Sequence
atgc intronic sequence ATGC exonic sequence...tttctagcttcttgtctcctttctcatctgttctttaatcagctaacacccggaaaaataattgaggtttcaatctgaataaagtctccttggatttcagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13870.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 20
------------------tttctagcttcttgtctcctttctcatctgttctttaatcag-ctaacacccggaaaaataattgaggtttcaatctgaataaagtctccttggattt--------cagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG-----
| | || || | || | | | | || | | | | | || | | || ||| || | | | | | || ||| ||||| || || |||| ||||||||||||||||||||||||||| | || ||| | | |||||||| || || || ||||| | ||||
gtatcctgttaattgaaatctttaattt-tcgtttggtacttgaaacattgtggagtgggattgacctattgggtataaaatgatgtatgattgtatgcctaactgttttactttttccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAGTATT
upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 20
------------------tttctagcttcttgtctcctttctcatctgttctttaatcag-ctaacacccggaaaaataattgaggtttcaatctgaataaagtctccttggattt--------cagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG
| | || || | || | | | | || | | | | | || | | || ||| || | | | | | || ||| ||||| || || |||| ||||||||||||||||||||||||||| | || ||| | | |||||||| || || || ||||| | ||||
gtatcctgttaattgaaatctttaattt-tcgtttggtacttgaaacattgtggagtgggattgacctattgggtataaaatgatgtatgattgtatgcctaactgttttactttttccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA
upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA08G20610.1 (Glycine max), 3'ss of exon 20
tttctagcttcttgtctcctttctcatctgttctttaatcagctaacacccggaaaaataattgaggtttcaatctgaataaagtctccttggatttcagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG
|| | || | || ||| || ||| | | |||| | || | || | |||| | ||| || |||||||| || ||| || || ||||||||| | || || ||||||||||| |||| ||||| |||| |||||||||||||||||||| || ||||
------gcatgatgcataagttatcaag-acatttgaatttcttgtt-----ggaaaacattttactaactgatgt-aatatattctttttat-tttcagGAGGCCAACAAGCGCAACAACAACTGGTTACCTCCCCCATGGGCAATAGTTGCTTTGGTTATTCTGGGATTTAATGAATTTATGACACTTCTAAG
upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA15G02780.1 (Glycine max), 3'ss of exon 20
--tttctagcttcttgtctcctttctcatctgttctttaatcagctaacacccggaaaaataattgaggtttcaatctgaataaagtctccttggatttcagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG
| | | | | | | | | ||| || | | | ||| | || | | ||| | || ||| | | || |||||||||||| ||| || | | ||||||| | || ||||||||||| || | || || || ||||||||||||||||||||||||| || |||||
acatcatggatgcatat-tatgtaggcatttgatttctg-tcactgatcaaacattttactaacttttacttattgatgatgtagtttatttttaatttcagGAAGCCAACAATCGTAGCAGCAACTGGTTACCTCCTCCATGGGCGATTGTGGCTTTGATTATTCTTGGATTTAATGAATTTATGACACTTTTAAG
upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA13G42650.1 (Glycine max), 3'ss of exon 21
tttctagcttcttgtctcctttctcatctgttctttaatcagctaacaccc--ggaaaaataattgaggtttcaatctgaata------aagtctccttggatttcagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG
| || | ||| | | || || || | | | || |||| | | ||| | | || || | || |||||||||||| ||| || | | ||||| | || || |||||||| || | || || || ||||||||||||||||||||||||| || |||||
-------aaatctatcccatttggtaatt-ttgaaaaaaaagtcatcccttttggtaaaaaagccaacttttacttattgatggtgtgtaatttctttttaatttcagGAAGCCAACAATCGTAGCAGGCACTGGTTACCTCCACCATGGGCGATTGTGGCTTTGCTTATTCTTGGATTTAATGAATTTATGACACTTTTAAG
upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 20
tttctagcttcttgtctcctttctcatctgttctttaatcagctaacacccggaaaaataattgaggtttcaatctgaataaagtctccttggatt-tcagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG
|| ||||| | | ||| | | | | ||| | | | || | | | | | | ||| || ||| ||||||||| ||| || |||||||||||| | ||||||||||||||||| |||| |||| || || ||||| |||||||||||||| || ||||
-caatattttctttgagaaacagtatcaaaatatttcactaaccatgccccattaccgtcaatggtatctaattgttttcacttcctctttcaattatcagGAAGCCAACAAGCGTAATAACAACTGGTTACCACCTCCATGGGCAATTGTTGCTATGGTCGTCCTGGGATTCAATGAATTTATGACACTTCTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acacccggaaaaataattgaggtttcaatctgaataaagtctccttggatttcagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG
agctaac putative branch site (score: 2)
tctcctt putative PPT
aaaaataattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttctagcttcttgtctcctttctcatctgttctttaatcagctaacacccggaaaaataattgaggtttcaatctgaataaagtctccttggatttcagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG
- - - - - - - - -cctttct
- - - - - - - - - - - - - -ctgttct
- - - - - - - - - - - - - - - - - - - - - ctaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaataaa