Sequence
atgc intronic sequence ATGC exonic sequence...gtgcataagagttttaagtgtattatgtgaacaaaaaaagtttaatatatgatttgctggtatcaattcatttctgacgctgaggcactgcttatgacagATACGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71220.2 |
intron # | 30 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 30
lower sequence: GLYMA08G13400.1 (Glycine max), 3'ss of exon 33
gtgcataagagttttaagtgtattatgtgaacaaaaaaagtttaat--atatgatttgctggtatcaattcatttctgacgctgaggcactgctta---tgacagATACGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTT
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-----tggattctataatattttttcatatttagttggagcctggtggattttacttgtcatcaggaatgcaatcttcactttgtgcttcttgtcaatttgccagATATGAACGCTTTATGAAGATTATGATTCTAAGTGTTCTAAAGAATACTCATCGTCCTGTTAAATTCTGGTTCATAAAGAACTACCTCTCTCCTCCTTTT
upper sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 30
lower sequence: GLYMA05G30230.1 (Glycine max), 3'ss of exon 31
---gtgcataagagttttaagtgtattatgtgaacaaaaaaagtttaatatatgatttgctggtatcaattcatttctgacgctgaggcactgctta---tgacagATACGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTT
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ggattctataatattttttcatatttagttggagcctgg------tggtattttatttgtaatcagggatgcaatcttcactatgtgcttcttgtcaatttgccagATATGAACGCTTTATGAAGATTATGATTCTAAGTGTTCTAAAGAATACTCATCGTCCAGTTAAATTCTGGTTCATAAAGAACTACCTCTCTCCTCCTTTT
upper sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 30
lower sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 31
gtgcataagagttttaagtgtattatgtgaacaaaaaaagtttaatatatgatttgctggtatcaattcattt-ctgacgctgag-gcactgcttatgacagATACGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTT
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-tttctacagggagggagtctgcgctaattcctgtttatgttttgtttgtt-tgtagtaccagaaattgctctgctaatatttaatggtttgctttctgcagATATGAACGTTTTCTGAAAATCATGATTCTAAGTGTCCTGAAGAACAGCAATCGCCCCGTAAAATTCTGGTTTATAAAGAACTATCTTTCTCCTCAATTT
upper sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 30
lower sequence: EFJ07070 (Selaginella moellendorffii), 3'ss of exon 27
gtgcataagagttttaagtgtattatgtgaacaaaaaaagtttaatatatgatttgctggtatcaattcatttctgacgctgaggcactgcttatgacagATACGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTT
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-----------------------------------------gtaa-gtcttagatgtttgaat-gatccgactttctcacagaaggtttgc-------agATACGAGCGTTTTCTAAAGATTATGATGCTCAGCGTTTTGAAGAATACTAGACGGCCAGTGAAATTTTGGTTTATCAAGAATTATCTTTCTCCACAATTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatgatttgctggtatcaattcatttctgacgctgaggcactgcttatgacagATACGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTT
ttctgac putative branch site (score: 2)
aattcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcataagagttttaagtgtattatgtgaacaaaaaaagtttaatatatgatttgctggtatcaattcatttctgacgctgaggcactgcttatgacagATACGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC