Sequence
atgc intronic sequence ATGC exonic sequencegtagtttcttaagtacactacacattcctgatttacacaactaattgccttggtcactttacgcagggagAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G04600.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os12g35570.3 (Oryza sativa), 3'ss of exon 6
------------------------------gtagtttcttaagtacactacacatt-cctgatttacacaactaattgccttggtcactt---tacgcagggagAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
|| || || || | || | | || | | || || || | | || | ||||| ||||| ||||||||| || ||||||||||||||||| || |||||||| ||| || || || || || | |||
ctcatgtccattgctcagcatttatttttcttatttcctattttagatagcataatatttgggacattgatttatgtgagctgcttatttccatttacagGGGGAGAACACAAAAATGTCGGCCAGTGATCCAAATTCTGCAATATATGTGACAGATAGTGCTAAAGAAATAAAGACAAAG
upper sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os12g35570.2 (Oryza sativa), 3'ss of exon 6
------------------------------gtagtttcttaagtacactacacatt-cctgatttacacaactaattgccttggtcactt---tacgcagggagAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG-------------------
|| || || || | || | | || | | || || || | | || | ||||| ||||| ||||||||| || ||||||||||||||||| || |||||||| ||| || || || || || | |||
ctcatgtccattgctcagcatttatttttcttatttcctattttagatagcataatatttgggacattgatttatgtgagctgcttatttccatttacagGGGGAGAACACAAAAATGTCGGCCAGTGATCCAAATTCTGCAATATATGTGACAGATAGTGCTAAAGAAATAAAGACAAAGGTTTGCTTTAAGCATTGTA
upper sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G11390.1 (Glycine max), 3'ss of exon 6
---------------------------gtagtttct-taagtacactacacattcctgatttaca--caactaattgccttgg----tcactttacgcagggagAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
| ||||| | | || | || |||||| | | | || | | || | | || ||||||||| | |||||||||||||| |||||||| |||||||| || |||||||| ||||| ||||| || || || ||||||
ggaaactgcagttacatatagactttgaaattttctctgaataaggtccaaattcctttgtagctgttatctcacatctttaaaatataaattcttgcagGGAGAAACAGGAAAAATGTCTGCCAGTGATCCCAATTCTGCAATATATGTGACCGATTCTGCAAAAGATATAAAGAACAAG
upper sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 6
---------------------------gtagtttcttaagtacactacacattcctgatttaca---caactaattgccttg----gtcactttacgcagggagAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
| ||||| | | | | | || || || | | || | | || | | || |||||| || | |||||||||||||| |||||||| |||||||| || |||||||| ||||| ||||| || || || ||||||
ggaaactgaagttacatataggttttgaaattttctctgaaaaaggtctaaattcttatgtagatgttatctcacatctttataatataaattcttgcagGGGGAAACAGGAAAAATGTCTGCCAGTGATCCCAATTCTGCAATATATGTGACCGATTCTGCAAAAGATATAAAGAACAAG
upper sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 7
---------------gtagtttct-----taagtacactacacattcctgatttacacaactaattgccttggtcactt--------------tacgcagggagAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
|| |||||| | | || | ||| ||| || | || || | || | | |||||| |||| ||||||||||||||||||||||| |||||||| || || ||||||||||| | |||||||||||| ||||||
cttctttgatgcttggtggtttctacatatggctgcatcattaattttctttttgtgtaaatcatggctcttgtttttccttgaatttgtatatctgcagGGGGAGACAGGAAAAATGTCTGCTAGTGATCCCAATTCTGCAATATACGTGACTGATTCTGGAAAGGACATTAAGAACAAG
upper sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ24416 (Selaginella moellendorffii), 3'ss of exon 7
gtagtttcttaagtacactacacattcctgatttacacaactaattgccttggtcactttacgcagggagAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
| ||| | || | ||| | ||||| || || || || |||||||||| ||| |||||||||||||||||| | || ||||| || || |||| ||| || ||| || || || || |||
--------gtgagtgcttc---tttttaaaacttatagcactaag-gcgttccacattt----cagGGAGAGAGTGGCAAAATGTCTGCTAGTGATACGAACTCTGCAATTTACGTGAAGGATACCCAAAAAGAGATCAAGAAAAAG
upper sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ23832 (Selaginella moellendorffii), 3'ss of exon 7
gtagtttcttaagtacactacacattcctgatttacacaactaattgccttggtcactttacgcagggagAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
| ||| | || ||| | ||||| || || ||| || |||||||||| ||| |||||||||||||||||| | || ||||| || || |||| ||| || ||| || || || || |||
--------gtgagtgcttc---tttttaaagcttatagcactaag-gcgttcctcattt----cagGGAGAGAGTGGCAAAATGTCTGCTAGTGATACGAACTCTGCAATTTACGTGAAGGATACCCAAAAAGAGATCAAGAAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactacacattcctgatttacacaactaattgccttggtcactttacgcagggagAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
aactaat putative branch site (score: 2)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtttcttaagtacactacacattcctgatttacacaactaattgccttggtcactttacgcagggagAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG