Sequence
atgc intronic sequence ATGC exonic sequence...ttttgtgtaaatagtagaaaataagattttaaggtaccaatctgttggtttttcgatttaaattgtagttactgatcgaaaacggaaaccttttgtgcagGTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTAGCTCAGAGGGTTTTGATAAATCCAAGAAAGATTGACT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G16950.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
-----ttttgtgtaaatagtagaaaataagattttaaggtaccaatctgttggtttttcgatttaaattgtagttactgatcgaaaacggaaaccttttgtgcagGTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTAGCTCAGAGGGTTTTGATAAATCCAAGAAAGATTGACT
| | ||| || || ||||| | | |||||| | | || | || | | | ||| | ||| ||||| |||||| | |||||||| |||||| | |||||||| |||||||||||||| || | || || ||| || | || ||||| | || |||||||
catgttaaattctaattaaccatctatgctgttttatgattaaggcctgttgtcatctgatgatatttcacctgtatttacctaaatt-----tcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 5
ttttgtgtaaatagtagaaaataagattttaaggtaccaatctgttg--gtttttcgatttaaattgtagttactgatcgaaaacggaaacctt--ttgtgcagGTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTAGCTCAGAGGGTTTTGATAAATCCAAGAAAGATTGACT
| || | | ||| | | ||| ||| | | | | | | ||||| || | | || | | || || | ||||| |||||| | ||||| || || |||||||||||||| ||||||||||| || || |||| ||||| || | || || || | || || ||||
----tttcaacttacacaaatgattctattacagtagtattgtatcactgcatgctgatttttgttttcacatgccccctgaattgacagttttcattcttcagGTTACTTTTGTTGAAGCTCTTGACCAGCTAATGCCTGGTTTTGATCCTGAAATTGCAAAATTAGCCCAGAGAGTCCTTATCAACCCTCGGAATATAGACT
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 5
ttttgtgtaaatagtagaaaa----taagattttaaggtaccaatctgt-tggtt-tttcgatttaaattgtagttactgatcgaaaacggaaaccttttgtgcagGTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTAGCTCAGAGGGTTTTGATAAATCCAAGAAAGATTGACT
|| | ||| ||||| | ||| | | || | || || || | |||| | | | | || | || ||| |||||| |||||| | ||||| || || ||||| |||||||||||||||||||| || || |||| ||||| ||| | || ||||| | || |||||||
-gctggatgaattctagaatgctccttagacatctgttgcctgatgaatatgattgttctcagttaattcacttgaatttactcaattcaaaa-----ttgggcagGTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAAATTGCAAAATTAGCCCAGAGAGTTCTTATCAATCCTCGGAAAATTGACT
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 5
-ttttgtgtaaatagtagaaaataagattttaaggtaccaatctgttggtttttcgatttaaattgtagttactgatcgaaaacggaaacc-ttttgtgcagGTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTAGCTCAGAGGGTTTTGATAAATCCAAGAAAGATTGACT
| | | || | | | | | |||| || ||| | | | | ||||| | | | | || || | || ||||||| |||||||||||||| | ||||| || |||||||||||||||||||| || || ||| | ||||||||||| | |||||||| | || |||||||
agtccaagaagttaaaaaatatttaatctttattttaaaaatttat--gatccctaatttatccctgaaaagataagcaaagtaataattggtattctgcagGTTACTTTTATAGAAGCTTTAGATCAACTTATGCCTGGATTTGATCCTGAAATTAGCAAGTTGGCTCAGAGGGTCCTTATAAATCCCCGGAATATTGACT
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------------------------ttttgtgtaaatagtagaaaataagattttaaggtaccaatctgttgg----tttttcgatttaaattgtagttactgatcgaaaacggaaacc----ttttgtgcagGTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTAGCTCAGAGGGTTTTGATAAATCCAAGAAAGATTGACT
|||| | || | | ||||| || | |||| | || | ||| |||| | | || || | | ||||||| |||||||| ||||| | || ||||| |||||||||||||||||||| || || ||| | |||||||||||| | |||||||| | || |||||||
gtagtacttctcttctgatatatttttttttatcctttctcaattgtattttgttcatgagaagaactgacaatagttttccaatttttcttttatgacgtttgaaagttttttatattatctcattgtttgaaaagttagaaacctaatttgtgcagaagagatatagttggtaataatggtactctgcagGTTACTTTTATTGAAGCTTTAGACCAGCTCATGCCTGGATTTGATCCTGAAATTAGCAAGTTGGCTCAGAGGGTTCTCATAAATCCCCGGAATATTGACT
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 5
ttttgtgtaaatagtagaaaataagattttaaggtaccaatctgttggtttttcgatttaaat-tgtagttactgatcgaaaacggaaaccttttgtgcagGTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTAGCTCAGAGGGTTTTGATAAATCCAAGAAAGATTGACT
| | ||| || | || |||| || || | | | ||||| || | | | | | | | || ||||||| |||||||||||||| | ||||| || |||||||||||||||||||| || || ||| | ||||||||||| | |||||||| | || |||||||
-aatatttaatctttatactatttcctttttttttaaaaaaaattatgatccctaatttattcctgaaaagattagcaaattaataattggtattctgcagGTTACTTTTATAGAAGCTTTAGATCAACTTATGCCTGGATTTGATCCTGAAATTAGCAAGTTGGCTCAGAGGGTCCTTATAAATCCCCGGAATATTGACT
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 5
ttttgtgtaaatagtagaaaataagattttaaggtaccaatctgttggtttttcgatttaaattgtagttactgatcgaaaacggaaaccttttgtgcagGTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTAGCTCAGAGGGTTTTGATAAATCCAAGAAAGATTGACT
| || ||||||| || || || || | ||| ||| | ||||||||| |||||| | ||||| |||||||| || ||||| || ||||||||||| ||| | ||||| ||||||||| | |||| ||||| |||| ||||| |
---------------------------------------gtttgcgagtttttcttctttcctt----tttct-acagaatacgcga------tgtgcagGTGACTTTTGTGGAAGCTCTGGATCAACTGATGCCAGGCTTTGATCCTGAAATCGGGAAGCTTGCTCAGAGGCTGCTGATCAATCCTCGAAAAATTGATT
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 5
ttttgtgtaaatagtagaaaataagattttaaggtaccaatctgttggtttttcgatttaaattgtagttactgatcgaaaacggaaaccttttgtgcagGTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTAGCTCAGAGGGTTTTGATAAATCCAAGAAAGATTGACT
|| ||||||| || || || || || ||| ||| | ||||||||| |||||| | ||||| |||||||| || ||||| || ||||||||||| ||| | ||||| ||||||||| | |||| || || |||| ||||| |
------------------------------------------gtttagtttttcttctttcctt----tttct-atagaatacgcga------tgtgcagGTGACTTTTGTTGAAGCTCTGGATCAACTGATGCCAGGCTTTGATCCTGAAATCGGGAAGCTTGCTCAGAGGCTCCTGATCAACCCTCGAAAAATTGATTMapped 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|125320557|gb|EL334642.1|EL334642EST: TATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAG GTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGA
genomic: TATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAGgtaacatgat ... ttttgtgcagGTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtttttcgatttaaattgtagttactgatcgaaaacggaaaccttttgtgcagGTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTAGCTCAGAGGGTTTTGATAAATCCAAGAAAGATTGACT
tactgat putative branch site (score: 2)
ccttttgt putative PPT
atttaaattgtagtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttgtgtaaatagtagaaaataagattttaaggtaccaatctgttggtttttcgatttaaattgtagttactgatcgaaaacggaaaccttttgtgcagGTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTAGCTCAGAGGGTTTTGATAAATCCAAGAAAGATTGACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA