Sequence
atgc intronic sequence ATGC exonic sequence...tctacatgtgacaacagatggaaacaataggtctccttagtatgatatggctgttcaattgagctagtcaggctgatgtgttttcattctctttaaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTGCAGCAGCTGCGACTTTTTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06670.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06670.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA17G03570.1 (Glycine max), 3'ss of exon 13
------tctacatgtgacaac-agatggaaacaataggtctccttagtatgatatggctgttcaattgagctagtcaggctgatgtgttttcattctctttaaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTGCAGCAGCTGCGACTTTTTAG
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tggctgcatttctgtagtgcttaaatgtaaatgct-gccttgtttaatctaccatagattcttattctaaatagt------gtttgcctcttatgtgagatgagcagGTTTATTTCTTACACGAGTTTTGTAGTTTGAGCAAGAGCCTGCAGATGGTCCAGCAGCTTCGGCTTTTTAG
upper sequence: AT3G06670.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA07G37040.1 (Glycine max), 3'ss of exon 11
tctacatgtgacaacagatggaaacaataggtctccttagtatgatatggct-gttcaattgag--ctagtcaggctgatgtgt---tttcattctctttaaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTGCAGCAGCTGCGACTTTTTAG
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tct-tgtatggttgtattt-----ctatagtgcttaaatgtaaatgctgccttgtttaatcgattcttattctaaatactgtttgccttttatgtgggatgaacagGTTTATTTCTTACACGAGTTTTGTAGTTTGAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTTTTTAG
upper sequence: AT3G06670.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA15G15270.1 (Glycine max), 3'ss of exon 12
tctacatgtgacaacagatggaaacaataggtctccttagtatgatatggctgttcaattgagctagtcaggctgatgtgttttcattctcttt-----aaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTGCAGCAGCTGCGACTTTTTAG
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---ttaaactgcttta-atgttaatgacatcttttttatgttcatgattgatgtt-actggtgattcttatgttaaatatttttgcctctctatttggtggacagGTTCATTTCTTGCACGAGTTTTGTAGTTTAAGCAAGAGCTTACAGATGGTACATCAGCTTCGGTTTTTTCG
upper sequence: AT3G06670.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA09G04260.1 (Glycine max), 3'ss of exon 13
-tctacat--gtgacaacagatggaaacaataggtctccttagtatgatatggctgttcaattgagctagtcaggctgatgtgttttcattctctttaaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTGCAGCAGCTGCGACTTTTTAG
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aactgctttaatgttaatgccatctttttttttatgttcatgat-tgatgttgctggtaattcttat--gttaaatatttttgtctctctatttggtggacagGTCCGTTTCTTGCATGAGTTTTGTAGTTTAAGCAAGAGCTTACAGATGGTTCAACAGCTTCGGCTTTTTTG
upper sequence: AT3G06670.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv05s0077g01200.t01 (Vitis vinifera), 3'ss of exon 13
tctacatgtgacaacagatggaaacaataggtctccttagtatgatatggctgt-tcaatt--gagctagtcaggctgatgtgttttcattctctttaaat--agGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTGCAGCAGCTGCGACTTTTTAG
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-----atgagtttatcttttcagtacttaagtgatgtgtggatgttttttctgggttaactcagagtgtgctattcttattgacctttgttttaaataaatgtagGTATTTTTCTTATATGAGTTTTGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGMapped 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|164230009|gb|ES178537.1|ES178537EST: CCAAGAAAAATTTG GTATATTTCTTGCACGAA-TTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTG
genomic: CCAAGAAAAATTTGgtatttcccg ... ctttaaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTG
EST:
gi|125299385|gb|EL313470.1|EL313470EST: TGCAAGGTTGAGGTCGCCTTCTACTTCTATGGAATCCAAGAAAAAATTTG GTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGT
genomic: TGCAAGGTTGAGGTCGCCTTCTACTTCTATGGAATCCAAGAAAAA-TTTGgtatttcccg ... ctttaaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatggctgttcaattgagctagtcaggctgatgtgttttcattctctttaaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTGCAGCAGCTGCGACTTTTTAG
ggctgat putative branch site (score: 4)
tgttttcattctcttt CT-rich tract
attctctttaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctacatgtgacaacagatggaaacaataggtctccttagtatgatatggctgttcaattgagctagtcaggctgatgtgttttcattctctttaaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTGCAGCAGCTGCGACTTTTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - -caacaga
- - - - - - - - - - gaaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - ctgttca