Sequence
atgc intronic sequence ATGC exonic sequencegtttggtttattatctttcccaccaatgtttttatgttgattctgtgttaaaatcttttactcacaatcagatgttttctctctcgaatttgggttaaggcatcatgattaatgagtgctggttccatactttgtgcttaaagccggattttgtttttgttacagTGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G09090.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g61050.1 (Oryza sativa), 3'ss of exon 2
gtttggtttattatctttcccaccaatgtttttatgttgattctgtgttaaaatcttttactcacaatcagatgttttctctctcgaatttgggttaaggcatcatgattaatgagtgctggttccatactttgtgcttaaagccggattttgtttttgttacagTGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAG
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-----------------------------------------------------ttggatttttaaacgtggatgacttttttctagttattgtcttaa--tttcttctttagtctgctctggg--cacactttaatgataa--------tcttttggtgtattagCGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGTTCTTGAAGGCTCTGATGGGGACAAATTGCCAG
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G14690.1 (Glycine max), 3'ss of exon 2
gtttggtttattatctttcccaccaatgtttttatgttgattctgtgttaaaatcttttactcacaatcagatgttttctctctcgaatttgggttaaggcatcatgattaatgagtgctggttccatact--ttgtgcttaaagccggattttgtttttgttacagTGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAG
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----------------------------------------------------------------------------------gtattgtttgtgctttg-ctttttgagtgatttgtgtttgtgtgattttcattttgttgaatgtctgcctttttgttt--tgcagTGATGGGAAGCTTGAGATTGTGGTTCCGTCTTTTGTTCACTACCTTGAGGTTCTAGAAGGTGCTGATGGGGACAAAATGCCAG
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G27250.1 (Glycine max), 3'ss of exon 2
gtttggtttattatctttcccaccaatgtttttatgttgattctgtgttaaaatcttttactcacaatcagatgttttctctctcgaatttgggttaaggcatcatgattaatgagtgctggttccatactttgtgcttaaagccggattttgtttttgttacagTGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAG
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------------------------------------------------------------------gtaagttgtttatgtgctttgcttt---ttgag------tgatttgtgtttgtgtaattttcattttgt--tgaatgtctgcctttttgttt--tgcagTGATGGGAAGCTTGAGATTGTGGTTCCGTCTTTTGTTCACTACCTTGAGGTTCTAGAAGGTGCTGATGGGGACAAAATGCCAG
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g01790.t01 (Vitis vinifera), 3'ss of exon 2
gtttggtttattatctttcccaccaatgtttttatgttgattctgtgttaaaatcttttactcacaatcagatgttttctctctcgaatttgggttaaggcatcatgattaatgagtgctggttccatactttgtgcttaaagccggattttgtttt-tgttacagTGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAG
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-------------------------------gtgagaaaaatcccccttgttactattatctaactatgag------cttcccttgatcattgatt----catttggcataggatcttatattcttagattttg-atatggggcctttctatgttttgtttctcagTGATGGAAAGCTTGATATAGTGGTTCCTTCTTTTGTTCATTATCTGGAGGTCTTAGAAGGTTCTGATGGAGATAAAATGCCTG
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S334_25V6.1 (Physcomitrella patens), 3'ss of exon 2
gtttggtttattatctttcccaccaatgtttttatgttgattctgtgttaaaatcttttactcacaatcagatgttttctctctcgaatttgggttaaggcatcatgattaatgagtgctggttccatactttgtgcttaaagccggattttgtttttgttacagTGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAG
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--------------------------------------------------ataccttgctcccatcttgcgccatctactccctcgcccccaaataaaacca--attcttcaaaaaagctgactac-tgcattttgtcgaacgc------------ttattgcagAGATGGCAAACTGGAAATTGTTGTTCCTTCCTTTGTACATTACCTGGAAGTTTTAGAAGGCTCTGATGGAGAAAAGCTGCCAG
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ25263 (Selaginella moellendorffii), 3'ss of exon 2
gtttggtttattatctttcccaccaatgtttttatgttgattctgtgttaaaatcttttactcacaatcagatgttttctctctcgaatttgggttaaggcatcatgattaatgagtgctggttccatactttgtgcttaaagccggattttgtttttgttacagTGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAG
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--------------------------------------------------------------------------------------------------------gtgagta-tccttgtttctttctcttgatgcgaagaaaaatgtggattgatttgatacaagGGATGGGAAACTGGACATTGTTGTGCCGTCTTTCGTTCACTACCTCGATGTTCTTGAAGGAGCAGATGGTGAAAAAATGCAAG
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ23254 (Selaginella moellendorffii), 3'ss of exon 2
gtttggtttattatctttcccaccaatgtttttatgttgattctgtgttaaaatcttttactcacaatcagatgttttctctctcgaatttgggttaaggcatcatgattaatgagtgctggttccatactttgtgcttaaagccggattttgtttttgttacagTGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAG
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--------------------------------------------------------------------------------------------------------gtgagta-tccttgtttctttctcttgatgcgaagaaaactgtggattgatttgatacaagGGATGGGAAACTGGACATTGTTGTGCCGTCTTTCGTTCACTACCTCGATGTTCTTGAAGGAGCAGATGGGGAAAAAATGCAAGMapped 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|152035986|gb|AU236941.2|AU236941EST: GAAGTCACTTCTAGCGTTTATGCTACACCCTTGATTGCTGATATTAACAG TGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGT
genomic: GAAGTCACTTCTAGCGTTTATGCTACACCCTTGATTGCTGATATTAACAGgtttggttta ... tttgttacagTGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgagtgctggttccatactttgtgcttaaagccggattttgtttttgttacagTGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAG
gattaat putative branch site (score: 3)
ttttgttttt putative PPT
attttgtttttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggtttattatctttcccaccaatgtttttatgttgattctgtgttaaaatcttttactcacaatcagatgttttctctctcgaatttgggttaaggcatcatgattaatgagtgctggttccatactttgtgcttaaagccggattttgtttttgttacagTGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG