Sequence
atgc intronic sequence ATGC exonic sequencegtacaaattgcacacgttgtctggatgaaactactagcttatctttgttctaatgtgatatatatttgtattatacttataaacaaagttgagcaatctccgtgttactgttcagctatctgctttgaattttcttaattatttctcttttgttgatgaacactattactggccttgcagGCCAAAGGTTACCGGGTTGGACCTGTATATGACGATGTATTATCAATGGCGTGGTTTTTCCTCGAGTTGATTGTTAAATCAATGGCATTGGAGCAAGCAC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16340.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16340.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv11s0016g00100.t01 (Vitis vinifera), 3'ss of exon 17
gtacaaattgcacacgttgtctggatgaaactactagcttatctttgttctaatgtgatatatatttgtattatacttataaacaaagttgagcaatctccgtgttactgttcagctatctgctttgaattttcttaattatttctcttttgttgatgaacactattactggccttgcagGCCAAAGGTTACCGGGTTGGACCTGTATATGACGATGTATTATCAATGGCGTGGTTTTTCCTCGAGTTGATTGTTAAATCAATGGCATTGGAGCAAGCAC
| | | | ||| || | | || | | |||| | || | ||| || | | | | | || || || | | || ||| ||||||| ||||| ||||| || || || || ||||| ||||| || ||||||| ||||||||||||||| | ||||| || ||||||||||||||||| | |
----------------------------------------------------------------------tggttgctgtgtttaaa-ttaatta--cttca-gacactgcatgggcattt--tttatatgcatctgact-tgtttcattcaatgttttcatccatgact---tctgcagGCTAAAGGCTACCGTGTAGGGCCAGTGTATGATGATGTCTTGGCAATGGCTTGGTTTTTCCTCGAGCTAATTGTCAAGTCAATGGCATTGGAGCAGACTC
upper sequence: AT4G16340.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: PP1S318_8V6.1 (Physcomitrella patens), 3'ss of exon 18
------gtacaaattgcacacgttgtctggatgaaactactagcttatctttgttctaatgtgatatatatttgtattatacttataaacaaagttgagcaatctccgtgttactgttcagctatctgctttgaattttcttaattatttctcttttgttgatgaacactattactggccttgcagGCCAAAGGTTACCGGGTTGGACCTGTATATGACGATGTATTATCAATGGCGTGGTTTTTCCTCGAGTTGATTGTTAAATCAATGGCATTGGAGCAAGCAC
| || || || | || | | |||| | | | | | |||||| ||| | | || | | || | || || | | || | | | || ||| ||||| | |||| ||| || ||||||||||||||||| |||| || || || |||||||| ||| |||||||| | |||||||| || || | ||||| || || |||||| | |||||||| |
gtaatgctgtaagttctcaacctctgttgctttgataaactatttcgtttcagctgtaatgtcgcataaacgtagtttttggaactgaataggcttaagaagcgagtaggacac------gttctttgggatgagc---cttaaccgtctctc-------gattaa---------------tgcagGCCAAAGGTTACAGGGTAGGTCCCGTCTATGACGACGTACTATCAATGTCATGGTTTTTTCTTGAACTCATTGTGAAGTCTATGGCACTTGAGCAAGCTC
upper sequence: AT4G16340.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: PP1S302_69V6.1 (Physcomitrella patens), 3'ss of exon 18
gtacaaattgcacacgttgtctggatgaaactactagcttatctttgttctaatgtgatatatatttgtattatacttataaacaaagttgagcaatctccgtgttactgttcagctatctgctttgaattttcttaattatttctcttttgttgatgaacactattactggccttgcagGCCAAAGGTTACCGGGTTGGACCTGTATATGACGATGTATTATCAATGGCGTGGTTTTTCCTCGAGTTGATTGTTAAATCAATGGCATTGGAGCAAGCAC
| | | | | || | | || | |||| | || | ||| || ||||| || | || | || || ||| | |||||||| ||||| ||| |||| || ||||| || ||||| |||||||||||| | |||||||| || || | ||||| ||||| |||||| | ||||| || |
---------------------------------------------------------------------accgtg-tggttatcatattaataatatgactaagttagt-ttgaaaaatcagcacgacccattcttgcccatg-----tatgctaattggca--attgtcga--ttgcagGCAAAAGGCTACAGGGTAGGCCCTGTCTACGACGACGTATTATCAATGTCATGGTTTTTTCTTGAACTCATTGTGAAATCCATGGCACTTGAGCAGGCCC
upper sequence: AT4G16340.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: PP1S60_296V6.1 (Physcomitrella patens), 3'ss of exon 14
gtacaaattgcacacgttgtctggatgaaactactagcttatctttgttctaatgtgatatatatttgtattatacttataaacaaagttgagcaatc-tccgtgttactgttcagctatctgctttgaattttcttaattatttctcttttgttgatgaacactattactggccttgcagGCCAAAGGTTACCGGGTTGGACCTGTATATGACGATGTATTATCAATGGCGTGGTTTTTCCTCGAGTTGATTGTTAAATCAATGGCATTGGAGCAAGCAC
| | | | | | | | |||| | | || |||| || | | || || | | | | | | | || | |||| || || | | | ||| | | || || | | || || |||| ||||| ||||| || | || |||||||||||||||||||| | |||||||| ||||| ||||| |||||||| || || ||||||||| | || || | |
------------------------gtatggtttcaaaccca--ataaatgtaattt--tttaggattgt-ttgaggacgtgcccttaggtggccttttattcatttacttatttattcatctatttatgatgataatgacgattattatatt-ttaaacagtgttaata-tggc---acagGCTAAAGGGTATAGAGTCGGACCTGTATATGACGATGTCCTCTCAATGGCTTGGTTCTTCCTGGAGTTGATCGTAAAGTCAATGGCACTTGAACAGTCTC
upper sequence: AT4G16340.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: PP1S25_205V6.1 (Physcomitrella patens), 3'ss of exon 17
gtacaaattgcacacgttgtctggatgaaactactagcttatctttgttctaatgtgatatatatttgtattatacttataaacaaagttgagcaatctccgtgttactgttcagctatctgctttgaattttcttaattatttctcttttgttgatgaacactattactggccttgcagGCCAAAGGTTACCGGGTTGGACCTGTATATGACGATGTATTATCAATGGCGTGGTTTTTCCTCGAGTTGATTGTTAAATCAATGGCATTGGAGCAAGCAC
|||| | | | | | | | || || | | || | || | || || || ||||| | | |||| |||| | |||||||||||| ||| | ||||||||||| || |||||||| || || ||||| ||||| ||||| ||||||||||| || |||||| || | ||||| | |
-------------------------------------------------------------------gtatgacattcaggcataggg------gatttctttcaaatagtgaggata---agatcaaaggtt-ttggttattcgcggtct------taaca-tattgtcg-tgacgcagGCCAAAGGCTACAGAGTTGGACCTGTGTACGACGATGTGTTGTCCATGGCTTGGTTCTTCCTTGAGTTGATTGTGAAGTCAATGACACTCGAGCAGTCTC
upper sequence: AT4G16340.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: PP1S145_21V6.1 (Physcomitrella patens), 3'ss of exon 16
gtacaaattgcacacgttgtctggatgaaactactagcttatctttgttctaatgtgatatatatttgtattatacttataaacaaagttgagcaatctccgtgttactgttcagctatctgctttgaattttcttaattatttctcttttgttgatgaacactattactggccttgcagGCCAAAGGTTACCGGGTTGGACCTGTATATGACGATGTATTATCAATGGCGTGGTTTTTCCTCGAGTTGATTGTTAAATCAATGGCATTGGAGCAAGCAC
|| ||| | ||| | | | | | || | || | | ||| || |||| | || | || || | ||| | | | ||||||| ||||| ||| | ||||||||||| ||||| || || | |||||||| ||||| ||||| ||||||||||| || || |||||| | |||||| | |
--------------------------------------------------------------------------------gtacgaag---atcaagcattgggatctttttaa---atttacgaggaaattatttaaatccttgttttgtggagcccttacaaatttattgtcatgcagGCAAAAGGCTACAGAGTTGGACCTGTGTATGATGACGTGCTGTCAATGGCTTGGTTCTTCCTTGAGTTGATTGTGAAGTCCATGGCACTTGAGCAATCTC
upper sequence: AT4G16340.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: EFJ04870 (Selaginella moellendorffii), 3'ss of exon 17
gtacaaattgcacacgttgtctggatgaaactactagcttatctttgttctaatgtgatatatatttgtattatacttataaacaaagttgagcaatctccgtgttactgttcagctatctgctttgaattttcttaattatttctcttttgttgatgaacactattactggccttgcagGCCAAAGGTTACCGGGTTGGACCTGTATATGACGATGTATTATCAATGGCGTGGTTTTTCCTCGAGTTGATTGTTAAATCAATGGCATTGGAGCAAGCAC
| | | | || || | | | |||| || | | || ||||||||| ||||| ||||| ||||||||||||||||| || || | |||||||| ||| | ||| |||| |||| |||| ||| ||||| || ||||||||
---------------------------------------------------------------------------------------------------------------------------gtagcagtatcggaact-tcgttagcttgtcatgaaatagtttt------cttgcagGCAAAAGGCTACCGAGTTGGACCTGTATATGATGACGTGCTGTCAATGGCTTGGGTGTTCTTCGAACTGATCGTTAGATCTATGGCTTTAGAGCAAGCTA
upper sequence: AT4G16340.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: EFJ09916 (Selaginella moellendorffii), 3'ss of exon 16
gtacaaattgcacacgttgtctggatgaaactactagcttatctttgttctaatgtgatatatatttgtattatacttataaacaaagttgagcaatctccgtgttactgttcagctatctgctttgaattttcttaattatttctcttttgttgatgaacactattactggccttgcagGCCAAAGGTTACCGGGTTGGACCTGTATATGACGATGTATTATCAATGGCGTGGTTTTTCCTCGAGTTGATTGTTAAATCAATGGCATTGGAGCAAGCAC
| | | | || || | | | |||| || | | || ||||||||| ||||| ||||| ||||||||||||||||| || || | |||||||| ||| | ||| |||| |||| |||| ||| ||||| || || |||||
---------------------------------------------------------------------------------------------------------------------------gtagcagtatcggaact-tcgttagcttgtcatgaaatagtttt------cttgcagGCAAAAGGCTACCGAGTTGGACCTGTATATGATGACGTGCTGTCAATGGCTTGGGTGTTCTTCGAACTGATCGTTAGATCTATGGCTTTAGAACAAGCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaattttcttaattatttctcttttgttgatgaacactattactggccttgcagGCCAAAGGTTACCGGGTTGGACCTGTATATGACGATGTATTATCAATGGCGTGGTTTTTCCTCGAGTTGATTGTTAAATCAATGGCATTGGAGCAAGCAC
tttcttaattatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaaattgcacacgttgtctggatgaaactactagcttatctttgttctaatgtgatatatatttgtattatacttataaacaaagttgagcaatctccgtgttactgttcagctatctgctttgaattttcttaattatttctcttttgttgatgaacactattactggccttgcagGCCAAAGGTTACCGGGTTGGACCTGTATATGACGATGTATTATCAATGGCGTGGTTTTTCCTCGAGTTGATTGTTAAATCAATGGCATTGGAGCAAGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG