Sequence
atgc intronic sequence ATGC exonic sequencegttagtggcctctttactaagcaggaacgccaatcttcttcctagtaggagtttctttgtcatgacagatttacttaacaatctatgaattttccctgaagGTGGTACGCTAAGCGATTTCTTCATCCTGACATAGTTGCCCCCTATGAATATATCTTCATATGGGATGAGGATCTTGGCGTGGAACACTTTGATTCGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G27470.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G27470.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G08270.1 (Glycine max), 3'ss of exon 6
---gttagtggcctctttactaagcaggaacgccaatcttct---tcctagtaggagtttctttgtcatgacagatttacttaacaatctatgaattttccctgaagGTGGTACGCTAAGCGATTTCTTCATCCTGACATAGTTGCCCCCTATGAATATATCTTCATATGGGATGAGGATCTTGGCGTGGAACACTTTGATTCGGAA
|||||| | || | | || || | | | | || || | | || | || || | | |||| || || || | ||||||||| ||||| || ||||| ||||||||||| || || || ||||| || ||||| || ||||||||||||||||| ||||| || |||||| | |||
gtttgtagtggatcttgtattgaattttttgtttcattttacaaattttgatcaggcttcctat-ttatcaagttttgacatga-aatccataaaattctgtttaagGTGGTATGCTAAACGCTTTCTGCATCCTGACATTGTGGCTCCTTATGACTACATCTTTATTTGGGATGAGGATCTTGGTGTGGAGCATTTTGATGCAGAA
upper sequence: AT3G27470.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv14s0066g00310.t01 (Vitis vinifera), 3'ss of exon 5
gttagtggcctcttta-ctaagcaggaacgccaatcttct-tcctagtaggagtttct---ttgtcat---gacagattta---------cttaacaa-tctatgaattttccctgaagGTGGTACGCTAAGCGATTTCTTCATCCTGACATAGTTGCCCCCTATGAATATATCTTCATATGGGATGAGGATCTTGGCGTGGAACACTTTGATTCGGAA
|| || || ||||| | | ||| |||| ||| | || | |||| | | || |||| | || ||| | || || | || |||| ||| | | ||||||||| || ||||| ||| | ||||||||||| || || |||||||| || || || || |||||||| || ||||| ||||| || |||||| | |||
gtgggtagctactttatcctcttaagaattccaaacttttatcattataggccatagtggattatcattgaggcatattgaagtcatgtttttcacgactccctgaaatttgcttcaagGTGGTATGCCAAGCGGTTTTTGCATCCTGACATTGTGGCACCCTATGACTACATATTTATGTGGGATGAAGACCTTGGGGTGGAGCATTTTGATGCAGAA
upper sequence: AT3G27470.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 7
gttagtggcctctttactaagcaggaacgccaatctt-cttcctagtaggagtttctttgtcatgacagatttacttaacaatctatgaattttccctgaagGTGGTACGCTAAGCGATTTCTTCATCCTGACATAGTTGCCCCCTATGAATATATCTTCATATGGGATGAGGATCTTGGCGTGGAACACTTTGATTCGGAA
| | | || | | ||| |||||| || | | || | || ||| | || | || ||||| | | | || |||||||| | ||||||||| | |||||||| | || || | ||||||||||||||||| |||||||||||||||| || || || || ||
-atgcctgtttgttacttgtggtggattctcaatctgactacatttctggctctgctctgttgtcgaagttgtagttaactgatt-ttaggggcaattgcagGTGGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATATATCTTCATTTGGGATGAGGATCTTGATTTGACTCATTTCAATGCGCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggagtttctttgtcatgacagatttacttaacaatctatgaattttccctgaagGTGGTACGCTAAGCGATTTCTTCATCCTGACATAGTTGCCCCCTATGAATATATCTTCATATGGGATGAGGATCTTGGCGTGGAACACTTTGATTCGGAA
acttaac putative branch site (score: 3)
ttttccct putative PPT
atttacttaacaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtggcctctttactaagcaggaacgccaatcttcttcctagtaggagtttctttgtcatgacagatttacttaacaatctatgaattttccctgaagGTGGTACGCTAAGCGATTTCTTCATCCTGACATAGTTGCCCCCTATGAATATATCTTCATATGGGATGAGGATCTTGGCGTGGAACACTTTGATTCGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT