Sequence
atgc intronic sequence ATGC exonic sequencegcatggatctttatttacctcttgatcaaaacttatgtccgttttatctttatgttctaataagctttttccaatttttagGGTAACATCGCCAGGTGGCTGAAAAAAGAAGGTGATAAAGTTGCTCCTGGGGAAGTACTCTGTGAAGTTGAAACT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G54220.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G54220.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G03930.1 (Glycine max), 3'ss of exon 6
gcatggatctt--tatttacctcttgatcaaaacttatgtccgttttatctttatgttctaataagctttttccaa---tttttagGGTAACATCGCCAGGTGGCTGAAAAAAGAAGGTGATAAAGTTGCTCCTGGGGAAGTACTCTGTGAAGTTGAAACT
| || | ||||| |||| | | | ||| | || | || |||| ||| | || |||| | || |||||||||| || || ||| |||| ||||||||||||||| | ||||||| ||||| ||||||||||||||||||
-----gttcctactattttaatctta--tgagattgctgtatagtgggtcatgat-ttctcctaaattattcccaatgatattcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
upper sequence: AT1G54220.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 6
gcatggatctttatttacctcttgatcaaaacttatgtccgttttatctttatgttctaataagctttttcca---atttttagGGTAACATCGCCAGGTGGCTGAAAAAAGAAGGTGATAAAGTTGCTCCTGGGGAAGTACTCTGTGAAGTTGAAACT
| | || | | |||| | | | ||| | || | || |||| ||| | || || || |||||||||| || || ||| |||| ||||||||||||| | | ||||||| ||||| ||||||||||||||||||
--gttcctacttttctgaatctta--tgagattgctgtatagtgggtcatgat-ttctcctaaattattctcactgatacgcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAGAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
upper sequence: AT1G54220.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 7
gcatggatctttatttacctctt-gatcaaaacttatgtccgttttatc--tttatgttctaataagctttttccaatttttagGGTAACATCGCCAGGTGGCTGAAAAAAGAAGGTGATAAAGTTGCTCCTGGGGAAGTACTCTGTGAAGTTGAAACT
||||| |||| | | || | || | || ||| | |||| |||||| | ||| | ||| | | |||||||||| || |||||| |||| ||||| ||||||||| | ||||||| ||||| |||||||||||||| |||
gcatgtgcctttctgaagctatgagaatacaaaccatgctcaatttactgttttatgattgaatgttttgtttatcaaatgcagGGTAACATTGCGAGGTGGTTGAAGAAAGAGGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAGACT
upper sequence: AT1G54220.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 6
----------------gcatggatctttatttacctcttgatcaaaacttatgtccgttttatctttatgttctaataagctttttccaatttttagGGTAACATCGCCAGGTGGCTGAAAAAAGAAGGTGATAAAGTTGCTCCTGGGGAAGTACTCTGTGAAGTTGAAACT
|||| | | ||||| | || | || | |||| | | || ||| || || | || ||| | |||| || || || ||||||||||| ||||| || |||||| || ||||||| |||||| | ||||||||||||||
gcatgtacctttagaagcattcaaaatcatttagattctgggtacaaagt-tgtctttgccaactagatg--cttatgtattgttgcca---tgcagGGAAATATTGCGAGGTGGCTGAAGAAAGAGGGAGATAAAATTTCTCCTGGAGAAGTATTGTGTGAAGTTGAAACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaaacttatgtccgttttatctttatgttctaataagctttttccaatttttagGGTAACATCGCCAGGTGGCTGAAAAAAGAAGGTGATAAAGTTGCTCCTGGGGAAGTACTCTGTGAAGTTGAAACT
ttctaat putative branch site (score: 2)
ctttttccaattttt putative PPT
ttttatctttatgttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatggatctttatttacctcttgatcaaaacttatgtccgttttatctttatgttctaataagctttttccaatttttagGGTAACATCGCCAGGTGGCTGAAAAAAGAAGGTGATAAAGTTGCTCCTGGGGAAGTACTCTGTGAAGTTGAAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG