Sequence
atgc intronic sequence ATGC exonic sequencegtgtgaattcatagagtttctttatgaatgcaagaaggtgcattgtggttgaaaacaatgttcttactcttttttttttctttgtatctcttagGATTTTGAATTTAAGGAAATTGATGAAGTGTTGAAATACTACCCTCAAGGACACCATGGAGTCGACAAGGAAGGAAGACCGGTGTACATTGAGAGGCTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G18180.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G18180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G37640.1 (Glycine max), 3'ss of exon 2
-------------------------------------------gtgtgaattcatagagtttctttatgaatgcaagaaggtgcattgtggttgaaaacaatgttcttactcttttttttttctttgtatctctta-----gGATTTTGAATTTAAGGAAATTGATGAAGTGTTGAAATACTACCCTCAAGGACACCATGGAGTCGACAAGGAAGGAAGACCGGTGTACATTGAGAGGCTAG
| | | | || | | || | | | || | || | | | | | || |||||||| | ||||| | ||| |||||||||||| || |||||||||||||| ||| |||| || || |||||||| |||||||| ||||| || |||||||| |||||||| ||||| |||
gtacttgtaacgacaatattttgtggggcttgaggggatttgtttattatattattgtatcctattgcttttcttgttggcagtttttttttttagca-agtttattttctctttttaactcttttgtgccctttataccagGATTTTGAATTCAAAGAAATTGATGAAGTATTGCAATATTATCCCCAAGGACATCATGGAGTGGACAAAGATGGAAGACCTGTGTACATAGAGAGATTAG
upper sequence: AT2G18180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G05980.1 (Glycine max), 3'ss of exon 2
----------------------------gtgtgaattcatag-agtttctttatgaatgcaagaaggtgcattgtggttgaaaacaatgttct-tactcttttttttttctttgtatctcttagGATTTTGAATTTAAGGAAATTGATGAAGTGTTGAAATACTACCCTCAAGGACACCATGGAGTCGACAAGGAAGGAAGACCGGTGTACATTGAGAGGCTAG
||| ||||||| | | | | | | | | | ||| | ||| | |||| | ||| || | | || | | | |||||||||||||| |||||| | || ||||| || ||||||| ||||| ||||| |||||||| || || || ||| |||| || ||||||||||| | |
gtatttgtgtttttgaacaatgatatttgtgagaattcaggggaatgtgacccttattctcacttatttaattatagttttgttcctccttctatttacttaattggtgccttttttatactagGATTTTGAATTCAAGGAACTCGAAGAAGTCCTGCAATACTATCCTCATGGACATCATGGAGTTGATAAAGATGGACGACCAGTTTACATTGAGAGAATTG
upper sequence: AT2G18180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G24670.1 (Glycine max), 3'ss of exon 2
-----------------------------------------gtgtgaattcatag--agtttctttatgaatgcaagaaggtgcattg-tggttgaaaacaatgttcttactctttttttttt-ctttgtatctctta-----gGATTTTGAATTTAAGGAAATTGATGAAGTGTTGAAATACTACCCTCAAGGACACCATGGAGTCGACAAGGAAGGAAGACCGGTGTACATTGAGAGGCTAG
| | | ||| || ||||| | || | | | | | ||| | | | || || | || | ||| | ||||| || ||| |||||||||||| |||||| | |||||||| || |||| || ||||||||||| |||||||| || || || ||| |||| | ||||||||||| | |
gtatttttgttttatatataacaatgatatttgtgagaaatgaggggatttattactagttttatcatatacttgacccttttccccacttgtttatagtattgctcctccttctgtttactaattttgtgccttttatactagGATTTTGAATTCAAGGAACTCGATGAAGTCCTGCAATATTATCCTCAAGGACATCATGGAGTTGATAAAGATGGACGACCAATTTACATTGAGAGATTGG
upper sequence: AT2G18180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv03s0038g04480.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------gtgtgaattcatagagtttctttatgaat-gcaagaaggtgcattgtggttgaaaacaatgttcttactcttttttttttctttgtat-ctcttagGATTTTGAATTTAAGGAAATTGATGAAGTGTTGAAATACTACCCTCAAGGACACCATGGAGTCGACAAGGAAGGAAGACCGGTGTACATTGAGAGGCTAG
|| || | | || | || || ||| |||| | | ||| | | |||| || | || | | || |||||||||||||| |||||||||||||| || | |||||||||| |||||||| |||||||| || || || || | || || || |||||||| || |
gtatcatcttgggaaaaagtcaattatagttggtttagatcacttgtatagaaaccacaattgggtggagtccaaccatttacattttctgagttcttaaccttataattctctgttcctagGATTTTGAATTCAAGGAAATTGATGATGTCCTTGAATACTACCCACAAGGACATCATGGAGTTGATAAAGATGGGCGGCCTGTTTATATTGAGAGACTTG
upper sequence: AT2G18180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------gtgtgaattcatagagtttctttatga-atgcaagaaggtgcattgtggttgaaaacaat-gttcttactcttttttttttctttgtatctcttagGATTTTGAATTTAAGGAAATTGATGAAGTGTTGAAATACTACCCTCAAGGACACCATGGAGTCGACAAGGAAGGAAGACCGGTGTACATTGAGAGGCTAG
| | | | | ||| || | | || | | || | || | | | | |||| | | | | | | |||| || | || | ||| | ||| ||| |||||||| ||||||||||||||||| || ||||| ||||||||||| || || |||||| | |||
gttttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaatttgcggatactgaggctcctgttatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG
upper sequence: AT2G18180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ28804 (Selaginella moellendorffii), 3'ss of exon 2
gtgtgaattcatagagtttct-ttatgaatgcaagaaggtgcattgtggttgaaaacaatgttcttactcttttttttttctttgtatctcttagGATTTTGAATTTAAGGAAATTGATGAAGTGTTGAAATACTACCCTCAAGGACACCATGGAGTCGACAAGGAAGGAAGACCGGTGTACATTGAGAGGCTAG
|| | || || || | | | ||||| |||||| | || || ||||||| | |||||||| | || || || | || |||||| ||||||||| || ||||| ||||||||||| ||||| |||||||| || || || ||||||||| | |
---------------gtcggtgccatccatttaaaagcttacggc-tggttctctttaatgttttg------ttcttcttctttggactgtctagGATTTCCATTTCAAAGAGCTGGAGGAAGTGAGGAAATACTATCCACAAGGCCACCATGGAGTGGACAAAGAAGGAAGGCCTGTATATATTGAGAGGATCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcattgtggttgaaaacaatgttcttactcttttttttttctttgtatctcttagGATTTTGAATTTAAGGAAATTGATGAAGTGTTGAAATACTACCCTCAAGGACACCATGGAGTCGACAAGGAAGGAAGACCGGTGTACATTGAGAGGCTAG
ttcttac putative branch site (score: 2)
tgttcttactcttttt CT-rich tract
ttttttttttctttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgaattcatagagtttctttatgaatgcaagaaggtgcattgtggttgaaaacaatgttcttactcttttttttttctttgtatctcttagGATTTTGAATTTAAGGAAATTGATGAAGTGTTGAAATACTACCCTCAAGGACACCATGGAGTCGACAAGGAAGGAAGACCGGTGTACATTGAGAGGCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG