Sequence
atgc intronic sequence ATGC exonic sequence...gtaatgagcaaagtatacaccattaatcatcttcattgtgctgaaaaatacttattccagctagcttacctttctagtacctctggcttatggttttcagGGAGCATGCACCATCAATCATCTTCATGGATGAAATCGATAGTATCGGGTCTGCTCGTATGGAATCTGGTAGTGGAAATGGTGACAGTGAGGTGCAAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G20000.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 5
----gtaatgagcaaagtata-caccattaatcatcttcattgtgctgaaaaatacttattc-cagctagcttacctttctagtacctctggcttatggttttcagGGAGCATGCACCATCAATCATCTTCATGGATGAAATCGATAGTATCGGGTCTGCTCGTATGGAATCTGGTAGTGGAAATGGTGACAGTGAGGTGCAAAGG
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attagttgtttgtgagttgaagcataattttgcatattcat-attctgttattagctttttcattgtgggcttagtttgtta-----tcgggttcacttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT
upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 5
gtaatgagcaaagt-atacaccattaatcatcttcattgtg---ctgaaaaatacttattccagctagcttacctttctagtacctctggcttatggttttcagGGAGCATGCACCATCAATCATCTTCATGGATGAAATCGATAGTATCGGGTCTGCTCGTATGGAATCTGGTAGTGGAAATGGTGACAGTGAGGTGCAAAGG
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ttgcttaactttttgattcattaattttcatgttatttggagacttgcctaaccattattatatatgaat-attattatggaacacttgtcttct---tcccagGGAACATGCTCCATCAATTATCTTCATGGACGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAATGGTGATAGTGAGGTACAGCGT
upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 5
gtaatgagcaaagtatacaccattaatcatcttcattgtgctgaaaaatacttattccagctagcttacctttctagtacctctgg---cttatggttttc--agGGAGCATGCACCATCAATCATCTTCATGGATGAAATCGATAGTATCGGGTCTGCTCGTATGGAATCTGGTAGTGGAAATGGTGACAGTGAGGTGCAAAGG
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-----aactttttgattcattaattttcatgtttatgttatttggagccttgcctaaccattattatatatgaatattatcatggaacacttgtcttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGT
upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 5
gtaatgagcaaagtatacaccattaatcatcttcattgtgctgaaaaatactt-attccagctagcttacctttctagtacctctggcttatggttttcagGGAGCATGCACCATCAATCATCTTCATGGATGAAATCGATAGTATCGGGTCTGCTCGTATGGAATCTGGTAGTGGAAATGGTGACAGTGAGGTGCAAAGG
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gtagagcccatcatcaacaataacaaaaaggaaaaaaaaaatgttgctttctttgttgctgtttgtttaaactt-tactttttgaactatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG
upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------------------------------------------------------gtaatgagcaaagtatacaccattaatcatcttcattgtgctgaaaaatacttattccagctagcttacctttctagtacctctg--gcttatggttttcagGGAGCATGCACCATCAATCATCTTCATGGATGAAATCGATAGTATCGGGTCTGCTCGTATGGAATCTGGTAGTGGAAATGGTGACAGTGAGGTGCAAAGG
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gtttgtttaatatctttagtggaaaccatgacttgtgatacacctagaggatttatttttcactcataagataatattttatatgttacctctcctgggtaattgtttagagtcacatttttttcctgggttattgaattttgttttaaatctcccttttatcttgtccttatggtctcttctctgctgctttattacagGGAGCATGCTCCATCAATCATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGAATGGAATCTGGAACTGGAAATGGTGATAGTGAAGTGCAGCGA
upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S245_17V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaatgagcaaagtatac-accattaatc-atcttcattgtgctgaaaaatacttattccagctagcttacctttctagtacctctggcttatggttttcagGGAGCATGCACCATCAATCATCTTCATGGATGAAATCGATAGTATCGGGTCTGCTCGTATGGAATCTGGTAGTGGAAATGGTGACAGTGAGGTGCAAAGG
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-taagatgtgtttttgattgccatcaacggaacttgtctctacctggaaacttcatgtcaagaacgtataagatgttaacaagttatttttgta-tggttagGGAACATGCACCATCAATCATCTTCATGGATGAAATTGATAGTATTGGATCAGCTCGTGTGGAGTCTGGGAATGGCAATGGAGATAGTGAAGTTCAGCGGMapped 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|125032640|gb|EL104909.1|EL104909EST: GTTCTAGAATGGTCAGAGAACTTTTTGTGATGGCAAG GGAGCATGCACCATCAATCATCTTCATGG
genomic: GTTCTAGAATGGTCAGAGAACTTTTTGTGATGGCAAGgtttgtacat ... tggttttcagGGAGCATGCACCATCAATCATCTTCATGG
EST:
gi|124934033|gb|EL011138.1|EL011138EST: CTTTTTGTGATGGCAAG GGAGCATGCACCATCAATCATCTTCATGGATGAAATCGATAGTATTGGGTC
genomic: CTTTTTGTGATGGCAAGgtttgtacat ... tggttttcagGGAGCATGCACCATCAATCATCTTCATGGATGAAATCGATAGTATCGGGTC
EST:
gi|124847090|gb|EH931527.1|EH931527EST: TACATTGGAGAAGGTTCTAGAATGGTCAGAGAACTTTTTGTGATGGCAAG GGAGCATGACACCATCAATCATCTTCATGGA
genomic: TACATTGGAGAAGGTTCTAGAATGGTCAGAGAACTTTTTGTGATGGCAAGgtttgtacat ... tggttttcagGGAGCATG-CACCATCAATCATCTTCATGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatacttattccagctagcttacctttctagtacctctggcttatggttttcagGGAGCATGCACCATCAATCATCTTCATGGATGAAATCGATAGTATCGGGTCTGCTCGTATGGAATCTGGTAGTGGAAATGGTGACAGTGAGGTGCAAAGG
agcttac putative branch site (score: 3)
ttttc putative PPT
ttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgagcaaagtatacaccattaatcatcttcattgtgctgaaaaatacttattccagctagcttacctttctagtacctctggcttatggttttcagGGAGCATGCACCATCAATCATCTTCATGGATGAAATCGATAGTATCGGGTCTGCTCGTATGGAATCTGGTAGTGGAAATGGTGACAGTGAGGTGCAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - caaagta
- - - - - - - -tacacca
- - - - - - - - - - - - - -catcttc
- - - - - - - - - - - - - - - - - - - - - -aaaaata