Sequence
atgc intronic sequence ATGC exonic sequencegtagatatgccgatgagcactgattgtattgcttacagtatttggttcagtgttgtccttctaacttattcttgaacgcaaatatatatagctctgcatggtcgtctcagatgtttaaatgctttccaagtttttgtcaacttatttttacctcattctcttttttcaagGATGTAGAAGGTATGATGTCAATTTCTGTTGAAGCTGCTGCGGCTAGGGATTCTTTGAGTGATGATAAAGAAATCGTTAACACTTATGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71820.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g51430.1 (Oryza sativa), 3'ss of exon 4
gtagatatgccgatgagcactgattgtattgcttacagtatttggttcagtgttgtccttctaacttattcttgaacgcaaatatatatagctctgcat-ggtcgtctcagatgtttaaatgctttccaagtttttgtcaacttatttttacctcattctcttttttcaagGATGTAGAAGGTATGATGTCAATTTCTGTTGAAGCTGCTGCGGCTAGGGATTCTTTGAGTGATGATAAAGAAATCGTTAACACTTATGAG
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--------------gtgtgctgaccttact-ttagcaataacaactgtattaaggttgtacttgcttgtttttta---ctaacgttcttatcaatacattaagctaaccaagttatcgagcacga---aaatttcatctgacatgttgat-tgtcaatgcctatt----agGATGTGGGAGGTATGATGTCTATTTCTGTTGAAGCAGCTGCAGCACGCGACTCGCTAAGTGATGATAAAGAGTTAATTCGCACTTATGAG
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G33880.1 (Glycine max), 3'ss of exon 4
gtagatatgccgatgagcactgattgtattgcttacagtatttggttcagtgttgtccttctaacttattcttgaacgcaaatatatatagctctgcatggtcgtctcagatgtttaaatgctttccaagtttttgtcaacttatttttacctcattctcttttttcaagGATGTAGAAGGTATGATGTCAATTTCTGTTGAAGCTGCTGCGGCTAGGGATTCTTTGAGTGATGATAAAGAAATCGTTAACACTTATGAG
| ||| ||||| ||| || | | | | || || | | || ||| | | || ||| | || || || || | || | | |||||| |||||||||||||| || |||| ||| || || | |||| ||||||||||||||||||| ||||||||||| |||||||| |||
-----------------------------------------------------------------tcatt-ttgaat--aaacatggttggaacctagttgtacacttatactggtatgtgcatatcctgtctttatggttttggctt-gtttctttatgttctgata-gGATGTTGAAGGTATGATGTCTATCTCTGATGAGGCAGCCGAGGCTCGGGATTCTTTGAGTGATGACAAAGAAATCGTCAACACTTACGAG
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 5
gtagatatgccgatgagcactgattgtattgcttacagtatttggttcagtgttgtccttctaacttattcttgaacgcaaatatatatagctctgcatggtcgtctcagatgtttaaatgctttccaagtttttgtcaacttatttttacctcattctcttttttcaagGATGTAGAAGGTATGATGTCAATTTCTGTTGAAGCTGCTGCGGCTAGGGATTCTTTGAGTGATGATAAAGAAATCGTTAACACTTATGAG
| | ||||| ||| || | | | | || || || || ||| | || ||| | || | | | || | |||| | ||||||||||||||||||||| || |||| ||| || || | |||| ||||||||||||| ||||| |||||||| || |||||||| |||
------------------------------------------------------------------tcatattgaat--aaacatgattggaacctagttgttcacttgtattggtatgtgcaaatcctgtctttatggttttgtctg-atttcttggtcttcggata-gGATGTAGAAGGTATGATGTCTATCTCTGATGAGGCAGCAGAGGCTCGGGATTCTTTGAGCGATGACAAAGAAATTGTCAACACTTACGAG
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 4
gtagatatgccgatgagcactgattgtattgcttacagtatttggttcagtgttgtccttctaacttattcttgaacgcaaatatatatagctctgcatggtcgtctcagatgtttaaatgctttccaagtttttgtcaacttatttttacctcattctcttttttcaagGATGTAGAAGGTATGATGTCAATTTCTGTTGAAGCTGCTGCGGCTAGGGATTCTTTGAGTGATGATAAAGAAATCGTTAACACTTATGAG
|||| || | | | | | |||| || | | | | | || || | | || | | | | ||| | || | |||| ||||||| ||||| ||||||||||||||||||||||| ||| |||| |||||||||||||||||||||||||| || | ||||| || |||
-----------------------------------------------------------------ttatcctatcaaaaagaaaaacttagcacttttttgaccttgttatcttctattaatgttgtatg-----gtgaccatctagttatgttcttaaatcttttacagGATGTGGAAGGGATGATGTCAATTTCTGTTGAAGCATCTGAGGCTCGGGATTCTTTGAGTGATGATAAAGAACTCATCAACACGTACGAG
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 4
gtagatatgccgatgagcactgattgtattgcttacagtatttggttcagtgttgtccttctaacttattcttgaacgcaaatatatatagctctgcatggtcgtctcagatgtttaaatgctttccaagtttttgtcaacttatttttacctcattctcttttttcaagGATGTAGAAGGTATGATGTCAATTTCTGTTGAAGCTGCTGCGGCTAGGGATTCTTTGAGTGATGATAAAGAAATCGTTAACACTTATGAG
| | || | | | | | | ||| || | ||| || | | | |||||| | ||| | || | |||| || || | || |||| |||| || ||||| ||||||||||||||||||||||| | | |||| |||||||||||||||||||||||||| || | ||||| ||||||
-------------------------------------------------------------caccactttttatagccctgaaacttatcactttttgacctcg-ctatcttctattaatgctg-catagtgactatctagttatctt---cttaatc----ttttacagGACGTGGAAGGCATGATGTCAATTTCTGTTGAAGCATCCGAGGCTCGGGATTCTTTGAGTGATGATAAAGAACTCATCAACACGTATGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaatgctttccaagtttttgtcaacttatttttacctcattctcttttttcaagGATGTAGAAGGTATGATGTCAATTTCTGTTGAAGCTGCTGCGGCTAGGGATTCTTTGAGTGATGATAAAGAAATCGTTAACACTTATGAG
cttatttttacctcat CT-rich tract
tcaacttattttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagatatgccgatgagcactgattgtattgcttacagtatttggttcagtgttgtccttctaacttattcttgaacgcaaatatatatagctctgcatggtcgtctcagatgtttaaatgctttccaagtttttgtcaacttatttttacctcattctcttttttcaagGATGTAGAAGGTATGATGTCAATTTCTGTTGAAGCTGCTGCGGCTAGGGATTCTTTGAGTGATGATAAAGAAATCGTTAACACTTATGAG
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