Sequence
atgc intronic sequence ATGC exonic sequencegttagtcattagttttacacctttccaagaaacgtttgcttatatttatttatattctctgatcaaaatacttgggcttgtgtttgcttttagATGTTGGCCAAGAAGGTTGAAACACTAACAAAGGCGATGGAAGTGGAAGCAAAGAAGATGCGAAGAGAAGTAGCAGCAATGGAGAAAGAGGTTTCAGCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G01750.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G01750.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 9
gttagtcattagt---tttac-acctttccaagaaacgtttg--cttatatttatttat-attctctgatcaaaatacttgggcttgtgtttgctt-ttagATGTTGGCCAAGAAGGTTGAAACACTAACAAAGGCGATGGAAGTGGAAGCAAAGAAGATGCGAAGAGAAGTAGCAGCAATGGAGAAAGAGGTTTCAGCTA
|| | | || || |||| ||| | || ||| | ||||||| || || || | || | || | | | | | ||||||| || |||||||| || ||| | || || || |||||||| || |||||||||||| |||| |||||||| || |||||||| ||||| | ||||
gtaaatgtttggtctatttattgtatttggatataatccttgacttcttatttataaatgatagtccttgctaattgtttccaatggccatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
upper sequence: AT2G01750.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 9
-------gttagtc-attagttttacacctttccaagaaacgtttgcttatatttattt-atattctctgatcaaaatacttgggcttgtgtttgctt-ttagATGTTGGCCAAGAAGGTTGAAACACTAACAAAGGCGATGGAAGTGGAAGCAAAGAAGATGCGAAGAGAAGTAGCAGCAATGGAGAAAGAGGTTTCAGCTA
|| ||| ||| || | | || | | ||||| | || | ||| || || | || | || | || | | | ||||||| || |||||||| || ||| | || || || |||||||| || |||||||||||| |||| |||||||| || |||||||| ||||| | ||||
gtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgct--aattgtttccaatggtcatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
upper sequence: AT2G01750.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
gttagtcattagttttacacctttccaagaaacgtttgcttatatttatttat-attctctgatcaaaatacttgggcttgtgtttgcttttagATGTTGGCCAAGAAGGTTGAAACACTAACAAAGGCGATGGAAGTGGAAGCAAAGAAGATGCGAAGAGAAGTAGCAGCAATGGAGAAAGAGGTTTCAGCTA
|||||| || |||| | | | || | | || || || | || || ||| | | || | | |||| || | ||||| |||| ||||| || || ||| | || || || |||||||| || |||||||||||| ||||||||||||| | |||||||| ||||| | || |
gttagtattt--ttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
upper sequence: AT2G01750.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 9
gttagtcattagttttacacctttccaagaaacgtttgcttatatttatttat-attctctgatcaaaatacttgggcttgtgtttgcttttagATGTTGGCCAAGAAGGTTGAAACACTAACAAAGGCGATGGAAGTGGAAGCAAAGAAGATGCGAAGAGAAGTAGCAGCAATGGAGAAAGAGGTTTCAGCTA
|||||| ||| ||| | | || | | || || || | || || ||| | | || | | |||| || | ||||| |||| ||||| || || ||| | || || || |||||||| || |||||||||||| ||||||||||||| | |||||||| ||||| | || |
gttagtattta--tttgtttttggatattaatcttagatttctaattgataattataatcttagctaactgttgcaatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCGA
upper sequence: AT2G01750.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 9
gttagtcattagttttacacctttccaagaaacgtttgcttatatttatttatattctctgatcaaaatacttgggcttgtgtttgcttttagATGTTGGCCAAGAAGGTTGAAACACTAACAAAGGCGATGGAAGTGGAAGCAAAGAAGATGCGAAGAGAAGTAGCAGCAATGGAGAAAGAGGTTTCAGCTA
| ||| | ||| | || || ||| | | | || ||| |||| | ||||| || |||||||||| || || || || ||||| |||||||| || || ||||||||||| || || ||||||||||||||||| ||||| | || |
-------------------------------gtatatgcgtgggtttggctcta---ggtgctcatgacagtcggactt----ttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAGCAATGGAGAAGGAGGTGGCCGCGA
upper sequence: AT2G01750.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ36655 (Selaginella moellendorffii), 3'ss of exon 9
gttagtcattagttttacacctttccaagaaacgtttgcttatatttatttatattctctgatcaaaatacttgggcttgtgtttgcttttagATGTTGGCCAAGAAGGTTGAAACACTAACAAAGGCGATGGAAGTGGAAGCAAAGAAGATGCGAAGAGAAGTAGCAGCAATGGAGAAAGAGGTTTCAGCTA
| ||| | ||| | || || ||| | | | || ||| |||| | ||||| || |||||||||| || || || || ||||| |||||||| || || ||||||||||| || || |||||| |||||||||| ||||| | || |
-------------------------------gtatatgcgtgggtttggctcta---ggtgctcatgacagtcggactt----ttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAACAATGGAGAAGGAGGTGGCCGCGAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116485598|gb|EG528190.1|EG528190EST: CTGCTAATGATAAAGATCAAAGCCTTAGAGATAAAGACGAAGCTATTGAG ATGTTGGCCAAGAAGGTTGAAACACTAACAAAGGCGATGGAAGTGGAAGCA
genomic: CTGCTAATGATAAAGATCAAAGCCTTAGAGATAAAGACGAAGCTATTGAGgttagtcatt ... ttgcttttagATGTTGGCCAAGAAGGTTGAAACACTAACAAAGGCGATGGAAGTGGAAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttatatttatttatattctctgatcaaaatacttgggcttgtgtttgcttttagATGTTGGCCAAGAAGGTTGAAACACTAACAAAGGCGATGGAAGTGGAAGCAAAGAAGATGCGAAGAGAAGTAGCAGCAATGGAGAAAGAGGTTTCAGCTA
ctctgat putative branch site (score: 4)
tttgctttt putative PPT
atttatttatattctc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtcattagttttacacctttccaagaaacgtttgcttatatttatttatattctctgatcaaaatacttgggcttgtgtttgcttttagATGTTGGCCAAGAAGGTTGAAACACTAACAAAGGCGATGGAAGTGGAAGCAAAGAAGATGCGAAGAGAAGTAGCAGCAATGGAGAAAGAGGTTTCAGCTA
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