Sequence
atgc intronic sequence ATGC exonic sequencegtaaatacttggaacctattccatcctaagtgaatgatttgcctatgatatttcctttttggtctaaccttgagattgtttgttacaaatatttgcagATAGTGGTGCTGATATACACGTGATAGTGAAAATTGAGAGTGCAGACTCCATACCTAACTTGCACTCCATTATCACAGCATCAGATGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G52920.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 5
gtaaatacttggaacctattccatcctaagtgaatgatttgcctatgatatttcctttttggtctaaccttgagattgtttgttacaaatatttgcagATAGTGGTGCTGATATACACGTGATAGTGAAAATTGAGAGTGCAGACTCCATACCTAACTTGCACTCCATTATCACAGCATCAGATGGG
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--------gtaatcttcaacccaacttt-gtaaaaaatcatatcatgcacctttttttacaattta---ctgagctcattctattc---tattctcagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCATCCCCAACTTACATTCAATCATCACAGCATCTGATGGG
upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 5
gtaaatacttggaacctattccatcctaagtgaatgatttgcctatgatatttcctttttggtctaaccttgagattgtttgtt-acaaatatttgcagATAGTGGTGCTGATATACACGTGATAGTGAAAATTGAGAGTGCAGACTCCATACCTAACTTGCACTCCATTATCACAGCATCAGATGGG
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gtaaatattcaagatac-ttgtattttttttaattagtccatctgattaatttctctaattatttcaaaatgtgataaattgtccactcaacgctgcagGCTGTGATGCTGATATACACGTCATTGTAAAAATTGAAAGTGCAGACTCTATACCAAACTTGCATTCAATTATTACAGCGTCTGATGGG
upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 5
gtaaatacttggaacctatt----ccatcctaagtgaatgatttgccta-tgatatttcctttttggtctaaccttgagattg-tttgttacaaatatttgcagATAGTGGTGCTGATATACACGTGATAGTGAAAATTGAGAGTGCAGACTCCATACCTAACTTGCACTCCATTATCACAGCATCAGATGGG
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gtaaatatctaaaatattttaaaaatactttttaaaatttatccgattagttttgctgcatatttagattataaatatgataaattttccacttgatactgcagGCTGCGGTGCTGATATACATGTCATCGTAAAAATTGAAAGTGCAGACTCTATACCAAATTTGCATTCAATTATCACTGCATCTGATGGG
upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 5
gtaaatacttggaacctattccatcctaagtgaatgatttgcctatgatatttcctttttggtctaaccttgagattgtttgtt-acaaatatttgcagATAGTGGTGCTGATATACACGTGATAGTGAAAATTGAGAGTGCAGACTCCATACCTAACTTGCACTCCATTATCACAGCATCAGATGGG
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gtaaattttcaagatacttgtaatttttt-taattagttcgtctgattaatttctctaattattttaaagtatgataaattgtccactcaacactgcagGCTGTGATGCTGATATACATGTCATTGTAAAAATTGAAAGTGCAGACTCTATACCAAACTTGCATTCAATTATTACAGCGTCTGATGGG
upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 5
gtaaatacttggaacctattccatcctaagtgaatgatttgcctatgatatttcctttttggtctaaccttgagattgtt---tgttacaaatatt--tgcagATAGTGGTGCTGATATACACGTGATAGTGAAAATTGAGAGTGCAGACTCCATACCTAACTTGCACTCCATTATCACAGCATCAGATGGG
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gtaaatatctaaaatattttaaaaatactttttaacatttatccaattagtttgctgcatatattgattataaatatgataaattttccatttggtactgcagGCTGTGGTGCTGATATACATGTCATCGTAAAAATCGAAAGTGCAGACTCTATACCAAATTTGCATTCAATTATCACTGCGTCTGATGGGMapped 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|116479876|gb|EG522468.1|EG522468EST: CTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAAATACCTTCAAA ATAGTGGTGCTGATATACACGTGATAGTGAAAATTGAGAGTGCAGACTCCA
genomic: CTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAAATACCTTCAAAgtaaatactt ... atatttgcagATAGTGGTGCTGATATACACGTGATAGTGAAAATTGAGAGTGCAGACTCCA
EST:
gi|86057128|gb|DR352885.1|DR352885EST: CTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAAATACCTTCAAA ATAGTGGTGCTGA
genomic: CTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAAATACCTTCAAAgtaaatactt ... atatttgcagATAGTGGTGCTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgatatttcctttttggtctaaccttgagattgtttgttacaaatatttgcagATAGTGGTGCTGATATACACGTGATAGTGAAAATTGAGAGTGCAGACTCCATACCTAACTTGCACTCCATTATCACAGCATCAGATGGG
gtctaac putative branch site (score: 2)
tttgttacaaatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatacttggaacctattccatcctaagtgaatgatttgcctatgatatttcctttttggtctaaccttgagattgtttgttacaaatatttgcagATAGTGGTGCTGATATACACGTGATAGTGAAAATTGAGAGTGCAGACTCCATACCTAACTTGCACTCCATTATCACAGCATCAGATGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG