Sequence
atgc intronic sequence ATGC exonic sequencegtcggtatttttttcactcttaatctgttgaaaaggtattttgggtttattgaagggaatcatgttttgatgattttgttgcatgacttcacagTGGGATGATCATCCGGCTATTATGGCTGTTGGTGTTGTTGATGGAACCTCAGAAACTATTTTCCAAACGCTTCTTTCTCTTGGACCCTCAAGATCAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G28320.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G28320.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G069976_T01 (Zea mays), 3'ss of exon 8
gtcggtatttttttcactcttaatctgttgaaaaggtattttgggtttattgaagggaatcatgttttgatgattttgttgcatgacttcacagTGGGATGATCATCCGGCTATTATGGCTGTTGGTGTTGTTGATGGAACCTCAGAAACTATTTTCCAAACGCTTCTTTCTCTTGGACCCTCAAGATCAGA
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----gtatatcttactcacc-aacgtgttgtgcatgcacat-ggatttattgt------taaattcataataattaggttgtttc-ctcagTATTGGGATGATCATCCGGCTATAATGGCAGTTGGTGTGGTTGATGCGAATTCCGAGGCTGTCTTTCAGACTCTAATGTCCCTTGGCCAATCAAGATCTG-
upper sequence: AT2G28320.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G29750.1 (Glycine max), 3'ss of exon 7
gtcggtatttttttcactcttaatctgttgaaaaggtattttgggtttattgaagggaatcatgttttgatgattttgttgcatgacttcacag-
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gttggcagaatttgttttcagtaattattg--------ttttatatttat--gatagaaatatgaattcttgaatatgctcc-tatcttcagAAATGGGATGATCACCCTGCAATAATGGCTGTTGGTGTGGTTGATGGAACTTCAGAAGCCATCTTCCAGACTCTTATGTCGCTTGGTCCTTCAAGATCAG-
upper sequence: AT2G28320.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G40010.1 (Glycine max), 3'ss of exon 7
gtcggtatttttttcactcttaatctgttgaaaaggtattttgggtttattgaagggaatcatgttttgatgattttgttgcatgacttcacag-
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gttggcagaaattgttttcagtaattattg--------ttttatattttataatagaaat-acgaactcttgaatatggtcc-tatcttcagAAATGGGATGATCACCCTGCAATAATGGCTGTTGGTGTGGTTGATGGAACTTCAGAAGCCATCTTCCAGACTCTTATGTCGCTTGGTCCTTCAAGATCAG-
upper sequence: AT2G28320.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv06s0004g02720.t01 (Vitis vinifera), 3'ss of exon 7
gtcggtatttttttcactcttaatctgttgaaaaggtattttgggtttattgaagggaatcatgttttgatgattttgttgcatgacttcacagTGGGATGATCATCCGGCTATTATGGCTGTTGGTGTTGTTGATGGAACCTCAGAAACTATTTTCCAAACGCTTCTTTCTCTTGGACCCTCAAGATCAGA
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gttggtagctttctaattgactgcctgttgttaaaatatgaacatcacattgaa------catgcttt----atctt-----------caacagTGGGATGATCATCCTGCAATAATGGCTGTGGGTGTGGTTGATGGGACTTCAGAGGCCATTTTTCAGACACTTATGTCTCTTGGTCCCTCAAGATCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgggtttattgaagggaatcatgttttgatgattttgttgcatgacttcacagTGGGATGATCATCCGGCTATTATGGCTGTTGGTGTTGTTGATGGAACCTCAGAAACTATTTTCCAAACGCTTCTTTCTCTTGGACCCTCAAGATCAGA
ttttgat putative branch site (score: 4)
tttattgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcggtatttttttcactcttaatctgttgaaaaggtattttgggtttattgaagggaatcatgttttgatgattttgttgcatgacttcacagTGGGATGATCATCCGGCTATTATGGCTGTTGGTGTTGTTGATGGAACCTCAGAAACTATTTTCCAAACGCTTCTTTCTCTTGGACCCTCAAGATCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA