Sequence
atgc intronic sequence ATGC exonic sequencegtgagtaattttattttctctgcagacatcttcttcagcttcaagtacctttcttctgatgcaaatgttataaaaactgcagTCATTTCAACAAGAATCAGCTCTCTGGGACCATTCCACCAAAACTTTTCAGCTCTGAGATGATACTGATCCATGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79620.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79620.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G18090.1 (Glycine max), 3'ss of exon 6
-------------------------------------------------------------------------------------------gtgagtaattttattttctctgcagacatcttctt-cagcttcaagtacc-tttcttctgatgcaaatgttataaaaactgcagTCATTTCAACAAGAATCAGCTCTCTGGGACCATTCCACCAAAACTTTTCAGCTCTGAGATGATACTGATCCATGT
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gtgagttttttctttcttgtttttttttttttttcatttaacacttgtgattaccatttagttaatgcaggaaagagaaatgtgttaaaaacagcaccactttcatctttttgttgagttctagttgctacattgagtgctatatcaaccgtgttttgatttctatttaatgcagCCATTTCAACAAGAACCAGCTTTCAGGTTCCATTCCCCCCAAGCTTTTCAGCTCTGAGATGATACTCATACACAT
upper sequence: AT1G79620.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G34790.1 (Glycine max), 3'ss of exon 6
----------------------------------------------------------------------------------------gtgagtaattttattttctctgcagacatcttctt-cagcttcaagtacctttcttctgatg--caaatgttataaaaactgcagTCATTTCAACAAGAATCAGCTCTCTGGGACCATTCCACCAAAACTTTTCAGCTCTGAGATGATACTGATCCATGT
| | | ||| | | | || || ||| || | | ||| | | || | || || || | ||||| |||||||| ||||| || ||||| || ||||||| || || || |||||||||||||||||||| || || |
gtgagttttttctttcttgttttttttttttcatttaacacttgtgattaccttttagtttgtgcagcaaagagcagtgtgttaaaaatagcgccactttcatctttttgtcgagttctagttgctacactgagtgctatatcaacagtgttctgat-ttctatttaatgcagCCATTTCAATAAGAACCACCTCTCAGGTTCCATTCCTCCCAAGCTCTTCAGCTCTGAGATGATACTCATACACAT
upper sequence: AT1G79620.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0056g00100.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------gtgagtaattttattttctctgcagacatctt-cttcagcttcaagtacctttcttctgatgcaaatgttataaaaactgcagTCATTTCAACAAGAATCAGCTCTCTGGGACCATTCCACCAAAACTTTTCAGCTCTGAGATGATACTGATCCATGT
|| | || || || | ||| | || | || | | | | || || | | |||| || |||| |||||||| ||||||||||| || || ||||||| | ||||||||||||||||| ||| ||| || |||||
gtgagtatcattaggcttccctacctaatgtgttttggaatcatctttcttaatgtgctatggtattgcaccatttattaatgtgtaaatttgtatctgatttttatgaac-tggcagCCATTTCAATAAGAATCAGCTTTCAGGCCCCATTCCGCGGAAACTTTTCAGCTCTGACATGGAACTAATACATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcttcttcagcttcaagtacctttcttctgatgcaaatgttataaaaactgcagTCATTTCAACAAGAATCAGCTCTCTGGGACCATTCCACCAAAACTTTTCAGCTCTGAGATGATACTGATCCATGT
ttctgat putative branch site (score: 3)
aaatgttataaaaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtaattttattttctctgcagacatcttcttcagcttcaagtacctttcttctgatgcaaatgttataaaaactgcagTCATTTCAACAAGAATCAGCTCTCTGGGACCATTCCACCAAAACTTTTCAGCTCTGAGATGATACTGATCCATGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG