Sequence
atgc intronic sequence ATGC exonic sequencegtacagattaggcattgatattgattgcattgttgttgtttcgattatagacccatatattttgtttttccattgttgtagATAATGACTTGCAGACCAAGATCAGATCTTTATGTTAACCTCCCAGCTCTCAGGAAACTAGATAACATGCTTCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G02010.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G02010.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G16610.2 (Glycine max), 3'ss of exon 2
-----------------gtacagattaggcattgatattgattgcattgttgttgtttcgattatagacccatatattttgtttttccat---tgttgtagATAATGACTTGCAGACCAAGATCAGATCTTTATGTTAACCTCCCAGCTCTCAGGAAACTAGATAACATGCTTCTT
| ||||| | || ||| | | | | | | | | || ||| | | | ||| || || || | ||||| ||||| || |||||||||||||| ||||| |||||| | |||||| ||||||||||||||||
catgctttcttctttttagattgattaaac-ttcataccaaataaagtacatatagatagttcttaatgtttaataatgtttcttttcacatgtgaatcagGTCATGACCACTAGACCTAGGTCAGATCTTTATGTCAACCTGCCAGCTTTGAGGAAATTAGATAACATGCTTCTG
upper sequence: AT5G02010.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G26010.1 (Glycine max), 3'ss of exon 2
-----------------gtacagattaggcattgatattgattgcattgttgttgtttcgattatagacccatatattttgtttttccat---tgttgtagATAATGACTTGCAGACCAAGATCAGATCTTTATGTTAACCTCCCAGCTCTCAGGAAACTAGATAACATGCTTCTT
| ||||| | || || | | | | | | | | | | || | | | ||| || || || | ||||| || || | |||||||||||||| ||||| |||||| | |||||| ||||||||||||||||
catgctttcttcattttagattgattaaactttc-taccaaataaagtatatatagatagttcttgatatttagtactgtttcttttcacatgtgaatcagGTCATGACCACTAGGCCTCGGTCAGATCTTTATGTCAACCTGCCAGCTTTGAGGAAATTAGATAACATGCTTCTG
upper sequence: AT5G02010.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G41330.1 (Glycine max), 3'ss of exon 3
------------------gtacagattaggcattgatattg-attgcattgttgttgtttcgattatagacccatatattttgtttttccattgttg--tagATAATGACTTGCAGACCAAGATCAGATCTTTATGTTAACCTCCCAGCTCTCAGGAAACTAGATAACATGCTTCTT
| || |||| ||||| | | | | | | | | || | || || | |||||||| | ||| || | ||||||||| | ||| | |||||||||||||| || || |||||||| | ||| |||||||||||||||||
catgctttttgcttcattttttaggttag-cattgcttcaggaaagggggatggacaaatagtttgttgatggtta-acattgtttttgaaatgtgaatcagGTCATGACTTGCCGTCCACGTTCAGATCTTTATGTCAATCTTCCAGCTCTGCGAAAATTAGATAACATGCTTCTT
upper sequence: AT5G02010.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G16790.1 (Glycine max), 3'ss of exon 3
--gtacagattaggcattgatattgattgcattg--------ttgttgtttcgattatagacccat--atattttgtttttccattgttgt-------agATAATGACTTGCAGACCAAGATCAGATCTTTATGTTAACCTCCCAGCTCTCAGGAAACTAGATAACATGCTTCTT
|| || || || | ||| | |||||| | | | | ||| | | | || || ||| ||| | || | ||||| || ||||| | |||||||||||||| || || |||||||| | ||| |||||||||||||||||
cagtgcattttgtttcttctttttgttagcattgcctcagggtagggggatggatgaataatttgttgatggttaacaattcttttgaaatgtgaatcagGTCATGACCTGTCGACCACGCTCAGATCTTTATGTCAATCTTCCAGCTCTGCGCAAATTAGATAACATGCTTCTT
upper sequence: AT5G02010.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0007g01380.t01 (Vitis vinifera), 3'ss of exon 3
----------------gtacagattaggcattgatattgattgcattgttgttgtttcgattatagacccatatattttgtttttccattgttgt-----agATAATGACTTGCAGACCAAGATCAGATCTTTATGTTAACCTCCCAGCTCTCAGGAAACTAGATAACATGCTTCTT
| || | ||| || ||| | ||||| || || | | | || |||| ||| | | || | |||||||||||||| ||||||||||||| |||| ||||||||||| | ||| ||||||||||||| |||
aaatgaaatgctggaaaatctaatgaaacatcaat--tgactatgatgttgaatggatgactaattttttgtgtttgttacacttcctttgatatgattcagGTCATGACTTGCAGACCCCGATCAGATCTTTACATTAATCTCCCAGCTCTGCGTAAATTAGATAACATGCTACTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcattgttgttgtttcgattatagacccatatattttgtttttccattgttgtagATAATGACTTGCAGACCAAGATCAGATCTTTATGTTAACCTCCCAGCTCTCAGGAAACTAGATAACATGCTTCTT
ttttgtttttccatt CT-rich tract
atatattttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacagattaggcattgatattgattgcattgttgttgtttcgattatagacccatatattttgtttttccattgttgtagATAATGACTTGCAGACCAAGATCAGATCTTTATGTTAACCTCCCAGCTCTCAGGAAACTAGATAACATGCTTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC