Sequence
atgc intronic sequence ATGC exonic sequence...tgattgggaaatagttttacactattagttagtctactaatgcataaccttttttctctatttctatttgctaattcctagaatcttcatcaacttgcagATATGTGATATGGTTGCAGTGGCAAAAATAATGAATGCCACCCTTGTGCTTCCCTCTCTTGACCATGATTCATTTTGGACTGATCCAAG
Basic information
species | Glycine max |
transcript | GLYMA01G27000.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G27000.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g37880.1 (Oryza sativa), 3'ss of exon 3
tgattgggaaatagttttacactattagttagtctact-aatgcataaccttttttctctatttctatttgctaattcctagaatcttcatcaacttgcagATATGTGATATGGTTGCAGTGGCAAAAATAATGAATGCCACCCTTGTGCTTCCCTCTCTTGACCATGATTCATTTTGGACTGATCCAAG
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----------------gtacgtatctatttaaacggtttaacatgcaacgcttttcagctaaccca------tactccttcgaaatt--att--cttacagATAAGTGATATGGTTGCAGTGGCAAAGATCATGAATGCATCACTAGTAATTCCCACTCTAGATCATCAGTCATTCTGGACTGATCCAAG
upper sequence: GLYMA01G27000.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g01650.t01 (Vitis vinifera), 3'ss of exon 3
--------------tgattgggaaatagttttacactattagttagtctactaatgcataaccttttttctctatttctattt--gctaattcctagaatcttcatcaacttgcagATATGTGATATGGTTGCAGTGGCAAAAATAATGAATGCCACCCTTGTGCTTCCCTCTCTTGACCATGATTCATTTTGGACTGATCCAAG
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gtaagcattcggtgtcaccaactttttagaatgctttattatatggtct-cttccctttattgtttcattcatagtactttttaagctaacctcttgt-tacttattgaaatccagATATGTGATATGGTTGCTGTTGCCAAGATTATGAATGCCACTCTTGTTCTTCCTTCTCTTGATCATGAGTCCTTTTGGACAGACCTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaccttttttctctatttctatttgctaattcctagaatcttcatcaacttgcagATATGTGATATGGTTGCAGTGGCAAAAATAATGAATGCCACCCTTGTGCTTCCCTCTCTTGACCATGATTCATTTTGGACTGATCCAAG
tgctaat putative branch site (score: 2)
tcttcatc putative PPT
tatttctattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgattgggaaatagttttacactattagttagtctactaatgcataaccttttttctctatttctatttgctaattcctagaatcttcatcaacttgcagATATGTGATATGGTTGCAGTGGCAAAAATAATGAATGCCACCCTTGTGCTTCCCTCTCTTGACCATGATTCATTTTGGACTGATCCAAG
- - - - - - - - - - - - - - - - - - - - tgcataa