Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttccttcttcctacatacaaaagttatactgtgactgtaatgtaccctgacaagatcatttcgttgataaaccagGCTTCTGATTACCGGGAAAACAAAATACACACTGGTTGGTTGGACAGTAGGATTGCTATGCGGGTCAGAGCAGAGAGACCTCCATGGTATCTCTCTGTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G36180.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os10g21910.1 (Oryza sativa), 3'ss of exon 9
gtatgtttccttcttcctacatacaaaagttatactgtgactgtaatgtaccctgacaagatcatttcgttgataaaccagGCTTCTGATTACCGGGAAAACAAAATACACACTGGTTGGTTGGACAGTAGGATTGCTATGCGGGTCAGAGCAGAGAGACCTCCATGGTATCTCTCTGTAG
||| | | || | | | ||| | || | | || | || | || | ||||| | | |||||| | || || |||||||| || || |||||||||||| | ||||| || ||||||||||| || ||||| ||||| || |||||||| || || || |
gtaagataactccattgaa---gtaaatggtacagttattcttttattttcctaatatatgccattttcatattt--tcagGCTGCAGAATATCGGGAAAATAAGATCCACACTGGTTGGCTAGACAGCAGAATTGCTATGCGTGTTAGAGCTGAGAGGCCCCCATGGTACCTTTCAGTTG
upper sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 11
gtatgtttccttcttcctacatacaaaagttatactgtgactgt--aatgtaccctgacaagatcatttcgttgataaacc--agGCTTCTGATTACCGGGAAAACAAAATACACACTGGTTGGTTGGACAGTAGGATTGCTATGCGGGTCAGAGCAGAGAGACCTCCATGGTATCTCTCTGTAG
||| || | | | || || || || | |||| || | | | || | | | | | | ||||||| || ||| | ||||||||||| ||||| |||||| |||||||||| ||||| |||||||| ||||||||||| ||||| |||||||| ||||| |
gtaaattactcacatg--acgagaaattattttatagaagctgtttaaaatgctgaattgacattagtaaaatatttgatctcagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAGAGGCCTCCCTGGTATCTTTCTGTCG
upper sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 11
gtatgtttccttcttcctacatacaaaagttatactgtgactgtaatgtacc---ctgacaagatcatttcgttgataaaccagGCTTCTGATTACCGGGAAAACAAAATACACACTGGTTGGTTGGACAGTAGGATTGCTATGCGGGTCAGAGCAGAGAGACCTCCATGGTATCTCTCTGTAG
||| || | | | | | | ||||| | ||| | | ||||| | || || || |||||||| || ||| | ||||||||||| ||||| |||||| |||||||||| ||||| |||||||| |||||||| || ||| | |||||||| || || |
gtaaattactcacatggtgacaaattattttataaaagttgtttaacatgctgaattgacattaccacaatattt-tatctcagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAAAGGCCTGCCTGGTATCTTTCGGTCG
upper sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 12
-----------------------gtatgtttccttcttcctacatacaaaagttatactgtgactgtaatgtaccctgacaagatcatttcgttgataaaccagGCTTCTGATTACCGGGAAAACAAAATACACACTGGTTGGTTGGACAGTAGGATTGCTATGCGGGTCAGAGCAGAGAGACCTCCATGGTATCTCTCTGTAG
| || | || || | | | || | | | ||| | || | | | | | | | |||||||||||||| | || || ||||| ||||| ||||||||||||||||| ||||||||| |||| |||||||| || || || |||||||| ||||| |
gtaaagttctaatctattgacaatcaaattccatttatcatcctttttcaataatttttaaccttagaatacaaactaaagaaaagaaaaaccttttctgc-agGCTTCTGATTACAGAGAGAATAAAATCCACACCGGTTGGTTGGACAGTAGAATTGCTATGAGGGTTAGAGCAGAAAGGCCGCCTTGGTATCTTTCTGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagttatactgtgactgtaatgtaccctgacaagatcatttcgttgataaaccagGCTTCTGATTACCGGGAAAACAAAATACACACTGGTTGGTTGGACAGTAGGATTGCTATGCGGGTCAGAGCAGAGAGACCTCCATGGTATCTCTCTGTAG
ttgataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttccttcttcctacatacaaaagttatactgtgactgtaatgtaccctgacaagatcatttcgttgataaaccagGCTTCTGATTACCGGGAAAACAAAATACACACTGGTTGGTTGGACAGTAGGATTGCTATGCGGGTCAGAGCAGAGAGACCTCCATGGTATCTCTCTGTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG