Sequence
atgc intronic sequence ATGC exonic sequencegtaaggtgcactagagtccatctctacacagaatgcatctgatttctgcctttcacgtgtttctctccctttatttccggcgtagTAAGCTTATAAATGTAGCTGTTCCCGGGACAATTGATGAACGAGCGATCAACACTAAGAGGGTACTTAATCCGTGGGAGAGAAATGAGAATCACACGCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G26700.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G26700.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g37580.1 (Oryza sativa), 3'ss of exon 4
--------------------------gtaaggtgcactagagt--ccatctctacacagaatgcatct---gatttctgc-ctttcacgtgtttctctccct-ttattt-ccggcgtagTAAGCTTATAAATGTAGCTGTTCCCGGGACAATTGATGAACGAGCGATCAACACTAAGAGGGTACTTAATCCGTGGGAGAGAAATGAGAATCACACGCTT
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gttagtttgttcttgtcagtgtccatatatattattttagtacgacgatattttcgtcgttttgatccaaggataactgttctctaaggcagttatttccttatcatgcactgaatcagCAAGTTGATCAATGTCGCTGTTCCGGGTACAATCGATGAGAGAGCAATCAATACAAAGAAGGACCCTAACCCGTGGGAGAGGAATGAGAATCACACCCTT
upper sequence: AT4G26700.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv19s0090g01440.t01 (Vitis vinifera), 3'ss of exon 3
-------------gtaaggtgcactagagtccatctctacacag-aatgcatctgatttctgcctttcacgtgtttctctccctttatttccggcgtagTAAGCTTATAAATGTAGCTGTTCCCGGGACAATTGATGAACGAGCGATCAACACTAAGAGGGTACTTAATCCGTGGGAGAGAAATGAGAATCACACGCTT
|| | | | | | || | | | |||| || || | | || | | | | | | || | || | | ||||||||||| || || || || || |||||||| ||||||||||| || ||||| || ||||||| ||||| |||||||| ||||| || || || |||
gtacttaagcatggtctgcttgataatactctactttgttatgtcaatgaatatgctgtg-gcttataaagaacatatgtcttgtggctt--gatgcagTAAGCTTATCAACGTTGCAGTGCCAGGGACAATAGATGAACGAGCTATTAACACCAAACGGGTACTAAATCCATGGGAGAGGAATGAAAACCATACCCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatgcatctgatttctgcctttcacgtgtttctctccctttatttccggcgtagTAAGCTTATAAATGTAGCTGTTCCCGGGACAATTGATGAACGAGCGATCAACACTAAGAGGGTACTTAATCCGTGGGAGAGAAATGAGAATCACACGCTT
atctgat putative branch site (score: 4)
tttctgcctttcacgt CT-rich tract
tttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggtgcactagagtccatctctacacagaatgcatctgatttctgcctttcacgtgtttctctccctttatttccggcgtagTAAGCTTATAAATGTAGCTGTTCCCGGGACAATTGATGAACGAGCGATCAACACTAAGAGGGTACTTAATCCGTGGGAGAGAAATGAGAATCACACGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG