Sequence
atgc intronic sequence ATGC exonic sequencegtcgcgatgtcaattgttgtttcttcctttgttttgttgttgtaaatactgaatttcctaacaaaagctagcttgtatggtctgagtacagGACATTCATCATAAAATTAAGCCAGAACAAGTAGAGCTTGTGCGTCGTGATTACACTGCCAATGAAGGTTGGGAGACGTTCCTTTCTTATGAAGATACAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50320.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 6
gtcgcgatgtcaattgttgtttcttcctttgttttgttgttgtaaatactgaatttcctaacaaaagctagcttgtatggtctgagtacagGACATTCATCATAAAATTAAGCCAGAACAAGTAGAGCTTGTGCGTCGTGATTACACTGCCAATGAAGGTTGGGAGACGTTCCTTTCTTATGAAGATACAC
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--------gtaaataaaaaatacagtaaaatcactttcacggcctaaaatggatgtccttttattattctaactgtgca-tctgtatgtagGATATCCATCACAAGATCAGGCCTGATGAAGTAGAGCTTGTTAGACGTGACTATGCTGCAAATGAGGGCTGGGAGACGTTCCTCTCTTATGAGGATACAC
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G36790.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------------gtcgcgatgtcaattgttgtttcttccttt--gttttgttgttgtaaat-----actgaatttcct-----aacaaaagctagcttgtatggtctgagtacagGACATTCATCATAAAATTAAGCCAGAACAAGTAGAGCTTGTGCGTCGTGATTACACTGCCAATGAAGGTTGGGAGACGTTCCTTTCTTATGAAGATACAC
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gttattatatagaactggttttgtttgggaattttctgtagtggttttgtttgggaattttctgtagcaaagattgcaaatgctttgaaattctgctgacacaatttgttcacttgatacctttttggagcaccaacaaacattttgtatttctctttagGATATTCACCACCAAATTAAGCCAGAAGAGGTGGAGCTTGTTCGGCGTGATTATATGGCAAATGAGGGTTGGGAAACATTTCTATCATATGAAGATACAC
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv17s0000g10190.t01 (Vitis vinifera), 3'ss of exon 6
gtcgcgatgtcaattgttgtttcttcctttgttttgttgttgtaaatactgaatttcctaacaaaagctagcttgtatggtctgagtacagGACATTCATCATAAAATTAAGCCAGAACAAGTAGAGCTTGTGCGTCGTGATTACACTGCCAATGAAGGTTGGGAGACGTTCCTTTCTTATGAAGATACAC
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gtgttgcacacaactatgttcacttgacatgttatttataaaagtttacaacaatttgaaatccttgttaacttgcctgtgatgaatctagGACATCCACCACAAAATTAAGCCAGAGGAGGTTGAGCTTGTTCGCCGTGATTATACAGCAAATGAAGGTTGGGAAACTTTTCTTTCATATGAGGATATACMapped 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|164156925|gb|ES084629.1|ES084629EST: GCTGGAATTCAG GACATTCATCATAAAATTAAGCCAGAACAAGTAGAGCTTGTGCGTCGTGAT
genomic: GCTGGAATTCAGgtcgcgatgt ... ctgagtacagGACATTCATCATAAAATTAAGCCAGAACAAGTAGAGCTTGTGCGTCGTGAT
EST:
gi|86084702|gb|DR380461.1|DR380461EST: ACTTGGGCCTTAAATGCCGTGATGTCCGTACTCGTGAAGCTGGAATTCAG GACATTCATCATAAAATTAAGCCAGAACAAGTAGAGCTTGTGCGTCGTGAT
genomic: ACTTGGGCCTTAAATGCCGTGATGTCCGTACTCGTGAAGCTGGAATTCAGgtcgcgatgt ... ctgagtacagGACATTCATCATAAAATTAAGCCAGAACAAGTAGAGCTTGTGCGTCGTGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttgtaaatactgaatttcctaacaaaagctagcttgtatggtctgagtacagGACATTCATCATAAAATTAAGCCAGAACAAGTAGAGCTTGTGCGTCGTGATTACACTGCCAATGAAGGTTGGGAGACGTTCCTTTCTTATGAAGATACAC
tcctaac putative branch site (score: 1)
taaatactgaattt 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 |
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gtcgcgatgtcaattgttgtttcttcctttgttttgttgttgtaaatactgaatttcctaacaaaagctagcttgtatggtctgagtacagGACATTCATCATAAAATTAAGCCAGAACAAGTAGAGCTTGTGCGTCGTGATTACACTGCCAATGAAGGTTGGGAGACGTTCCTTTCTTATGAAGATACAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA