGGCTGCACATTGCTTAACCTCTATCCAG                         TTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATG
genomic: TGTCCCGGGCAATTAGGGCTGCACATTGCTTAACCTCTATCCAGgttagccaca ... ttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATG
EST: gi|125303257|gb|EL317342.1|EL317342
EST:     CAATTAGGGCTGCACATTGCTTAACCTCTATCCAG                         TTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGT
genomic: CAATTAGGGCTGCACATTGCTTAACCTCTATCCAGgttagccaca ... ttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttcacttgtatttttgtgatgaaatactttataattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT
                                            tttccgt  CT-rich tract
        ttgtatttttgtgatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagccacaatttggttggattaaataaatttgttagacataagtctctgttgcaacttttttctagacataacattgttcaagtacttcataactgcaaagttccttgagatttcacccctaatagtaaatagagttgttcacttgtatttttgtgatgaaatactttataattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA