Sequence
atgc intronic sequence ATGC exonic sequencegtatattggattctagctcctattaccatggttttgtagattatatagttcaggatagctattagctagttcgatttattggtgatgtctagttttgcatggttagaaacatgtctcttggtgtttgttagactgttaaagatggctgtttgaactttgtagATTTGGCATGCAAACATGCCATATAACAAAATTGCTGACCGGAAAGGTCATCAAGGATGGATGAAAAGGGAAGGGGAATACTTTACTTTCCCAGGCGGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G00740.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G00740.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G01870.1 (Glycine max), 3'ss of exon 1
gtatattggattctagctcctattaccatggttttgtagattatatagttcaggatagctattagctagttcgatttattggtgatgtctagttttgcatggttagaaacatgtctcttggtgtttgttagactgttaaagatggctgtttgaactttgtagATTTGGCATGCAAACATGCCATATAACAAAATTGCTGACCGGAAAGGTCATCAAGGATGGATGAAAAGGGAAGGGGAATACTTTACTTTCCCAGGCGGTG
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-----------------------------------gca-attatgtgtctcagaaaaaatatttaccttttagaat-gttgttgatgttt----------------------gccatttagtgatctat---ctatctaaaagcactgatgtattcatgtagATATGGCACAGCAACATGCCATACAACAAGATTGCTGACAGGAAAGGTCACCAAGGATGGATGAAGCTTGAAGGTCCTCACTTTATATTCCCTGGAGGTG
upper sequence: AT4G00740.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G08360.1 (Glycine max), 3'ss of exon 1
gtatattggattctagctcctattaccatggttttgtagattatatagttcaggatagctattagctagttcgatttattggtgatgtctagttttgcatggttagaaacatgtctcttggtgtttgttagactgttaaagatggctgtttgaactttgtagATTTGGCATGCAAACATGCCATATAACAAAATTGCTGACCGGAAAGGTCATCAAGGATGGATGAAAAGGGAAGGGGAATACTTTACTTTCCCAGGCGGTG
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---------------------------------------------------------attatgtgtcagaaaaatgtttt--taatttttagaatgttgttgattgatgtttgttatttagtgatctat---ctatctaaaagcactgatgtattcatgtagATATGGCACAGCAACATGCCATACAACAAGATTGCTGACAGGAAAGGTCACCAAGGATGGATGAAGCTTGATGGTCCTCACTTTATATTCCCTGGAGGTG
upper sequence: AT4G00740.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G45990.1 (Glycine max), 3'ss of exon 1
gtatattggattctagctcctattaccatggttttgtagattatatagttcaggatagctattagctagttcgatttattggtgatgtctagttttgcatggt-tagaaacatgtctcttggt-gtttgttagactgttaaagatggctgtttgaactttgtagATTTGGCATGCAAACATGCCATATAACAAAATTGCTGACCGGAAAGGTCATCAAGGATGGATGAAAAGGGAAGGGGAATACTTTACTTTCCCAGGCGGTG-
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----------------------------------------------------------------aagaatacaagatatca-tgtactctagtttagaatgccgctgggatttatcactcatttgattcatccatccaaaacattgatggtatattctgtgcagaTATGGCACAGCAACATGCCATACAACAAGATTGCTGACAGGAAAGGTCACCAGGGATGGATGAAACTAGAAGGTCAACACTTTATATTCCCTGGTGGTGG
upper sequence: AT4G00740.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G40110.2 (Glycine max), 3'ss of exon 1
gtatattggattctagctcctattaccatggttttgtagattatatagttcaggatagctattagctagttcgatttattggtgatgtctagttttgcatggt-tagaaacatgtctcttggtgtttgttagactgttaaagatggctgtttgaactttgtagATTTGGCATGCAAACATGCCATATAACAAAATTGCTGACCGGAAAGGTCATCAAGGATGGATGAAAAGGGAAGGGGAATACTTTACTTTCCCAGGCGGTG
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--------------------------------------------------------------gaacatcatcaagatatcatatac-tctaatttagaatgatgttgggatttatcactcattgattcatccatccaaaatattgataatatattatgtgcagATATGGCACAGCAACATGCCGTACAACAAGATTGCTGACAGGAAAGGTCACCAGGGATGGATGAAACTAGAAGGTCAACACTTTATATTCCCTGGTGGTG
upper sequence: AT4G00740.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0048g01990.t01 (Vitis vinifera), 3'ss of exon 1
gtatattggattctagctcctattaccatggttttgtagattatatagttcaggatagctattagctagttcgatttattggtgat-gtctagttttgcatggttagaaacatgtctcttggtgtttgttagactgttaaagatggctgtttgaactttgtagATTTGGCATGCAAACATGCCATATAACAAAATTGCTGACCGGAAAGGTCATCAAGGATGGATGAAAAGGGAAGGGGAATACTTTACTTTCCCAGGCGGTG
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---------------------------------------------------------------ccttgttttaatatattgctttttaaccatcaaaaaatgctttctttcaatgccataaattattacaactacttgaagtatatgtctatctcctttgcagATCTGGCACAGCAACATGCCACACAATAAAATTGCTGACAGGAAAGGTCACCAGGGATGGATGAAAGAAGAAGGCATGTACTTCATTTTCCCTGGGGGTGMapped 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|116482787|gb|EG525379.1|EG525379EST: CGCCTTCTGGTTATAAAATTCCTGTTCCGTGGCCTGAGAGTCTTCACAAG ATTTGGCATGCAAACATGCCATATAACAAAATTGCTGACCGGAAAGGTCAT
genomic: CGCCTTCTGGTTATAAAATTCCTGTTCCGTGGCCTGAGAGTCTTCACAAGgtatattgga ... aactttgtagATTTGGCATGCAAACATGCCATATAACAAAATTGCTGACCGGAAAGGTCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacatgtctcttggtgtttgttagactgttaaagatggctgtttgaactttgtagATTTGGCATGCAAACATGCCATATAACAAAATTGCTGACCGGAAAGGTCATCAAGGATGGATGAAAAGGGAAGGGGAATACTTTACTTTCCCAGGCGGTG
ttaaagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatattggattctagctcctattaccatggttttgtagattatatagttcaggatagctattagctagttcgatttattggtgatgtctagttttgcatggttagaaacatgtctcttggtgtttgttagactgttaaagatggctgtttgaactttgtagATTTGGCATGCAAACATGCCATATAACAAAATTGCTGACCGGAAAGGTCATCAAGGATGGATGAAAAGGGAAGGGGAATACTTTACTTTCCCAGGCGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA