Sequence
atgc intronic sequence ATGC exonic sequencegtaggtgcttgccttgtttgattagttagtcgcatattttggcatctagttgatatttttcattcatctactttagCTATATGGCTCCTGAATATGCATCAAGTGGAAAATTAACAGAGAAATCAGATGTATTCTCCTTTGGGGTTGTTCTGCTGGAGTTAATCACTGGACGTAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G68690.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g01040.1 (Oryza sativa), 3'ss of exon 5
----gt-aggtgcttgccttgttt---gattagttagtcgcatattttggcatctagttgatatttttcattcatctactttagCTATATGGCTCCTGAATATGCATCAAGTGGAAAATTAACAGAGAAATCAGATGTATTCTCCTTTGGGGTTGTTCTGCTGGAGTTAATCACTGGACGTAAA
|| | || || || | || | |||| || | || || ||| ||| || || | || || |||||||| || |||||||||||||| ||||| || |||| ||| ||||| ||||| ||||| |||||||| | ||| | |||||||| | |||
gttagtgaagtactggcaattttcagaagcagatctgtcgtgatcttacagagataattaataaaattcgtttttcc-ttgcagGTACATGGCTCCAGAGTATGCATCAAGTGGGAAATTGACTGAGAGATCTGATGTGTTCTCTTTTGGTGTTGTTCTCTTAGAGCTTATCACTGGTAGAAAA
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G14310.1 (Glycine max), 3'ss of exon 5
--------------------------------------gtaggtgcttgccttgtttgattagttagtcgcatattttggc-------atctagttgatatt--tttcattcatctactt-----------tagCTATATGGCTCCTGAATATGCATCAAGTGGAAAATTAACAGAGAAATCAGATGTATTCTCCTTTGGGGTTGTTCTGCTGGAGTTAATCACTGGACGTAAA
| | ||| ||| ||| ||||||| | | | || | ||| |||| | | | ||| |||||||| ||||||||||| |||||||| ||||| || ||||| || ||||||| || ||||| ||||| || |||| |||| |||||||| ||
gtgggtattcatcaatatgtctccaaacttctcttttcttttttactttttcatttttcatagactaaaatatattttagtgcaaaaaactttattaacattgatttcccccccccccccccccccccttatagGTATATGGCCCCTGAATATGCGTCAAGTGGCAAATTGACTGAGAAGTCCGATGTATATTCTTTTGGAGTTGTGCTTTTGGAACTAATTACTGGACGGAAG
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0011g02460.t01 (Vitis vinifera), 3'ss of exon 5
-------------------gtaggtgc-ttgccttgtttgattag--ttagtcgcatattttggcatctagttgatatttttcattcatct--actttagCTATATGGCTCCTGAATATGCATCAAGTGGAAAATTAACAGAGAAATCAGATGTATTCTCCTTTGGGGTTGTTCTGCTGGAGTTAATCACTGGACGTAAA
| || ||| | | ||| || || || | || | ||| | | || || | | | || || ||||||||||| || |||||||||||||| || ||||| |||||||| ||||| ||||| ||||| ||||| || |||||| | || |||||||| |||
cagagggcacttactatttagggatgaattgtccagaatgactaagatttgttttacatgccatatccatgttcaaagattccaattgattgaatttcagATATATGGCTCCCGAGTATGCATCAAGTGGCAAGTTAACTGAGAAATCTGATGTCTTCTCTTTTGGAGTTGTCCTTCTGGAGCTTATTACTGGACGGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagttagtcgcatattttggcatctagttgatatttttcattcatctactttagCTATATGGCTCCTGAATATGCATCAAGTGGAAAATTAACAGAGAAATCAGATGTATTCTCCTTTGGGGTTGTTCTGCTGGAGTTAATCACTGGACGTAAA
agttgat putative branch site (score: 5)
tttttcattcatct CT-rich tract
ttgatatttttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggtgcttgccttgtttgattagttagtcgcatattttggcatctagttgatatttttcattcatctactttagCTATATGGCTCCTGAATATGCATCAAGTGGAAAATTAACAGAGAAATCAGATGTATTCTCCTTTGGGGTTGTTCTGCTGGAGTTAATCACTGGACGTAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA