Sequence
atgc intronic sequence ATGC exonic sequencegtcagttatttattcttttctgctcacttctttatctgcatattccttaactacattcgtacctgcaacaaatttggtggtcagattgatagatttttttcgttcttctcatctagGATGTTGAAGCTCACACCTCAGATGCATCACAATTAATTCCACAACACAATTACAAGCTTGATGTGCATGCTCTAAATAGCCGTCACCCAGGAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G51050.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G51050.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g01070.1 (Oryza sativa), 3'ss of exon 4
---------------------------------------gtcagttatttattcttttctgctcacttctttatctgcatattccttaac-tacattcgtacctgca----acaaatttggtggtcagattg--atagatttttttcgttcttctcatct--------agGATGTTGAAGCTCACACCTCAGATGCATCACAATTAATTCCACAACACAATTACAAGCTTGATGTGCATGCTCTAAATAGCCGTCACCCAGGAGAG
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gtgcacccatcctgtagtccatgacttttactttatagtttatactactatttatttcaaggatgttgccacttctgtgcattttgtgtcatgcattagcatgcacaggacatgaatagcttggaaagcttgccatacattattcatgtgtttctgttttgacaaaacagAATATCCCATCGCAACCATCCGATGCTTCAGTGCTGATACCACAACACAATTACAAGCTTGATGCCCATGCCCTTAATAGTCGTCATCCTGGTCAG
upper sequence: AT3G51050.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G07720.1 (Glycine max), 3'ss of exon 6
gtcagttatttattcttttctgctcacttctttatctgcatattcc-ttaactacattcgtacctgcaacaaatttggtggtcagattgatagatttttttcgttcttctcatctagGATGTTGAAGCTCACACCTCAGATGCATCACAATTAATTCCACAACACAATTACAAGCTTGATGTGCATGCTCTAAATAGCCGTCACCCAGGAGAG
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-------aaacaa-cattaatgttcaataatctaa-tgcctattttgttgaatactctg-----tgtagtgttatccttattctaattactg---ctattgtcttttcattatttagAACATTGAAGCACATTCTTCAGATGCATCACAGTTACTTCCACAGCATAACTACAAGCTTGATGTTCATGCTCTGAATACCCGTCAACCTGGAGAG
upper sequence: AT3G51050.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G37580.1 (Glycine max), 3'ss of exon 6
gtcagttatttattcttttctgctcacttctttatctgcatattccttaactacattcgtacctgcaacaaatttggtggtcagattgatagatttttttcgttcttctcatctagGATGTTGAAGCTCACACCTCAGATGCATCACAATTAATTCCACAACACAATTACAAGCTTGATGTGCATGCTCTAAATAGCCGTCACCCAGGAGAG
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----------acaacattaatgttcactaatctaacatctattatgttgaatactcttgt----gtagtgttatcctttattctaatgactggtattgtc--ttttcattatttagAACATTGAAGTGCATTCTTCAGATGCATCACAGTTACTTCCGCAACATAACTACAAGCTTGATGTTCATGCTCTGAATACCCGCCAACCTGGAGAGMapped 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|86060085|gb|DR355842.1|DR355842EST: ATGCATTTGCTGGCAAGACTGGCCTTCTTCGATGGAGTAAAAAGACTGAT GATGTTGAAGCTCACACCTCAGATGCATCACAATTAATTCCACAACACAAT
genomic: ATGCATTTGCTGGCAAGACTGGCCTTCTTCGATGGAGTAAAAAGACTGATgtcagttatt ... tctcatctagGATGTTGAAGCTCACACCTCAGATGCATCACAATTAATTCCACAACACAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgcaacaaatttggtggtcagattgatagatttttttcgttcttctcatctagGATGTTGAAGCTCACACCTCAGATGCATCACAATTAATTCCACAACACAATTACAAGCTTGATGTGCATGCTCTAAATAGCCGTCACCCAGGAGAG
gattgat putative branch site (score: 4)
tttttttcgttcttct putative PPT
attgatagattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagttatttattcttttctgctcacttctttatctgcatattccttaactacattcgtacctgcaacaaatttggtggtcagattgatagatttttttcgttcttctcatctagGATGTTGAAGCTCACACCTCAGATGCATCACAATTAATTCCACAACACAATTACAAGCTTGATGTGCATGCTCTAAATAGCCGTCACCCAGGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA