Sequence
atgc intronic sequence ATGC exonic sequencegtaagtatctagtatttactgctgtatgtttcaacaaacctttgaccagcttgtaagactctctaatggcttggtaatgaacattttcagCCTCGATGGAGTGACCTAGATGTTAACCAGCATGTGAATAATGTAAAGTACATTGGGTGGATCCTGGAGAGTGCTCCAGTGGGAATAATGGAGAGGCAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G08510.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G08510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g43820.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------gtaagtatctag-tatttactgctgta-tgtttcaacaaacctttgaccagcttgtaagactctctaatggcttggtaatgaacattttcagCCTCGATGGAGTGACCTAGATGTTAACCAGCATGTGAATAATGTAAAGTACATTGGGTGGATCCTGGAGAGTGCTCCAGTGGGAATAATGGAGAGGCAGA
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gtaagtcagctagacatagttacatactaaattatcattatgcctcaactgcaatcatttatctaagaaaaatagtaatatttgatctcacccctcatttattttaaatgatctttgatggactcttgtttactgcaa-cagCCTAGATGGGGTGACCTCGATGTCAATCAGCATGTGAACAATGTTAAATATATTGGGTGGATCCTTGAG-------------------------------
upper sequence: AT1G08510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g43090.1 (Oryza sativa), 3'ss of exon 6
------------------------------------------------------gtaagtatctagtatttactgctgtatgtttcaacaaacctttgaccagcttgtaagactctctaatggcttggtaatgaacattttcagCCTCGATGGAGTGACCTAGATGTTAACCAGCATGTGAATAATGTAAAGTACATTGGGTGGATCCTGGAGAGTGCTCCAGTGGGAATAATGGAGAGGCAGA
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gtaagtcagctagacatggttacatactgaattatcattatgcctcaactgctatcatttatctaagaaaaacagtaataa--ttgatctcacccctcatttattttaaatgatatttgatggactcttgtttactgcaa-cagCCTAGATGGGGTGACCTCGATGTCAATCAGCATGTGAACAATGTTAAATATATTGGGTGGATCCTTGAG-------------------------------
upper sequence: AT1G08510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g05130.1 (Oryza sativa), 3'ss of exon 5
gtaagt-atctagtatttactgctgt-atgtttcaacaaacctttgaccagcttgta-agactctctaatggcttggtaatgaacattttcagCCTCGATGGAGTGACCTAGATGTTAACCAGCATGTGAATAATGTAAAGTACATTGGGTGGATCCTGGAGAGTGCTCCAGTGGGAATAATGGAGAGGCAGA
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gtaagtcagttaatattgcttgttaccgtcattcattttgctggtggttctcatgcataaaatttctcatgagggatcctttgttcatgtcagCCGAAGTGGAGTGACCTTGATGTCAACCAGCATGTGAACAATGTGAAGTATATTGGTTGGATACTTGAG-------------------------------
upper sequence: AT1G08510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G08060.2 (Glycine max), 3'ss of exon 4
gtaagt-atctagtatttactgctgtatgtttcaacaaacc-tttgaccagcttgt--aagac-----tctctaat-ggcttg-gtaatgaa----catttt-cagCCTCGATGGAGTGACCTAGATGTTAACCAGCATGTGAATAATGTAAAGTACATTGGGTGGATCCTGGAGAGTGCTCCAGTGGGAATAATGGAGAGGCAGA
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gtatgtcaactagttttttttctaattgctgtcattaatttattttctcaaattatttcagatgttgttttctaattagtttacataatgcatcttcattttgcagCCTAGGTGGAGTGATCTAGATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAG-------------------------------
upper sequence: AT1G08510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S121_22V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------gtaagtatctagtatttactgctgtatgtttcaacaaacctttgaccagctt--gtaagactctctaat-------ggcttggtaatgaacatttt-------cagCCTCGATGGAGTGACCTAGATGTTAACCAGCATGTGAATAATGTAAAGTACATTGGGTGGATCCTGGAGAGTGCTCCAGTGGGAATAATGGAGAGGCAGA
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gtgcagatcttttccttccccttcgtagatttagcttagttttttattttttaattttcaactttttttttgaatttgaacacacaacactcttttttccttaggcaggaatcaccaattttgacaagctgtctatctcccgtatttctgatgcagCCAAGACGCAGTGACTTGGACATGAACCAGCATGTGAACAACGTGAAGTACATTGGGTGGATGTTGGAG-------------------------------
upper sequence: AT1G08510.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S433_34V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------------gtaagtatctagtatttactgctgtatgtttcaacaaacctttgaccagcttgtaagactctctaatggcttggtaatgaacattttcagCCTCGATGGAGTGACCTAGATGTTAACCAGCATGTGAATAATGTAAAGTACATTGGGTGGATCCTGGAGAGTGCTCCAGTGGGAATAATGGAGAGGCAGA
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gtgcgaatattttccttccttcctgtgcctgagctttggctttttattttttaatttttttatctcattttacatgcgtctcccgtgggattatactcactctagctgtattgccattgaaagcaccaaagttttgatgagccctgcatgtttctccgtgtttgtggc--acagCCGAGACGCAGTGATTTGGACATGAACCAGCATGTGAATAATGTGAAGTACATTGGTTGGATGTTGGAG-------------------------------Mapped 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|124982189|gb|EL055013.1|EL055013EST: TAACAAAAATTGATGACAAGACTGCTGACTATGTTCGATCTGGTCTCACT CCTCGATGGAGTGACCTAGATGTTAAC
genomic: TAACAAAAATTGATGACAAGACTGCTGACTATGTTCGATCTGGTCTCACTgtaagtatct ... acattttcagCCTCGATGGAGTGACCTAGATGTTAAC
EST:
gi|125099418|gb|EL155236.1|EL155236EST: CTATGTTCGATCTGGTCTCACT CCTCGATGGAGTGACCTAGATGTTAACCAGCATGTGAATAATGTAAAGTAC
genomic: CTATGTTCGATCTGGTCTCACTgtaagtatct ... acattttcagCCTCGATGGAGTGACCTAGATGTTAACCAGCATGTGAATAATGTAAAGTAC
EST:
gi|86073234|gb|DR368991.1|DR368991EST: TAACAAAAATTGATGACAAGACTGCTGACTATGTTCGATCTGGTCTCACT CCTCGATGGAGTGACCTAGATGTTAACCAGCATGTGAATAATGTAAAGTAC
genomic: TAACAAAAATTGATGACAAGACTGCTGACTATGTTCGATCTGGTCTCACTgtaagtatct ... acattttcagCCTCGATGGAGTGACCTAGATGTTAACCAGCATGTGAATAATGTAAAGTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacctttgaccagcttgtaagactctctaatggcttggtaatgaacattttcagCCTCGATGGAGTGACCTAGATGTTAACCAGCATGTGAATAATGTAAAGTACATTGGGTGGATCCTGGAGAGTGCTCCAGTGGGAATAATGGAGAGGCAGA
ctctaat putative branch site (score: 3)
cattttc putative PPT
aacatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtatctagtatttactgctgtatgtttcaacaaacctttgaccagcttgtaagactctctaatggcttggtaatgaacattttcagCCTCGATGGAGTGACCTAGATGTTAACCAGCATGTGAATAATGTAAAGTACATTGGGTGGATCCTGGAGAGTGCTCCAGTGGGAATAATGGAGAGGCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG