Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttcttgaatgcctccactgatcagattaatcattagcatcctgtacttcaaccaatgacatattatgttaataaattattttctcgatgtaattatatggatgcatggtgcagGGTTTATTGCAATGTATGCTACTCTGGCCAGTAGGGATGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTCACCTTGAAGGTCCAGGTGGACTTTTTGA
Basic information
species | Glycine max |
transcript | GLYMA08G03570.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 9
gtaagtttcttgaatgcctccactgatcagattaatcattagcatcctgtacttcaaccaatgacatattatgttaataaattattttctcgatgtaattatatggatgcatggtgcagGGTTTATTGCAATGTATGCTACTCTGGCCAGTAGGGATGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTCACCTTGAAGGTCCAGGTGGACTTTTTGA
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-------------attcacatattcctcatgtgaatc-----catgatgaatttctaacttttttgtttta-gttatttcattatactgtccttattccttttctatggtaccttgcagGGTTTATTGCAATGTATGCTACTCTTGCAAGCAGAGACGTG-----------------------------------------------------------
upper sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 9
gtaagtttcttgaatgcctccactgatcagattaatcattagcatcctgtacttcaaccaatgacatattatgttaataaattattttctcgatgtaattatatggatgcatggtgcagGGTTTATTGCAATGTATGCTACTCTGGCCAGTAGGGATGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTCACCTTGAAGGTCCAGGTGGACTTTTTGA
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------tttttctgtatttcaa--gcttgaatgcttgattactctgctatctgttctctagt-atgtatt---tcagtctattgcccttaaactgttat-------attcatcttgcagGGTTCATTGCAATGTATGCTACTCTTGCAAGTCGAGATGTG-----------------------------------------------------------
upper sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 9
gtaagtttcttgaatgcctccactgatcagattaatcattagcatcctgtacttcaaccaatgacatattatgttaataaattattttctcgatgtaattatatggatgcatggtgcagGGTTTATTGCAATGTATGCTACTCTGGCCAGTAGGGATGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTCACCTTGAAGGTCCAGGTGGACTTTTTGA
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---------------cttgtcactgacagagctgtccattttctttctcctattta--tgtttctgttctaagtt--tgcattgctctctctacaatctaaattggatttgtggtgcagGGTTTATTGCAATGCATGCTACCCTGGCCAGCCGAGATGTGGACTGTTGCTTGATTCCAGAATCACCCTTTTATCTTGAAGGGCCAGGTGGACTTTTTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catattatgttaataaattattttctcgatgtaattatatggatgcatggtgcagGGTTTATTGCAATGTATGCTACTCTGGCCAGTAGGGATGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTCACCTTGAAGGTCCAGGTGGACTTTTTGA
tgttaat putative branch site (score: 3)
tatgttaataaattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttcttgaatgcctccactgatcagattaatcattagcatcctgtacttcaaccaatgacatattatgttaataaattattttctcgatgtaattatatggatgcatggtgcagGGTTTATTGCAATGTATGCTACTCTGGCCAGTAGGGATGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTCACCTTGAAGGTCCAGGTGGACTTTTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA