Sequence
atgc intronic sequence ATGC exonic sequencegcaagtagtttcttaagtacactacacattcctgatttacacaactaattgccttggtcactttacgcagGGAGAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G04600.3 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G04600.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os12g35570.3 (Oryza sativa), 3'ss of exon 6
------------------------------gcaagtagtttcttaagta-cactacacattcctgatttacacaactaattgccttggtcactttacgcagGGAGAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
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ctcatgtccattgctcagcatttatttttcttatttcctattttagatagcataatatttgggacattgatttatgtgagctgcttatttccatt-tacagGGGGAGAACACAAAAATGTCGGCCAGTGATCCAAATTCTGCAATATATGTGACAGATAGTGCTAAAGAAATAAAGACAAAG
upper sequence: AT3G04600.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os12g35570.2 (Oryza sativa), 3'ss of exon 6
------------------------------gcaagtagtttcttaagta-cactacacattcctgatttacacaactaattgccttggtcactttacgcagGGAGAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG-------------------
| | | | ||| || || | | | ||| | | | | ||| | | || ||||| ||||| ||||||||| || ||||||||||||||||| || |||||||| ||| || || || || || | |||
ctcatgtccattgctcagcatttatttttcttatttcctattttagatagcataatatttgggacattgatttatgtgagctgcttatttccatt-tacagGGGGAGAACACAAAAATGTCGGCCAGTGATCCAAATTCTGCAATATATGTGACAGATAGTGCTAAAGAAATAAAGACAAAGGTTTGCTTTAAGCATTGTA
upper sequence: AT3G04600.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G11390.1 (Glycine max), 3'ss of exon 6
------------------------gcaagtagtttcttaagtacactacacattcctgatttaca--caactaattgccttgg----tcactttacgcagGGAGAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
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ggaaactgcagttacatatagactttgaaattttctctgaataaggtccaaattcctttgtagctgttatctcacatctttaaaatataaattcttgcagGGAGAAACAGGAAAAATGTCTGCCAGTGATCCCAATTCTGCAATATATGTGACCGATTCTGCAAAAGATATAAAGAACAAG
upper sequence: AT3G04600.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 6
------------------------gcaagtagtttcttaagtacactacacattcctgatttaca---caactaattgccttg----gtcactttacgcagGGAGAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
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ggaaactgaagttacatataggttttgaaattttctctgaaaaaggtctaaattctt-atgtagatgttatctcacatctttataatataaattcttgcagGGGGAAACAGGAAAAATGTCTGCCAGTGATCCCAATTCTGCAATATATGTGACCGATTCTGCAAAAGATATAAAGAACAAG
upper sequence: AT3G04600.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 7
-----------gcaagtagtttct-----taagtacactacacattcctgatttacacaactaattgccttggtcactt--------------tacgcagGGAGAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
|| |||||| | | || | ||| ||| || | || || | || | | |||||| |||| ||||||||||||||||||||||| |||||||| || || ||||||||||| | |||||||||||| ||||||
cttctttgatgcttggtggtttctacatatggctgcatcattaattttctttttgtgtaaatcatggctcttgtttttccttgaatttgtatatctgcagGGGGAGACAGGAAAAATGTCTGCTAGTGATCCCAATTCTGCAATATACGTGACTGATTCTGGAAAGGACATTAAGAACAAG
upper sequence: AT3G04600.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ24416 (Selaginella moellendorffii), 3'ss of exon 7
gcaagtagtttcttaagtacactacacattcctgatttacacaactaattgccttggtcactttacgcagGGAGAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
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------------gtgagtgcttc---tttttaaaacttatagcactaag-gcgttccacattt----cagGGAGAGAGTGGCAAAATGTCTGCTAGTGATACGAACTCTGCAATTTACGTGAAGGATACCCAAAAAGAGATCAAGAAAAAG
upper sequence: AT3G04600.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ23832 (Selaginella moellendorffii), 3'ss of exon 7
gcaagtagtttcttaagtacactacacattcctgatttacacaactaattgccttggtcactttacgcagGGAGAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
| ||| | || ||| | ||||| || || ||| || |||||||||| ||| |||||||||||||||||| | || ||||| || || |||| ||| || ||| || || || || |||
------------gtgagtgcttc---tttttaaagcttatagcactaag-gcgttcctcattt----cagGGAGAGAGTGGCAAAATGTCTGCTAGTGATACGAACTCTGCAATTTACGTGAAGGATACCCAAAAAGAGATCAAGAAAAAGMapped 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|164235157|gb|EL975532.1|EL975532EST: GCTATAGCAAGCCCGCCCTGATTGAGTCAACATTTTT-CCTGCGTTGCAG GGAGAGAATGGAAAAATGTCTGCTAGTGATCCAAA
genomic: GCTATAGCAAGCCCGCCCTGATTGAGTCAACATTTTTTCCTGCGTTGCAGgcaagtagtt ... ctttacgcagGGAGAGAATGGAAAAATGTCTGCTAGTGATCCAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtacactacacattcctgatttacacaactaattgccttggtcactttacgcagGGAGAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
aactaat putative branch site (score: 2)
tcacttt putative PPT
aactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagtagtttcttaagtacactacacattcctgatttacacaactaattgccttggtcactttacgcagGGAGAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG