Sequence
atgc intronic sequence ATGC exonic sequencegtaaataccatagaatggtactgtattgaacaacgcctttgggaatcttgtcaatgtataaacaaatgattgaggggaaaaccctccaagcttggtgtttttgcttgtttctcaagtaataacttatgcatcatgtatcacaaatcaataatatggcctatacttttactaactgttgttcaacagGAAAGAAAATCAAGGTGATGAGGCGGCAGACAACATTTGTTTTCCATCACACTTCTCATCCATGGAGCAGGAGTCCAATCCTAAACTGGATG
Basic information
species | Glycine max |
transcript | GLYMA12G29080.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G29080.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g07912.1 (Oryza sativa), 3'ss of exon 5
gtaaataccatagaatggtactgtattgaacaacgcctttgggaatcttgtcaatgtataaacaaatgattgaggggaaaaccctccaagcttggtgtttttgcttgtttctcaagtaataacttatgcatcatgtatcacaaatcaataatatggcctatacttttacta-actgttgttcaacagGAAAGAAAATCAAGGTGATGAGGCGGCAGACAACATTTGTTTTCCATCACACTTCTCATCCATGGAGCAGGAGTCCAATCCTAAACTGGATG
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------------------------------------------------------------------------------------------------------gttaggccgtcaattaa-accatatgcttgcattagcttggtacagttagtttgctc-tacctgaataacgttcatatctctcagCTAGGAGAACTAAGGTGATGCAGAGGCAGTCTACCTTTGTGTTCCATCACACATCTCATCCATGGAGCAAAAATAAAATACTTATTTGGATG
upper sequence: GLYMA12G29080.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G11000.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaaataccatagaatggtactgtattgaacaacgcctttgggaatcttgtcaatgtataaacaaatgattgaggggaaaaccctccaagcttggtgtttttgcttgtttctcaagtaataacttatgcatcatgtatcacaaatcaataatatggcctatacttttactaactgttgttcaacagGAAAGAAAATCAAGGTGATGAGGCGGCAGACAACATTTGTTTTCCATCACACTTCTCATCCATGGAGCAGGAGTCCAATCCTAAACTGGATG
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-------------------------------------------------------------------------------------tttatcacaaacagctgattcattgttaaagatacttaatgcctaggatgctttagtttccagtcatatataccctagtcttcttgact-ttgttcaacagCAAAGAAGACCAAGGTGATGAAGCGTCAGTCTACATTTGTTTTCCATCATGCCTCTCATCCTTGGAGTAACAATCGTTTTCTCATTTGGATG
upper sequence: GLYMA12G29080.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0035g00260.t01 (Vitis vinifera), 3'ss of exon 5
gtaaataccatagaatggtactgtattgaacaacgcctttgggaatcttgtcaatgtataaacaaatgattgaggggaaaaccctccaagcttggtgtttttgcttgtttctcaagtaataacttatgcatcatgtatcacaaatcaataatatggcctatacttttactaactgttgttcaacagGAAAGAAAATCAAGGTGATGAGGCGGCAGACAACATTTGTTTTCCATCACACTTCTCATCCATGGAGCAGGAGTCCAATCCTAAACTGGATG
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---------------------------------------------------------------------------------ggatttatgtttgtagca--taattggttttcaa-taactttctctacttc-tctctaatttgttcatgatattagcttctccaataccggtt-ttattttgtagCAAAGGTAAACAAAGAGATGAGGAGACAATCCACCTTTGTTTTCCATCACACATCACACCCATGGAGCAGGAGCCGCATTCTCATTTGGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgtatcacaaatcaataatatggcctatacttttactaactgttgttcaacagGAAAGAAAATCAAGGTGATGAGGCGGCAGACAACATTTGTTTTCCATCACACTTCTCATCCATGGAGCAGGAGTCCAATCCTAAACTGGATG
tactaac putative branch site (score: 0)
acaaatcaataatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaataccatagaatggtactgtattgaacaacgcctttgggaatcttgtcaatgtataaacaaatgattgaggggaaaaccctccaagcttggtgtttttgcttgtttctcaagtaataacttatgcatcatgtatcacaaatcaataatatggcctatacttttactaactgttgttcaacagGAAAGAAAATCAAGGTGATGAGGCGGCAGACAACATTTGTTTTCCATCACACTTCTCATCCATGGAGCAGGAGTCCAATCCTAAACTGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG