Sequence
atgc intronic sequence ATGC exonic sequencegtttgctagtgtttggccttttttcctgttctttgccgcctttatatgaaatgttgtataatataagtctaaagatatgggttgtgtatatttagATGTTGGCCAAGAAGGTTGAAACATTAACAAAGGCGATGGACGTTGAGGCAAAGAAGATGCGAAGAGAAGTAGCTGTAATGGGGAAAGAAGTTGCTGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G14840.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g50320.1 (Oryza sativa), 3'ss of exon 9
gtttgctagtgtttggccttttttcctgttctttgccgcctttatatga--aatgttgtataatataagtctaaagatatgggttgtgtatatttagATGTTGGCCAAGAAGGTTGAAACATTAACAAAGGCGATGGACGTTGAGGCAAAGAAGATGCGAAGAGAAGTAGCTGTAATGGGGAAAGAAGTTGCTGCAA
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--------gtatggcactagaattcctgtttattatggatttaatgggaccaatgctgtgggtcatgcctttgctaac-tgcctcttgtttac--agATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA
upper sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 9
------gtttg--ctagtgtttggccttttttcctgttctttgccgcctttatatgaaatgttgtataatataagtctaaagatatgggttgtgtatatttagATGTTGGCCAAGAAGGTTGAAACATTAACAAAGGCGATGGACGTTGAGGCAAAGAAGATGCGAAGAGAAGTAGCTGTAATGGGGAAAGAAGTTGCTGCAA
||||| ||| | ||| || | | ||| | | | | ||| || | || ||| | | | |||| | ||| ||||||| || |||||||| || ||||| || || || ||||| |||||||||||||||||| |||| |||||||||| |||| ||| || || ||||| |
gtaaatgtttggtctatttattgtatttggatataatccttgacttcttatttataaatgatagtccttgctaattgtttcca-atggccatcatctatc-agATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
upper sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 9
------gtttg--ctagtgtttggccttttttcctgttctttgccgcctttatatgaaatgttgtataatataagtctaaagatatgggttgtgtatatttagATGTTGGCCAAGAAGGTTGAAACATTAACAAAGGCGATGGACGTTGAGGCAAAGAAGATGCGAAGAGAAGTAGCTGTAATGGGGAAAGAAGTTGCTGCAA
||||| ||| | ||| || | | ||| | | | | ||| || | || ||| | | | |||| | ||| ||||||| || |||||||| || ||||| || || || ||||| |||||||||||||||||| |||| |||||||||| |||| ||| || || ||||| |
gtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgctaattgtttcca-atggtcatcatctatc-agATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
upper sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
gtttgctagtgtttggccttttttcctgttctttgccgcctttatatgaaatgttgtataatataagtctaaagatatgggttgtgtatatttagATGTTGGCCAAGAAGGTTGAAACATTAACAAAGGCGATGGACGTTGAGGCAAAGAAGATGCGAAGAGAAGTAGCTGTAATGGGGAAAGAAGTTGCTGCAA
||| | | |||| ||| | | |||| | || | || | | | | | ||| | | || ||| | | | ||||| |||| ||||| || || ||||| || || || ||||| |||||||||||||||||| |||||||||||||| |||| ||| || || |||||||
gttagtatttttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatggttgttatctgt---cagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
upper sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 9
gtttgctagtgtttggccttttttcctgttctttgccgcctttatatgaaatgttgtataatataagtctaaagatatgggttgtgtatatttagATGTTGGCCAAGAAGGTTGAAACATTAACAAAGGCGATGGACGTTGAGGCAAAGAAGATGCGAAGAGAAGTAGCTGTAATGGGGAAAGAAGTTGCTGCAA
||| | | |||| || | | |||| | || | || | | | | | ||| | | || ||| | | | ||||| |||| ||||| || || ||||| || || || ||||| |||||||||||||||||| |||||||||||||| |||| ||| || || ||||| |
gttagtatttatttgtttttggatattaatcttagatttctaattgataattataatcttagctaactgttgcaatggttgttatctgt---cagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatatgaaatgttgtataatataagtctaaagatatgggttgtgtatatttagATGTTGGCCAAGAAGGTTGAAACATTAACAAAGGCGATGGACGTTGAGGCAAAGAAGATGCGAAGAGAAGTAGCTGTAATGGGGAAAGAAGTTGCTGCAA
gtctaaa putative branch site (score: 3)
tataatataagtctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgctagtgtttggccttttttcctgttctttgccgcctttatatgaaatgttgtataatataagtctaaagatatgggttgtgtatatttagATGTTGGCCAAGAAGGTTGAAACATTAACAAAGGCGATGGACGTTGAGGCAAAGAAGATGCGAAGAGAAGTAGCTGTAATGGGGAAAGAAGTTGCTGCAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC