Sequence
atgc intronic sequence ATGC exonic sequencegtgagaatcatcataagtctttttatttctcgtttggttctgtattgttataatacttaattgtaaacctttgcagGTAGCTAGTTTTGGAGGTACTCTACTATCTCAAGGCATTCTAGCCCTCTCATTTGCTCCAAGAGATTCACATAAATCTCAAATTCAGTTCGCTTTGGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G00740.1 |
intron # | 2 |
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 2
lower sequence: LOC_Os04g48140.1 (Oryza sativa), 3'ss of exon 2
--------gtgagaatcatcataagtctttttatttctcgtttggttctgtattgttataatactta-attgtaaacctttgcagGTAGCTAGTTTTGGAGGTACTCTACTATCTCAAGGCATTCTAGCCCTCTCATTTGCTCCAAGAGATTCACATAAATCTCAAATTCAGTTCGCTTTGGAAA
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gtaataagctaaatcttcacatgaatcaatttatgttttacttt-taaagaaatggtatggtattaagatctttcctctctgaagGTGGCTAGTTTTGGTGGGTTTTTGCTTAAAGAGAATATCTTGACACTCTCTTTTGCCCCAAGAGATTCACATAAATCTCAAATACAATTTGCTCTGGAGA
upper sequence: AT4G00740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G076841_T01 (Zea mays), 3'ss of exon 2
gtgaga-atcatcataagtcttttt--atttctcgtttggttct---gtattgttataatacttaattgtaaacctttgcagGTAGCTAGTTTTGGAGGTACTCTACTATCTCAAGGCATTCTAGCCCTCTCATTTGCTCCAAGAGATTCACATAAATCTCAAATTCAGTTCGCTTTGGAAA
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gtaatatgttaatctgaacttgggaagacttctggttttacttttaggagttttggtcataatgatcttttcctctctgaagGTTGCTAGCTTTGGTGGATTTTTGCTTAAGGAGAATATCATGACACTTTCATTTGCACCAAGAGATTCACATAAGTCTCAAATACAATTTGCTTTGGAGA
upper sequence: AT4G00740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G45990.1 (Glycine max), 3'ss of exon 2
gtgagaatcatcataagtctt---tttatttctcgtttggttctgtattgttat------aatacttaattgtaaaccttt-----gcagGTAGCTAGTTTTGGAGGTACTCTACTATCTCAAGGCATTCTAGCCCTCTCATTTGCTCCAAGAGATTCACATAAATCTCAAATTCAGTTCGCTTTGGAAA-
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-taagagctgttatctatttttcctttggcacctttctagaattttattactgtttatttaatatgcaaatacatctctttttttcacaggTTGCTAGTTTTGGAGGATATATGCTATCTAAAAATATTTTAACCATGTCTTTTGCTCCAAGAGATTCACATAAAGCTCAAATACAATTTGCCTTGGAAAG
upper sequence: AT4G00740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G40110.2 (Glycine max), 3'ss of exon 2
--------gtgagaatcatcataag----tctttttatttctcgtttggttctgt-----attgttataatacttaattgtaaacctttgcagGTAGCTAGTTTTGGAGGTACTCTACTATCTCAAGGCATTCTAGCCCTCTCATTTGCTCCAAGAGATTCACATAAATCTCAAATTCAGTTCGCTTTGGAAA
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gtaagacagtaagagctgttatcttgttttcctttgagatcttactagaatttattcctgtttaacatgctaatacatcttattttttcacagGTTGCTAGTTTTGGAGGATATATGCTGTCTAAGAATATTTTAACCATGTCTTTTGCACCAAGAGATTCACATAAAGCTCAAATACAATTTGCCTTGGAAAMapped 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: TTCCGCTTAATGGTGGAACTTTGAGAACTGCTCTTGACATGGGATGCGGG GTAGCTAGTTTTGGAGGTACTCTACTATCTCAAGGCATTCTAGCCCTCTCA
genomic: TTCCGCTTAATGGTGGAACTTTGAGAACTGCTCTTGACATGGGATGCGGGgtgagaatca ... acctttgcagGTAGCTAGTTTTGGAGGTACTCTACTATCTCAAGGCATTCTAGCCCTCTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatttctcgtttggttctgtattgttataatacttaattgtaaacctttgcagGTAGCTAGTTTTGGAGGTACTCTACTATCTCAAGGCATTCTAGCCCTCTCATTTGCTCCAAGAGATTCACATAAATCTCAAATTCAGTTCGCTTTGGAAA
acttaat putative branch site (score: 4)
cctttgc putative PPT
tgtattgttataatac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagaatcatcataagtctttttatttctcgtttggttctgtattgttataatacttaattgtaaacctttgcagGTAGCTAGTTTTGGAGGTACTCTACTATCTCAAGGCATTCTAGCCCTCTCATTTGCTCCAAGAGATTCACATAAATCTCAAATTCAGTTCGCTTTGGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA