Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcaatttttagtctccaacttctacttcagtaaaaccattctgctctcagttttctagtcttattcaagtttttcatataatatactccttatcatgatttcgattaatatacttgagttttctctagGCTACTATTTCGGGTGCCAAATCTATGAAAGGAACTCCCTATTGGATGGCTCCAGAAGTTATTCTTCAAACCGGGCATAGCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G54960.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G39760.1 (Glycine max), 3'ss of exon 6
gtaagtcaatttttagtctccaacttctacttcagtaaaaccattctgctctcagttttctagtcttattcaagtttttcatataatatactccttatcatgatttcgattaatatacttgagttttctctagGCTACTATTTCGGGTGCCAAATCTATGAAAGGAACTCCCTATTGGATGGCTCCAGAAGTTATTCTTCAAACCGGGCATAGCTT
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------------gtaatctcagtcttatatgt-agctctactattgtgtatgtcgcttt--acctttgtgagggctcttctgtttgcacatttgtttaagcagtgccttttcct---------tttaatctagGCAACCATTTCTGGTGCCAAGTCCATGAAGGGTACTCCATATTGGATGGCTCCAGAAGTTATTCTCCAGACTGGGCATAGCTT
upper sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G42340.1 (Glycine max), 3'ss of exon 6
gtaagtcaatttttagtctccaacttctacttcagtaaaaccattctgctctcagttttctagtcttattcaagtttttcatataatatactccttatcatgatttcgattaatatacttgagttttctctagGCTACTATTTCGGGTGCCAAATCTATGAAAGGAACTCCCTATTGGATGGCTCCAGAAGTTATTCTTCAAACCGGGCATAGCTT
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------------gtaatctcagtcttat-ctatagctctactactgtgtatgttgcttg--acctttgtgagggcttttctgtttgcaaatttgtttaagcagtgtttttttttttttttataaataatccagGCAACCATTTCTGGTGCCAAGTCCATGAAAGGTACTCCATATTGGATGGCTCCAGAAGTTATTCTCCAGACTGGGCATTGCTT
upper sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv14s0128g00430.t01 (Vitis vinifera), 3'ss of exon 6
gtaagtcaatttttagtctccaacttctacttcagtaaaaccattctgctctcagttttctagtcttattcaagtttttca-----tataatatactccttatcatgatttcgattaat--atacttgagttttctctagGCTACTATTTCGGGTGCCAAATCTATGAAAGGAACTCCCTATTGGATGGCTCCAGAAGTTATTCTTCAAACCGGGCATAGCTT
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----------------------------------gtacacactatctgctctgtgtttattcat-ttattcagttgacttaatttttgtgat-tacttttgctcaaaatctcgtctgattgagacattggttgcca-tagGCTACCATTTCAGGTGCCAAGTCCATGAAAGGCACCCCGTATTGGATGGCTCCGGAAGTCATTCTCCAGACAGGCCATAGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatataatatactccttatcatgatttcgattaatatacttgagttttctctagGCTACTATTTCGGGTGCCAAATCTATGAAAGGAACTCCCTATTGGATGGCTCCAGAAGTTATTCTTCAAACCGGGCATAGCTT
gattaat putative branch site (score: 3)
ttttctct putative PPT
atttcgattaatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcaatttttagtctccaacttctacttcagtaaaaccattctgctctcagttttctagtcttattcaagtttttcatataatatactccttatcatgatttcgattaatatacttgagttttctctagGCTACTATTTCGGGTGCCAAATCTATGAAAGGAACTCCCTATTGGATGGCTCCAGAAGTTATTCTTCAAACCGGGCATAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT