Sequence
atgc intronic sequence ATGC exonic sequencegtaagaatcaatccaatcaatcagttcgcgctacaattttgtcacttttgaagttaaaagtatccaattttgcatctctctaatgttcatatgtaatgtgcagTGTTTGGGTTGCCCGTAGACCACCTGGTTACGCTTTTCTAGATTTCGAAGATCCTAGGGATGCCCGTGATGCTATCCGTGCTTTAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G31580.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G31580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g54770.1 (Oryza sativa), 3'ss of exon 2
gtaagaatcaatccaatcaatcagttcgcgctacaattttgtcacttttgaagttaaaagtatccaattttgcatctctctaatgttcatatgtaatgtgcagTGTTTGGGTTGCCCGTAGACCACCTGGTTACGCTTTTCTAGATTTCGAAGATCCTAGGGATGCCCGTGATGCTATCCGTGCTTTAGATG
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--tattcctgactcaatatagtggtaccccttgtactataagttatttggacgttgcgggtatgtttgttgatgtaattttcaagtgtatttttc-catgcagTGTCTGGGTTGCCCGTAAACCACCTGGTTTTGCATTTATCGATTTTGATGACAAGAGGGATGCTGAGGATGCACTCCGTGATTTAGATG
upper sequence: AT4G31580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G29080.2 (Glycine max), 3'ss of exon 2
gtaagaatcaatccaatcaatca-gttcgcgctacaattttgtcacttttgaagtt--aaaagtatccaattttgcatctctctaatgttcatatgtaatgtgcagTGTTTGGGTTGCCCGTAGACCACCTGGTTACGCTTTTCTAGATTTCGAAGATCCTAGGGATGCCCGTGATGCTATCCGTGCTTTAGATG
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-cggtttttgttgcagtggtttttatttgttttgtttttctaataggtctattttttgaaaaaaaaatgattttgtgttt----aatgct-atgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGATGCACAGGATGCTATCCGTGAATTGGATG
upper sequence: AT4G31580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G17930.4 (Glycine max), 3'ss of exon 2
-----gtaagaatcaatccaatcaatcagttcgcgctacaattttgtcacttttgaagttaaaagtatccaattttgcatctctctaatgttcatatgtaatgtgcagTGTTTGGGTTGCCCGTAGACCACCTGGTTACGCTTTTCTAGATTTCGAAGATCCTAGGGATGCCCGTGATGCTATCCGTGCTTTAGATG
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gttttgttgctgt-gattttattttttgttttgttctactattaggtttattttgaaa--aaaaatg----attttgtgtttaatgggtact-atgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGACGCACAGGATGCTATCCGTGAATTGGATGMapped 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|116418442|gb|EG461034.1|EG461034EST: ACTGAGCGTGAACTTGAGGATGAGTTCCGTGCCTTTGGAGTTGTCAGGAG TGTTTGGGTTGCCCGTAGACCACCTGGTTACGCTTTTCTAGATTTCGAAGA
genomic: ACTGAGCGTGAACTTGAGGATGAGTTCCGTGCCTTTGGAGTTGTCAGGAGgtaagaatca ... taatgtgcagTGTTTGGGTTGCCCGTAGACCACCTGGTTACGCTTTTCTAGATTTCGAAGA
EST:
gi|116418435|gb|EG461027.1|EG461027EST: GTGCCTTTGGAGTTGTCAGGAG TGTTTGGGTTGCCCGTAGACCACCTGGTTACGCTTTTCTAGATTTCGAAGA
genomic: GTGCCTTTGGAGTTGTCAGGAGgtaagaatca ... taatgtgcagTGTTTGGGTTGCCCGTAGACCACCTGGTTACGCTTTTCTAGATTTCGAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaagttaaaagtatccaattttgcatctctctaatgttcatatgtaatgtgcagTGTTTGGGTTGCCCGTAGACCACCTGGTTACGCTTTTCTAGATTTCGAAGATCCTAGGGATGCCCGTGATGCTATCCGTGCTTTAGATG
ctctaat putative branch site (score: 3)
ttaaaagtat 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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaatcaatccaatcaatcagttcgcgctacaattttgtcacttttgaagttaaaagtatccaattttgcatctctctaatgttcatatgtaatgtgcagTGTTTGGGTTGCCCGTAGACCACCTGGTTACGCTTTTCTAGATTTCGAAGATCCTAGGGATGCCCGTGATGCTATCCGTGCTTTAGATG
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