Sequence
atgc intronic sequence ATGC exonic sequence...cgttacatggtgaaacactgtataccttgtcatgtcaaactatttgtaattatcatgtctgtcctcacggtctgctcattgaattcaacaatctttccagATCAAGGACTGCCGGACACGTTACAACGGTGATGCTGACCATCATCAGCGACGTAAAAAGTTTACATTTCCTGCTCGCCTTATATGTGGAGATTGTTATG
Basic information
species | Glycine max |
transcript | GLYMA06G41190.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G41190.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G20650.2 (Arabidopsis thaliana), 3'ss of exon 4
---cgttacatggtgaaacactgtataccttgtcatgtcaaac-tatttgtaattatcatgtctgtcctcacggtctgctcattgaattcaacaatctttccagATCAAGGACTGCCGGACACGTTACAACGGTGATGCTGACCATCATCAGCGACGTAAAAAGTTTACATTTCCTGCTCGCCTTATATGTGGAGATTGTTATG
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gtaagtttactggctgaatgatagctgtatctttattttgcatatatgttttatctctatacctgag--aagtgcttctatgttgtacttaataa------cagATTGAAGATTGTCGCACGCGTTATAACGGTGATGCAGACCATCATCAACGGCGTAAAAAGTTCAGTTTTCCGTCTCGATTATTATGTGGGGATTGTTTTG
upper sequence: GLYMA06G41190.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g02860.t01 (Vitis vinifera), 3'ss of exon 2
-------------------cgttacatggtgaaacactgtat---accttg-tcatgtcaaactatttgtaattatcatgtctgtcct--cacggtctgctcattgaatt--caacaatctttcca-------gATCAAGGACTGCCGGACACGTTACAACGGTGATGCTGACCATCATCAGCGACGTAAAAAGTTTACATTTCCTGCTCGCCTTATATGTGGAGATTGTTATG--
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gtgtcctcattcagctttatgctctccgaggggatgctgttcttgattttgctcgtggcaagggtggtgatctaatcaaataggacaaggcaaagattggatactatgttggcaccaatattgctgaaggcttgatagaagACTGTTGTACACGCTATAATGGTGACATAGACCATCATCAAAGGCGCAAAAAGTTCACATTTCCGGCTCGCCTTATATGTGGAGATTATTTTGAG
upper sequence: GLYMA06G41190.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0014g04740.t01 (Vitis vinifera), 3'ss of exon 4
cgttacatggtgaaacactgtataccttgtcatgtcaaac-tatttgtaattatcatgtctgtcctcacggtct-gc---tcattgaattcaacaatctt-tccagATCAAGGACTGCCGGACACGTTACAACGGTGATGCTGACCATCATCAGCGACGTAAAAAGTTTACATTTCCTGCTCGCCTTATATGTGGAGATTGTTATG
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--aggcatggcaaga-attttgaatttttt--tctcaattgtctctgctgttg-catgtttgctgttataaacttgcctatcattgtgtttggcaactatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGGCGCAAAAAGTTCACATTTCCGGCTCGCCTTATATGTGGAGATTGTTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaattatcatgtctgtcctcacggtctgctcattgaattcaacaatctttccagATCAAGGACTGCCGGACACGTTACAACGGTGATGCTGACCATCATCAGCGACGTAAAAAGTTTACATTTCCTGCTCGCCTTATATGTGGAGATTGTTATG
tcctcac putative branch site (score: 2)
tctttcc putative PPT
attgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgttacatggtgaaacactgtataccttgtcatgtcaaactatttgtaattatcatgtctgtcctcacggtctgctcattgaattcaacaatctttccagATCAAGGACTGCCGGACACGTTACAACGGTGATGCTGACCATCATCAGCGACGTAAAAAGTTTACATTTCCTGCTCGCCTTATATGTGGAGATTGTTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - -catggtg
- - - - - - - -cactgta
- - - - - - - - - - - taccttg
- - - - - - - - - - - - - - -tcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaattc