Sequence
atgc intronic sequence ATGC exonic sequence...tgttgctttgacaaatcgatatacatttgcttacaggtgatatgaaagatatgataaacttattttcttttaattttttggggacctgtgcactttctagGGTTTTACATTTCCAGTTCGAGCACATTTTCTTGAGGATATTCTGGAAAGGACTGGATATCGGTTGACACCTTCTAATCAAATTGATGACTATGGTCAAG
Basic information
species | Glycine max |
transcript | GLYMA08G05480.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G05480.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 2
tgttgctttgacaaatcgatatacatttgcttac--aggtgatatgaaagatatgataaacttattttcttttaattttttggggacctgtg-cactttctagGGTTTTACATTTCCAGTTCGAGCACATTTTCTTGAGGATATTCTGGAAAGGACTGGATATCGGTTGACACCTTCTAATCAAATTGATGACTATGGTCAAG
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-atcagtagggttattcataagagagatcctaacctagcctagattaaag-catcttat-tttattaggatggccctcattggttgcatacatctcatttcagGGTTTCACTTATCCTGTTCGGAGTCGATTTCTAGAAGATATTCTCGAAATTACTGGGCACAGATTAACTCCTTACAATCAAATTGATGACTATGGTCAAG
upper sequence: GLYMA08G05480.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 8
tgttgctttgacaaatcgatatacatttgcttacaggtgatatgaaagatatgata-aacttattttcttttaattttttggggacctgtgcactttctagGGTTTTACATTTCCAGTTCGAGCACATTTTCTTGAGGATATTCTGGAAAGGACTGGATATCGGTTGACACCTTCTAATCAAATTGATGACTATGGTCAAG
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tgcaataaaatttgtttgaatgtcttgtgctttgctgtagcttcttgtgtaagttatatcttgacgtcctttcataaaaaacggttttat-ctcaacttagGGTTTTACATATCCTGTCCGGAGTCATTTTCTGGAAGATATTCTTGAAATTACTGGGCACTGGTTAACTCCATACAATCAAATTGATGACTATGGTCAAG
upper sequence: GLYMA08G05480.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv17s0000g03030.t01 (Vitis vinifera), 3'ss of exon 7
tgttgctttgacaaatcgatatacatttgcttacaggtgatatga---------aagatatgataaacttattttcttttaattttttggggacctgtgcactttctagGGTTTTACATTTCCAGTTCGAGCACATTTTCTTGAGGATATTCTGGAAAGGACTGGATATCGGTTGACACCTTCTAATCAAATTGATGACTATGGTCAAG
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--tttagtttattattgagtacaaattt-tttatatataacatgttgttcattcatggtgtgatggactaactcttctctctccctctactgttctac------tttagGGGTTTACGTACCCAGTACGAACTCATTTTCTGGAAAATATTCTGGAAATGACTGGATATAGATTGACTCCTTATAATCAAATTGATGATTATGGTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagatatgataaacttattttcttttaattttttggggacctgtgcactttctagGGTTTTACATTTCCAGTTCGAGCACATTTTCTTGAGGATATTCTGGAAAGGACTGGATATCGGTTGACACCTTCTAATCAAATTGATGACTATGGTCAAG
ttttaat putative branch site (score: 3)
cactttct putative PPT
atgataaacttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttgctttgacaaatcgatatacatttgcttacaggtgatatgaaagatatgataaacttattttcttttaattttttggggacctgtgcactttctagGGTTTTACATTTCCAGTTCGAGCACATTTTCTTGAGGATATTCTGGAAAGGACTGGATATCGGTTGACACCTTCTAATCAAATTGATGACTATGGTCAAG
tgttgct
- - - - - - - - - - - - - -tgcttac
- - - - - - - - - - - - - - - - - - -tgatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctgtg