Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttttacgcttcttccagtttgcatatgatttgtgttatagcgactatcagaccaacttcttcctgcttatgtagGTTTATGCACGAGAGGCTGAACACTCATGCTGAATCTATTGCATTCTTTGGAGGTGGAGCTCGAGAAAAGGCTGTAAGTTTCTTAATTGCCCTAGCTATA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39850.3 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39850.3 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA18G02110.1 (Glycine max), 3'ss of exon 18
---------gtaagttttttacgcttcttcca-gtttgcatatgatttgtgttatagcgactat-cagaccaactt--cttcctgcttatg-tagGTTTATGCACGAGAGGCTGAACACTCATGCTGAATCTATTGCATTCTTTGGAGGTGGAGCTCGAGAAAAGGCTGTAAGTTTCTTAATTGCCCTAGCTATA
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gtaaatccattatagtttccgctgtcctatcatggctctaaacaaatagtgctgttgtaatggttctgaccttttcaactttatgcttcttctagGTTCATGCATGAAAGACTCTGTACTCATGCTGAATCTGTTGCTTTCTTTGGAGGTGGAGCTCGAGAAAAAGCT---------------------------
upper sequence: AT4G39850.3 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA11G38160.1 (Glycine max), 3'ss of exon 18
gtaagtttttta-------cgcttcttcca-gtttgcatatgatttgtgttatagcgactat-cagaccaactt--cttcctgcttatg-tagGTTTATGCACGAGAGGCTGAACACTCATGCTGAATCTATTGCATTCTTTGGAGGTGGAGCTCGAGAAAAGGCTGTAAGTTTCTTAATTGCCCTAGCTATA
|||| | ||| |||| | |||| || | | | | ||| | | | | | | |||| | ||| ||||| || |||||| ||||| || || || |||||||||||||| |||| |||||||||||||||||||||||||| |||
gtaaatccattatagtttccgctgcctccatgtcactaaacaaatagtgctgttgtaatggttctgaccttttcaactttatgcttctgctagGTTCATGCATGAAAGACTCTGTACTCATGCTGAATCAGTTGCTTTCTTTGGAGGTGGAGCTCGAGAAAAAGCT---------------------------
upper sequence: AT4G39850.3 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA05G31270.1 (Glycine max), 3'ss of exon 16
gtaagttttttacgcttct---------tccagtttgcatatgatttgtgttatagcgactat-cagaccaacttcttcct--gcttatgtagGTTTATGCACGAGAGGCTGAACACTCATGCTGAATCTATTGCATTCTTTGGAGGTGGAGCTCGAGAAAAGGCTGTAAGTTTCTTAATTGCCCTAGCTATA
|||| || || || ||||| | | | | || | | | | ||| | || | |||| | |||| | |||||| ||||| || || || ||||||||||||||| |||| |||||||||||||| ||||||||||| |||
gtaaacttattctactgtcagctaacaatccaggtactaatcaaatagttctgttgaaattattctgatctgtttctctttatgcttttctagGTTCATGCATGAAAGACTTTGTACTCATGCTGAATCTGTTGCTTTCTTTGGAGGTGGTGCTCGAGAAAAAGCT---------------------------
upper sequence: AT4G39850.3 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA08G14480.1 (Glycine max), 3'ss of exon 14
--------gtaagttttttacgcttcttccagtttgcatatgatttgtgttatagcgactat-cagaccaacttcttcct--gcttatgtagGTTTATGCACGAGAGGCTGAACACTCATGCTGAATCTATTGCATTCTTTGGAGGTGGAGCTCGAGAAAAGGCTGTAAGTTTCTTAATTGCCCTAGCTATA
| | | | | | ||||| | | | ||||| | | | | ||| | || | |||| | |||| | |||||| ||||| || || || ||||||||||||||| |||| |||||||| ||||| ||||||||||| |||
gtaaactattctactgtctgctaataatccaggtactagtcaaattgtgctgttgaaattattctgatctgtttctctttatgcttttctagGTTCATGCATGAAAGACTTTGTACTCATGCTGAATCTGTTGCTTTCTTTGGGGGTGGTGCTCGAGAAAAAGCT--------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatatgatttgtgttatagcgactatcagaccaacttcttcctgcttatgtagGTTTATGCACGAGAGGCTGAACACTCATGCTGAATCTATTGCATTCTTTGGAGGTGGAGCTCGAGAAAAGGCTGTAAGTTTCTTAATTGCCCTAGCTATA
cttcttcctgcttat CT-rich tract
atgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttttttacgcttcttccagtttgcatatgatttgtgttatagcgactatcagaccaacttcttcctgcttatgtagGTTTATGCACGAGAGGCTGAACACTCATGCTGAATCTATTGCATTCTTTGGAGGTGGAGCTCGAGAAAAGGCTGTAAGTTTCTTAATTGCCCTAGCTATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT