Sequence
atgc intronic sequence ATGC exonic sequence...ttatgcttatggtagtgacctaaatctttttatctactttgtccatatccgagaacacaccttatataaagtgccaatatgttgctattgggtgatgcagGAATGTGCATTACTGACTGATGGTAGGTTCTCTGGTGGGTCACACGGTTTTGTTGTTGGCCACATTTGCCCTGAAGCTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23940.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os08g44530.1 (Oryza sativa), 3'ss of exon 11
ttatgcttatggtagtgacctaaatctttttatctactttgtccatatccgagaacacaccttatataaagtgccaatatgttgctattgggtgatgcagGAATGTGCATTACTGACTGATGGTAGGTTCTCTGGTGGGTCACACGGTTTTGTTGTTGGCCACATTTGCCCTGAAGCTCAG
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-----------gtagttatcttgctgtcttctgaatgtctgataactttccttgtgacagctgatcaatatt--taacttgtattcaaacatcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G014069_T01 (Zea mays), 3'ss of exon 11
ttatgcttatgg-tagtgacctaaatctttttatctactttgtccatatccgagaacacaccttatataaagtgccaatatgttgctattgggtgatgcagGAATGTGCATTACTGACTGATGGTAGGTTCTCTGGTGGGTCACACGGTTTTGTTGTTGGCCACATTTGCCCTGAAGCTCAG
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-tgcatgtgtgcctggcaactatcctcctttcatcagattagttattcttcactacagttgatgtgataacctcttaaccaatgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: AC234528.1_FGT005 (Zea mays), 3'ss of exon 11
ttatgcttatggtagtg-acctaaatctttttatctactttgtccatatccgagaacacaccttat-ataaagtgccaatatgttgctattgggtgatgcagGAATGTGCATTACTGACTGATGGTAGGTTCTCTGGTGGGTCACACGGTTTTGTTGTTGGCCACATTTGCCCTGAAGCTCAG
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-taccttgatctagatgcacgtgtgcctggcca-ctaccctggttattcttcactacagctgatgtgataacctcttaaccagtgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTTGTTGTCGGCCACATATGCCCTGAAGCACAG
upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv05s0051g00830.t01 (Vitis vinifera), 3'ss of exon 11
-ttatgcttatggtagtgaccta--aatctttttatctactttgtccatatccgagaacacaccttatataaagtgccaatatgttgctattgggtgatgcagGAATGTGCATTACTGACTGATGGTAGGTTCTCTGGTGGGTCACACGGTTTTGTTGTTGGCCACATTTGCCCTGAAGCTCAG
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tatgttctcttagacatattttatgaacctgcttaac-actgagtacctttgtttcatttgatgtaatgttacttatggaattttattccttatgtg--gcagGATGTTGCTTTGTTGACTGATGGTAGGTTTTCAGGAGGTTCACATGGATATGTTGTTGGCCACATATGTCCTGAAGCACATMapped 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|164220849|gb|ES164211.1|ES164211EST: CTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAAAG GAATGTGCATTA
genomic: CTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAAAGgtatgatatg ... ggtgatgcagGAATGTGCATTA
EST:
gi|86087681|gb|DR383440.1|DR383440EST: CTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAAAG GAATGTGCATTACTGACTGATGGTAGGTTCTCTGGTGGGTCACACGGTTTT
genomic: CTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAAAGgtatgatatg ... ggtgatgcagGAATGTGCATTACTGACTGATGGTAGGTTCTCTGGTGGGTCACACGGTTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatccgagaacacaccttatataaagtgccaatatgttgctattgggtgatgcagGAATGTGCATTACTGACTGATGGTAGGTTCTCTGGTGGGTCACACGGTTTTGTTGTTGGCCACATTTGCCCTGAAGCTCAG
ttatataaagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatgcttatggtagtgacctaaatctttttatctactttgtccatatccgagaacacaccttatataaagtgccaatatgttgctattgggtgatgcagGAATGTGCATTACTGACTGATGGTAGGTTCTCTGGTGGGTCACACGGTTTTGTTGTTGGCCACATTTGCCCTGAAGCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - -ctaaatc
- - - - - - - - - - - - - - - - - - - - - ccatatc
- - - - - - - - - - - - - - - - - - - - - - - - - - gaacaca