Sequence
atgc intronic sequence ATGC exonic sequencegtaataacaatgttccttgcttgggaattgtagtgaatggaagtttctgtggtgttctctctatctacttgatctaatctttgttttgtgtttctgttatgaactttagATGTAGAGAGAAACAAAGGAAAGAGGCTTCACGGCTTCAAGCTGTGAATCGGAAGTTGACGGCAATGAACAAGCTCTTGATGGAGGAGAATGACAGGTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52150.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52150.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G21610.1 (Glycine max), 3'ss of exon 2
--------gtaataacaatgttccttgcttgggaattg--tagtgaatggaagtttctgtggtgtt-ctctctatct--acttgatctaatctttgttttgtgtttctgttatgaactttagATGTAGAGAGAAACAAAGGAAAGAGGCTTCACGGCTTCAAGCTGTGAATCGGAAGTTGACGGCAATGAACAAGCTCTTGATGGAGGAGAATGACAGGTTG
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gtacctaccctaaactaaagttaccgtttttacaattactttactttttaaattttttatgttgttacttgttatgttgagttgaggtaacttttttgttttgtttttgtga-gttgttcagATGTAGAGAGAAGCAGAGGAAGGAGTCGTCGCGGCTGCAAGCTGTAAATAGGAAGTTGACTGCCATGAACAAGTTGCTCATGGAGGAGAATGATAGGTTG
upper sequence: AT1G52150.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G21620.2 (Glycine max), 3'ss of exon 1
-------gtaataac-aatgttccttgcttgggaattgtagtgaatggaagtttctgtggt--gttc---tctctatctacttgatct--aatctttgttttgtgtttctgttatgaac-tttagATGTAGAGAGAAACAAAGGAAAGAGGCTTCACGGCTTCAAGCTGTGAATCGGAAGTTGACGGCAATGAACAAGCTCTTGATGGAGGAGAATGACAGGTTG
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gtacctacccctaactgaagtctattgctttgattttcttttttaagccaattcatcaaattaatttaattctgtgtttgagtgaacttgaaaatgaatgttttgttaataaggtaactgttcagATGTAGAGAGAAGCAGAGGAAGGAGTCGTCGCGGCTGCAAGCTGTAAATAGGAAGTTGACTGCCATGAACAAGCTGCTCATGGAGGAGATTGATAGGTTG
upper sequence: AT1G52150.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G01950.1 (Glycine max), 3'ss of exon 1
gtaataacaatgttccttgcttgggaattgtagtgaatggaa---gtttctgtggtgttctctctatctacttgatctaatctttgttttgtgtttctgttatgaactttagATGTAGAGAGAAACAAAGGAAAGAGGCTTCACGGCTTCAAGCTGTGAATCGGAAGTTGACGGCAATGAACAAGCTCTTGATGGAGGAGAATGACAGGTTG
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-----------------------gtacctaccctaaacccaactcaccctttttacgattactttaccttttcatttttgaccttgttatgttgacttgacttg---tccagATGTAGAGAGAAGCAGAGAAAGGAGTCGTCGCGGCTCCAAGCTGTCAATAGGAAGCTGACTGCTATGAACAAGCTGCTGATGGAAGAGAATGATAGGTTG
upper sequence: AT1G52150.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G01940.1 (Glycine max), 3'ss of exon 1
gtaataacaatgttccttgcttgggaattgtagtgaatggaa---gtttctgtggtgttctctctatctacttgatctaatctttgttttgtgtttctgttatgaactttagATGTAGAGAGAAACAAAGGAAAGAGGCTTCACGGCTTCAAGCTGTGAATCGGAAGTTGACGGCAATGAACAAGCTCTTGATGGAGGAGAATGACAGGTTG
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-----------------------gtacctaccctaaacccaactcaccctttttacgattactttaccttttcaattttgaccttgttatgttgacttgacttg---tccagATGTAGAGAGAAGCAGAGAAAGGAGTCGTCGCGGCTGCAAGCTGTCAATAGGAAGCTGACTGCTATGAACAAGCTGCTGATGGAAGAGAATGATAGGTTG
upper sequence: AT1G52150.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv09s0002g03740.t01 (Vitis vinifera), 3'ss of exon 1
gtaataacaatgttccttgcttgggaattgtagtgaatggaagtttctgtggtgttctctctatctacttgatctaatctttgttttgtgtttctgttatgaacttta--gATGTAGAGAGAAACAAAGGAAAGAGGCTTCACGGCTTCAAGCTGTGAATCGGAAGTTGACGGCAATGAACAAGCTCTTGATGGAGGAGAATGACAGGTTG
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ggaatag--atggtt-ttatttgaataccccagt-----caagcattaat--taatagtcccgcatgcttaagaacattgtcattt-gcatttctgtttcgctttttacagATGCCGAGAGAAGCAGAGGAAAGAGGCGTCTCGCCTCCAAGCTGTGAATAGGAAGCTGACCGCCATGAACAAGCTTTTGATGGAGGAGAATGATAGGTTGMapped 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|86068368|gb|DR364125.1|DR364125EST: CTCTCCAACATTGAGCCTAAACAGATCAAAGTGTGGTTTCAGAACCGAAG ATGTAGAGAGAAACAAAGGAAAGAGGCTTCACGGCTTCAAGCTGTGAATCG
genomic: CTCTCTAACATTGAGCCTAAACAGATCAAAGTGTGGTTTCAGAACCGAAGgtaataacaa ... tgaactttagATGTAGAGAGAAACAAAGGAAAGAGGCTTCACGGCTTCAAGCTGTGAATCG
EST:
gi|125255537|gb|EL269622.1|EL269622EST: CATTGAGCCTAAACAGATCAAAGTGTGGTTTCAGAACCGAAG ATGTAGAGAGAAACAAAGGAAAGAGGCTTCACGGCTTCAAGCTGTGAATCG
genomic: CATTGAGCCTAAACAGATCAAAGTGTGGTTTCAGAACCGAAGgtaataacaa ... tgaactttagATGTAGAGAGAAACAAAGGAAAGAGGCTTCACGGCTTCAAGCTGTGAATCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctctctatctacttgatctaatctttgttttgtgtttctgttatgaactttagATGTAGAGAGAAACAAAGGAAAGAGGCTTCACGGCTTCAAGCTGTGAATCGGAAGTTGACGGCAATGAACAAGCTCTTGATGGAGGAGAATGACAGGTTG
atctaat putative branch site (score: 3)
taatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataacaatgttccttgcttgggaattgtagtgaatggaagtttctgtggtgttctctctatctacttgatctaatctttgttttgtgtttctgttatgaactttagATGTAGAGAGAAACAAAGGAAAGAGGCTTCACGGCTTCAAGCTGTGAATCGGAAGTTGACGGCAATGAACAAGCTCTTGATGGAGGAGAATGACAGGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA