Sequence
atgc intronic sequence ATGC exonic sequencegtagatttcgacatcaaccatgttttagatacttcatagtgtacttgttgagtatcttttatcaaatcttttccgtcattacaattgctagttcttgatatgtagTGGAAGTGACAGCACTGGAGAACAACATTGTTGTGTACAAATTTGTGCAAGATCTCCATTTCTTTGTTACGGGCGGTGAAGAGGAAAACGAGCTTATCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G60970.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G60970.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G02270.3 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------------------gtagatttcgacatcaaccatgttttagatacttcatagtgtacttgtt-gagtat--cttttatcaaatcttttccgtcattacaattgct-------agttcttgatatg-tagTGGAAGTGACAGCACTGGAGAACAACATTGTTGTGTACAAATTTGTGCAAGATCTCCATTTCTTTGTTACGGGCGGTGAAGAGGAAAACGAGCTTATCTT
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gtgtgtaaaacttatgtgatatggtcaatgatcaattgaccatgccataattcatgatgaagaattgtctgtgtgtttgatcaaattctgtatgtgattgggatagattgctgatcactgattcgtatatgacctcctttgagtattgact-tcatttcttttgccttcatgggctttttcatttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTT
upper sequence: AT1G60970.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G13190.3 (Glycine max), 3'ss of exon 2
----------------------------------------------------------------------------------------gtagatt-tcgacatcaaccatgttttagatacttcatagtgtacttgttgagtatcttttatcaaatcttttccgtcattacaattgctagttcttgatatgtagTGGAAGTGACAGCACTGGAGAACAACATTGTTGTGTACAAATTTGTGCAAGATCTCCATTTCTTTGTTACGGGCGGTGAAGAGGAAAACGAGCTTATCTT---
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gtgtgtaaaacttctgtgatatggtcaataatcaattgaccatgccataattcatgatgtgtttggtcaaattctgtctgtgattgtgatagattgctgatcactgatttgtatatgaccccattttgtaaacatgttgagtgttgact-tcatttttattgcctccttgggttttttcatttt------acagcagAAATAGCAATGTTTGAGAATAACATTGTTCTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTTAGC
upper sequence: AT1G60970.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G13190.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------------------------------------------gtagatt-tcgacatcaaccatgttttagatacttcatagtgtacttgttgagtatcttttatcaaatcttttccgtcattacaattgctagttcttgatatgtagTGGAAGTGACAGCACTGGAGAACAACATTGTTGTGTACAAATTTGTGCAAGATCTCCATTTCTTTGTTACGGGCGGTGAAGAGGAAAACGAGCTTATCTT
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gtgtgtaaaacttctgtgatatggtcaataatcaattgaccatgccataattcatgatgtgtttggtcaaattctgtctgtgattgtgatagattgctgatcactgatttgtatatgaccccattttgtaaacatgttgagtgttgact-tcatttttattgcctccttgggttttttcatttt------acagCAGAAATAGCAATGTTTGAGAATAACATTGTTCTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTT
upper sequence: AT1G60970.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv10s0003g02760.t01 (Vitis vinifera), 3'ss of exon 3
gtagatttcgacatcaaccatgt-tttagatacttcatagtgtacttgttgagtatcttttatcaaatcttttccgtcattacaattgctagttcttgatatgtagTGGAAGTGACAGCACTGGAGAACAACATTGTTGTGTACAAATTTGTGCAAGATCTCCATTTCTTTGTTACGGGCGGTGAAGAGGAAAACGAGCTTATCTT
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----cttaaaactagtgtggtgtgtttacaatgttcaaatttggcttcactgctgctctttg--aatgccttgcctttttttttttttttgttttttcatctacagCGGAGATAGCAATGTTTGAGAACAACATTGTTGTTTACAAATTTGTCCAAGACCTTCACTTCTTTGTTACTGGTGGTGAAGATGAAAATGAACTAATCTTMapped 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|152034836|gb|BP837875.2|BP837875EST: CGAAAAATCCGTGTTTACAAAGACTCAGAAAACAAATGCTAGGACCGAAG TGGAAGTGACAGCACTGGAGAACAACATTGTTGTGTACAAATTTGTGCAAG
genomic: CGAAAAATCCGTGTTTACAAAGACTCAGAAAACAAATGCTAGGACCGAAGgtagatttcg ... tgatatgtagTGGAAGTGACAGCACTGGAGAACAACATTGTTGTGTACAAATTTGTGCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtatcttttatcaaatcttttccgtcattacaattgctagttcttgatatgtagTGGAAGTGACAGCACTGGAGAACAACATTGTTGTGTACAAATTTGTGCAAGATCTCCATTTCTTTGTTACGGGCGGTGAAGAGGAAAACGAGCTTATCTT
tcttgat putative branch site (score: 4)
ttctt CT-rich tract
ttttatcaaatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagatttcgacatcaaccatgttttagatacttcatagtgtacttgttgagtatcttttatcaaatcttttccgtcattacaattgctagttcttgatatgtagTGGAAGTGACAGCACTGGAGAACAACATTGTTGTGTACAAATTTGTGCAAGATCTCCATTTCTTTGTTACGGGCGGTGAAGAGGAAAACGAGCTTATCTT
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