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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctttatggtgttaatttttgattttgattccctagtagtgttttaactttttgctggcatcttcgcacaaatttttaagttcatcttgtgagaaccttgacttacgtctagAGATCTGAATCACACGAACCAGTACATTGTGGGGCTTGCTCTCTGTGCTTTAGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTCGCCCCTGAAGTT

Basic information

species Arabidopsis thaliana
transcript AT1G60070.2
intron # 2
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G60070.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os06g07090.2 (Oryza sativa), 3'ss of exon 2
gtatcctttatggtgttaatttttg--attttgattccctagtagtgttttaactttttgctggcatcttcgcacaaatttttaagttcatcttgtgagaaccttgacttacgtctagAGATCTGAATCACACGAACCAGTACATTGTGGGGCTTGCTCTCTGTGCTTTAGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTCGCCCCTGAAGTT
            || |  |    |   ||  | || | | |    |||||| | ||||    |    ||  |  |     ||| ||  ||| | ||   |  ||| ||   ||   |||||||| || ||| ||||||||| ||||||||||||||| ||||||||| | || || ||||| || || |||||||| ||||||||  | ||||| || 
------------gtatccacccatactatacttatgctccatatctgttttgatttttcttagaatgctatgttctg--ctttgag--catttggtagta--cttaac--gcggacagAGATCTTAACCACTCGAACCAGTTCATTGTGGGGCTTGCACTCTGTGCTCTTGGCAACATTTGCTCCGCTGAAATGGCGCGTGATCTGTCACCTGAGGTG

upper sequence: AT1G60070.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g56110.2 (Oryza sativa), 3'ss of exon 2
gtatcctttatggtgttaatttttgattttgattccctagtagtgttttaactttttgctggcatcttcgcacaaatttttaagttcatcttgtgagaaccttgacttacgtctagAGATCTGAATCACACGAACCAGTACATTGTGGGGCTTGCTCTCTGTGCTTTAGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTCGCCCCTGAAGTT
|||  |     |    || | | |   |   || | ||  |     ||    |||| ||  | |  |  |     | |||| |||   | | ||||  |  |||     |    |||||||| |||||| ||||||||| ||| |||||||||||  | |||||  | || ||||| || || || |||||||| || |||||  | |||||||| 
gtacaccaccagactctattatct--ctgcaatgcgctgctgcgagttctgtttttcgcatgtaattctg-----agttttgagtaattttagtgattaatttggggggc----agAGATCTCAATCACTCGAACCAGTTCATCGTGGGGCTTGCATTGTGTGCGCTTGGGAATATCTGCTCCGCTGAAATGGCACGGGATCTGTCGCCTGAAGTG

upper sequence: AT1G60070.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G03890.1 (Glycine max), 3'ss of exon 2
---------------------------------gtatcctttatggtgt-taatttttgattttgattcccta---gtagtgttttaa-ctttttgctggcatcttc-----gcacaaattttta-agttcatcttgtgagaaccttgacttacgtctagAGATCTGAATCACACGAACCAGTACATTGTGGGGCTTGCTCTCTGTGCTTTAGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTCGCCCCTGAAGTT
                                  | |  |||||  |   | ||||||   ||  |||    |   ||  | |||| | ||  || |||  ||         | |||||| || | | |   |  |   ||| |||| ||| |     |||||||| |||||||| || ||||| || ||||| |||||||| |||||||||||||| ||||||||||||||||||||||||||||| || || || |||
gtatccagtttttagtcaaagttctgtttattttttttatttatattccctgatttttacattgcattttacaaatgtgttattttgatctacttactgaaataaaatgagggaacaaatattaataatgggttatagcagagccttaactgaatcacagAGATCTTAATCACACAAATCAGTATATAGTGGGACTTGCTCTTTGTGCTTTAGGAAACATTTGTTCAGCAGAAATGGCTCGTGATCTTGCACCAGAGGTT

upper sequence: AT1G60070.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 1
---------------------------gtatccttt-atggtgt-taatttttgattttgattcccta---gtagtgttttaactttttgctggcatcttcg----------cacaaatttttaagttcatcttgtgagaaccttgacttacgtctagAGATCTGAATCACACGAACCAGTACATTGTGGGGCTTGCTCTCTGTGCTTTAGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTCGCCCCTGAAGTT
                            |||| ||| ||  ||  | ||||||   ||| | |    |   ||  | |||| |  || | ||  |     |            | ||| | ||||       ||   ||| |||| ||| |     |||||||| |||||||| || ||||| || ||||| |||||||| |||||||||||||| |||||||||||||||||||| |||||||| || || || |||
gtatccagtttttagtcaaagttctgtttatctttttatattgcctgatttttacatttcactttacaaatgtgttattttgatcttctacttactgaaacaaaatgaagaaaaaaaaatattaataatgggttagtagagccttaactgaatcacagAGATCTTAATCACACAAATCAGTATATAGTGGGACTTGCTCTTTGTGCTTTAGGAAACATTTGTTCAGCAGAAATGGCCCGTGATCTTGCACCAGAGGTT

upper sequence: AT1G60070.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G39930.1 (Glycine max), 3'ss of exon 2
gtatcc---tttatggtgttaatt--tttgattttg-attccctagtagtgttttaactttttgctggcatcttcgca--caaatttttaagttcatc--ttgtgagaaccttgacttacgtctagAGATCTGAATCACACGAACCAGTACATTGTGGGGCTTGCTCTCTGTGCTTTAGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTCGCCCCTGAAGTT
||||||   || |||    |  ||  |||| |||||  |||| || |  |    |  | |||| |    ||  | |    | |    | | | | ||   || | | ||||||  || |     |||||||| |||||||| || || || || ||||| |||||||| ||||||||||||||||||| |||||| ||||||||||||||||| || || || |||
gtatccaaattcatgtcaatgtttcatttgtttttgtgttccttaatttttagattccattttacaaatatgctagggagctagcaataatggtgatgggttataaaaaccttagctaagtcacagAGATCTTAATCACACAAATCAATATATAGTGGGACTTGCTCTTTGTGCTTTAGGAAATATTTCTTCAGCCGAAATGGCTCGTGATCTTGCACCAGAGGTT

upper sequence: AT1G60070.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 2
gtatcctttatggtgttaatttttgattttgattccctagtagtgttttaactttttgctggcatcttcgcacaaatttttaagttcatcttgtgagaaccttgacttacgtctagAGATCTGAATCACACGAACCAGTACATTGTGGGGCTTGCTCTCTGTGCTTTAGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTCGCCCCTGAAGTT
                 ||      |   | || |  | |||   | ||        |  |  |       | ||| |  | | | |   |||   ||||||| |||||  | ||||||||| ||||| |  ||||||||||||||||| |||||||| |||||| | ||||||||||||||||||||||||||||||||||| || |||||||| 
-------------caaaaaaaaaaaaacattat-cgttggtacgatattcttacaaagtcgaaaagaaaaaaaaaaatcatcactcc--tttgcaggaaccttaacttatatttagAGATCTCAATCATAACAACCAGTACATTGTGGGACTTGCTCTTTGTGCTCTGGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTTGCACCTGAAGTG

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|116403651|gb|EG446243.1|EG446243
EST:     CTTGATGAAAGGCAAGAAGTATTAATGCTTGTCACCAACTCGCTGAAGCA                         AGATCTGAATCACACG
genomic: CTTGATGAAAGGCAAGAAGTATTAATGCTTGTCACCAACTCGCTGAAGCAgtatccttta ... ttacgtctagAGATCTGAATCACACG
EST: gi|19875009|gb|AU235840.1|AU235840
EST:     CTTGATGAAAGGCAAGAAGTATTAATGCTTGTCACCAACTCGCTGAAGCA                         AGATCTGAATCACACGAACCAGTACATTGTGGGGCTTGCTCTCTGTGCTTT
genomic: CTTGATGAAAGGCAAGAAGTATTAATGCTTGTCACCAACTCGCTGAAGCAgtatccttta ... ttacgtctagAGATCTGAATCACACGAACCAGTACATTGTGGGGCTTGCTCTCTGTGCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatcttcgcacaaatttttaagttcatcttgtgagaaccttgacttacgtctagAGATCTGAATCACACGAACCAGTACATTGTGGGGCTTGCTCTCTGTGCTTTAGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTCGCCCCTGAAGTT
 aaccttgac  putative branch site 
            aaatttttaagttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctttatggtgttaatttttgattttgattccctagtagtgttttaactttttgctggcatcttcgcacaaatttttaagttcatcttgtgagaaccttgacttacgtctagAGATCTGAATCACACGAACCAGTACATTGTGGGGCTTGCTCTCTGTGCTTTAGGAAATATTTGTTCAGCAGAAATGGCTCGTGATCTCGCCCCTGAAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG