Sequence
atgc intronic sequence ATGC exonic sequence...tttgttttagatgttgtgctcatatgcttagagagggtgtttactggtttagattaatgtattaacttcatgtaacttctcgtttcaatgtttactgtagGAAAGAGGTGAGAATATACCACCAGAAGATTCATTCGATGTAGCCCGTAAAGTGAAGGAAATGTACTGCTACACTTGTTCTGACATCGTAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G13180.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g38340.1 (Oryza sativa), 3'ss of exon 4
---tttgttttagatgttgtgctcatatgcttagagagggtgtttactggtttagattaatgtattaacttcatgtaacttctcgtttcaatgtttactgtagGAAAGAGGTGAGAATATACCACCAGAAGATTCATTCGATGTAGCCCGTAAAGTGAAGGAAATGTACTGCTACACTTGTTCTGACATCGTAAAG
||| | | | || | | | || | | | | | | | | || | | | | | || | || | | || || |||||||||||||| | || ||||||||||| || || ||||| || | | |||||| |||||||||||||| || ||||| || || || |||
aagtttacctcata-attttcttgagattttcatattttatata-gcgaatctgcataatggcagtgcacttata-agtcactgagccaattagttcttgcagGAAAGAGGTGAGCACATTCCACCAGAAGAATCTTTTGATGTGGCAAGGAGAGTGAAAGAAATGTACTGCTATACATGTTCAGATATTGTGAAG
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G092459_T02 (Zea mays), 3'ss of exon 4
--tttgttttagatgttgtgctcatatgcttagagagggtgtttactggtttagattaatgtattaacttcatgtaacttctcgtttcaatgtttactgtagGAAAGAGGTGAGAATATACCACCAGAAGATTCATTCGATGTAGCCCGTAAAGTGAAGGAAATGTACTGCTACACTTGTTCTGACATCGTAAAG
||| |||| | ||| || | | | | | | || ||| ||| || | | | || || || | | || | |||||||||||||||| || ||||||||||| || || |||||||| | | | || ||||||||||| || |||| ||| ||| | || |||
gaattgatttata-gtttaactttgacatagatacaaagcatccacctctttttctta-catagtttgataaagtcaccgagtcttgtattcttgcatccagGAAAGAGGTGAGAACATTCCACCAGAAGAATCTTTTGATGTAGCAAGGAGGATCAAAGAAATGTACTGTTATACTTCTTCAGACGTTGTGAAG
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------------------tttgttttagatgttgtgctcatatgcttagagagggtgt----ttactggtttagattaatgta---ttaacttcatgtaacttctcgtttcaatgt---ttactgtagGAAAGAGGTGAGAATATACCACCAGAAGATTCATTCGATGTAGCCCGTAAAGTGAAGGAAATGTACTGCTACACTTGTTCTGACATCGTAAAG
|| ||| | || ||| || | | | | | || | || ||| || | | |||||| | ||| || | | | || || |||||||||| |||||| ||||||||||||| || || || || || || ||||||||||||||||| |||||||| || |||||||| || |||
gtaggaaatccttgtggtataaatttaaaagttattgtgctcttcttgttaatgttgaaggatctcacaaactaccatttacatagctagtgaaatcaattg-taataatccatatccaattgtcaatctacattttgctaaagtcagattcatgaactgtcttgtgttgacatcgcttggtgcagGAAAGAGGAGAGAATGTACCACCAGAAGACTCTTTTGAAGTGGCACGGAAAGTGAAGGAAATGTATTGCTACACCTGCTCTGACATTGTGAAG
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 3
tttgttttagatgttgtgctcatatgcttagagagggtgtttactggtttagattaatgta--ttaacttcatgtaacttctcgtttcaa---tgtttactgtagGAAAGAGGTGAGAATATACCACCAGAAGATTCATTCGATGTAGCCCGTAAAGTGAAGGAAATGTACTGCTACACTTGTTCTGACATCGTAAAG
|||| | || | | || | | | || | | | ||| | | | |||| ||| | | || | | || || || |||||||||| || ||| ||||||| ||||| || || || || || || ||||||||||||||||| |||||||| || |||||||| || |||
--tgttgaactgactgagattgtaataatccatatc-caattgccaatctgcatttttccaagccagattcac--aacctgttgtgttgacattgcttcatgcagGAAAGAGGAGAAAATGTACCACCGGAAGACTCTTTTGAAGTGGCTCGGAAAGTGAAGGAAATGTATTGCTACACCTGCTCTGACATTGTGAAG
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 3
---tttgttttagatgttgtgctcatatgcttagagagggtgtttactggtttagattaatgtattaacttcatgtaacttctcgtttcaat---gtttactgtagGAAAGAGGTGAGAATATACCACCAGAAGATTCATTCGATGTAGCCCGTAAAGTGAAGGAAATGTACTGCTACACTTGTTCTGACATCGTAAAG
|| | |||| || | || | | | | ||| || ||| || | |||||| | ||| || | | | || || |||||||||| |||||| |||||| ||| || || || || || || || ||||||||||||||||| |||||||| || |||||||| || |||
tgaactgactgagat--tgcattaatccatatccaattgtcagt--ctgcattttgctaaagt--cagattcatgaactgtcttgtgttgacatcgcttcatgcagGAAAGAGGAGAGAATGTACCACTAGAGGACTCTTTTGAAGTGGCACGGAAAGTGAAGGAAATGTATTGCTACACCTGCTCTGACATTGTGAAG
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0137g00280.t01 (Vitis vinifera), 3'ss of exon 3
tttgttttagatgttgtgctcatatgcttagagagggtgtttactggtttagattaatgtattaacttcatgtaacttctcgtttcaatgtttac----tgtagGAAAGAGGTGAGAATATACCACCAGAAGATTCATTCGATGTAGCCCGTAAAGTGAAGGAAATGTACTGCTACACTTGTTCTGACATCGTAAAG
| | || || | || ||| || | || | || |||| |||| ||| ||| ||| || ||| ||||||||||||| ||| || | || || ||||| || || || ||||| || ||||||||||||||||| ||||| || | |||||| ||||| |||
-attatctatatatagtatctatacatactaggataaaaatcacgatctgtga--aatg-attaccttaatggtttcctgaattttgatatttgtgttgtgtagGAAAGAGGAGAGCATGTGCCGCCTGAAGACTCTTTTGAAGTAGCTCGAAAAGTGAAGGAAATGTATTGCTATACATCTTCTGATATCGTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtttagattaatgtattaacttcatgtaacttctcgtttcaatgtttactgtagGAAAGAGGTGAGAATATACCACCAGAAGATTCATTCGATGTAGCCCGTAAAGTGAAGGAAATGTACTGCTACACTTGTTCTGACATCGTAAAG
attaatgtattaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgttttagatgttgtgctcatatgcttagagagggtgtttactggtttagattaatgtattaacttcatgtaacttctcgtttcaatgtttactgtagGAAAGAGGTGAGAATATACCACCAGAAGATTCATTCGATGTAGCCCGTAAAGTGAAGGAAATGTACTGCTACACTTGTTCTGACATCGTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- -gttttag
- - - - - - - - - - - - - - - - - - - - - - -ggtttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacttca