Sequence
atgc intronic sequence ATGC exonic sequencegtactttcctctttccaacatgtgatatgcttgtggtttctcaaaattccgctataactcttgtcatattctcctagGGGGCAAATATTTTGGTCGATAACAAAGGTTGCATCAGACTCGCAGATTTTGGTGCTTCCAAGAAAGTTGTAGAGCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06030.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06030.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G39670.1 (Glycine max), 3'ss of exon 5
-----------gtactttcctctttccaacatgtgatatgcttgtggtttctcaaaattccgctataactcttgtcatattct-cctagGGGGCAAATATTTTGGTCGATAACAAAGGTTGCATCAGACTCGCAGATTTTGGTGCTTCCAAGAAAGTTGTAGAGCTA
|| ||| ||| || || | | |||| ||| || | | | | ||| | | ||||| || || ||| | || ||||||||||| ||||| | |||||| || |||||||| |||||||||||||| || ||
gtattgtgcttttatttttacttttttaagattttctgc-cttggtatttgtctctttatcatgttgatcaatgtgttgctggatatagGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCGCTGACTTTGGTGCATCCAAGAAAGTTGTTGAACTG
upper sequence: AT3G06030.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G28090.1 (Glycine max), 3'ss of exon 5
-----gtactttcctctttccaacatgtgatatgcttgtggtttctcaaaattccgctataactcttgtcatattct-cctagGGGGCAAATATTTTGGTCGATAACAAAGGTTGCATCAGACTCGCAGATTTTGGTGCTTCCAAGAAAGTTGTAGAGCTA
|| | || ||| || || | | |||| ||| || || | | | || | | ||||| || || ||| | || ||||||||||| ||||| | |||| |||| ||||| || |||||||||||||| || ||
gtattgtgcatttacttttataagattttctgc-cttggtgttcgtctctatatcatgttgatcaatgctttgctggatatagGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCACAGACTTTGGGGCATCCAAGAAAGTTGTTGAACTG
upper sequence: AT3G06030.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0020g02910.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------gtactttcctctttccaacatgtg-atatgcttgtggtttctcaaaattccgctataactctt----gtcatat-tctcctagGGGGCAAATATTTTGGTCGATAACAAAGGTTGCATCAGACTCGCAGATTTTGGTGCTTCCAAGAAAGTTGTAGAGCTA
| | | | | | | ||||| |||||| || ||||| | | ||||| ||| | | | | || ||||||||||||| |||| ||||| || || ||||| | ||| ||||| |||||||| || ||||||||||| |||||
gtatctccttttttcttgcaaatggtattattatggaactccattacttgtatatgtgcgcatgcttatgttttct--acttgtgtctatatctcataatggccgtgcatcattcagGGGGCAAATATCCTGGTTGATAATAAGGGATGCATTAAACTTGCAGACTTTGGTGCATCTAAGAAAGTTGTTGAGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatatgcttgtggtttctcaaaattccgctataactcttgtcatattctcctagGGGGCAAATATTTTGGTCGATAACAAAGGTTGCATCAGACTCGCAGATTTTGGTGCTTCCAAGAAAGTTGTAGAGCTA
ctataac putative branch site (score: 3)
tattctcct putative PPT
tcaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactttcctctttccaacatgtgatatgcttgtggtttctcaaaattccgctataactcttgtcatattctcctagGGGGCAAATATTTTGGTCGATAACAAAGGTTGCATCAGACTCGCAGATTTTGGTGCTTCCAAGAAAGTTGTAGAGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT