Sequence
atgc intronic sequence ATGC exonic sequencegtgtctaattgaattttactttttggttgctttaactttcacttgtttcgatcaaattttttttactggcgaaaaagtaataaaatgtaatctaattgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G51980.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g53700.1 (Oryza sativa), 3'ss of exon 6
------------------------------------------gtgtctaattgaattttactttttggttgctttaactttcacttgtttcgatcaaattttttttactggcgaaaaagtaataaaatgtaatctaattgctat-tagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
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gtattgttggcaaacatcaaatttaaccattattcagagacaaaactcaactatggtataccttttatgtagtttactgtctagtagactgccttatatgttcaccatttctttatacgcaatatgg-atggtcttgttattttgcagATGCTCATGGGAGGAGGTGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGT
upper sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G005036_T01 (Zea mays), 3'ss of exon 6
---gtgtctaattg-aattttactttttggttgctttaactttcacttgtttcgatcaaattttttttactggcgaaaaagtaataaaatgtaatctaattgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
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gccatttcttctagcggtgttaaaaaacaatcacatgtgctgttgcatatgctaatctaatagtgctt-----caaaggtatgttga----tcaatttgttgtctgtagATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGT
upper sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G43000.1 (Glycine max), 3'ss of exon 7
---------------gtgtctaattgaattttactttttggttgctt-taacttt---cacttgtttcgatcaaattttttttactggcgaaaaagtaataaaatg---taatctaattgcta------------ttagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
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gtactcactttgtgtgagtcattctgatttcaagatatagcatgtctatggatttgcatattttcttctgctggcattcatgcacaagaaaaggaggaaagaaacaatttaatagaagtaataattctgagtcgttcagATGCTTATGGGAGGAGGTGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGGATGCATTCAAGGCTGT
upper sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G21380.1 (Glycine max), 3'ss of exon 6
-----------------gtgtctaattgaatt-ttactttttggttgctttaacttt-cacttgtt--tcgatcaaattttttttactggcgaaaaagtaataaaatgtaatctaattgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
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gtacacattttgtgtctgagtgtgatagaaataccatgctttggttttttcgtccttacttttgttgctcaaaaaagtatgtacaaaatgattgaatggaactaataattcttgaatcatg--cagATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTAT
upper sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G02390.1 (Glycine max), 3'ss of exon 6
--------------------------gtgtctaattgaattttactttttggttgctttaactttcacttgtttcgatcaaattttttttactggcg--aaaaagtaataaaatgtaatc--taattgctatt----agATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
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gtactcactttgtgtgagccattctgatttcaagagatatcatgtctatggatttgcatatttttcttttgttggcattcgtgcacaagaaaaggaggaaagaaacaattgaatagaagtagtatttctgagtgtgcagATGCTTATGGGAGGAGGTGGGTCATTCTCAGCCGGAGGGCCTGGGAAAGGGATGCACTCAAGGCTGT
upper sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G01720.1 (Glycine max), 3'ss of exon 6
------------------gtgtctaattgaattttactttttggttgctttaactttcacttgtttcgatcaaattttttttactggcgaaaaagtaataaaatg-taatctaattgctat-tagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
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gtactccattttgtgtttgagtctgatagaattactgtattttgtt-ttttggtccttacttttgttgcacaataaaggacaaatgaaatgattgaatggaagtaataattcttgaattgtgcagATGCTTATGGGAGGAGGTGGATCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTAT
upper sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g03200.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------------------------------------gtgtctaattgaattttactttttggttgctttaactttcacttgtttcgatcaa--attttttttactggcgaaaaagtaataaaatgtaatctaattgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
| | || | || | | | | | || | ||| || |||| ||| | | ||| | | ||| |||||| || || ||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||| | || |
gtgctgcatttgatcttttcttcttaaagagattctgctatctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatattcatattccctcttttcattcatccaccatgttttccttttttgcattaa-gaaatgtgatagtcccgc----agATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGGGGCCCTGGAAAAGGAATGCACTCACGACTAT
upper sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv10s0003g03230.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------------------------------------------------gtgtctaattgaattttactttttggttgctttaactttcacttgtttcgatcaa--attttttttactggcgaaaaagtaataaaatgtaatctaattgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
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gtgctgcatttgatcttttcttcttaaagagattctgctatttggaaatctctctctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatatattccctcttttcattcatccaccatgttttccttttttgcattaa-gaaatgtgatagtcctgc----agATACTTATGGGAGGAGGTGGCTCATTCTCTACGGGGGGCCCTGGAAAAGGAATGCACTCACGACTATMapped 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|124879327|gb|EH958764.1|EH958764EST: AGCAGTCACCGCCACTGTTCTCCAG ATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGA
genomic: AGCAGTCACCGCCACTGTTCTCCAGgtgtctaatt ... ttgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcaaattttttttactggcgaaaaagtaataaaatgtaatctaattgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
atctaat putative branch site (score: 3)
aaaaagtaataaaatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtctaattgaattttactttttggttgctttaactttcacttgtttcgatcaaattttttttactggcgaaaaagtaataaaatgtaatctaattgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
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