Sequence
atgc intronic sequence ATGC exonic sequence...tacatctcttttgggagtaatggatatttgttctttatctgggttttgcctacaaatacttgcattttgaaattcactgatattttatacctgggagcagGATACTCACCTTTTACTTACTGGGGGAGTTGAGAAAATTCTCCGAATCTATGATATGAATCGGCCTGATGCACCACCCAGAGAAGTGGATAAATCTCCTG
Basic information
species | Glycine max |
transcript | GLYMA17G12770.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G12770.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g11060.1 (Oryza sativa), 3'ss of exon 3
tacatctcttttgggagtaatggatatttgttctttatctgggttttgcctacaaatacttgcattttgaaa-----ttcactgatattttatacctgggagcagGATACTCACCTTTTACTTACTGGGGGAGTTGAGAAAATTCTCCGAATCTATGATATGAATCGGCCTGATGCACCACCCAGAGAAGTGGATAAATCTCCTG
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-aca-ctgtttgttgcctattttgtcattaatttccactttg--ctggtcaaagttttctttcattcatagagaagcctgattaaaatgcta-atgttctttcagGACACCCACCTGTTACTTACTGGAGGTCTTGAGAAAATTTTACGTATATATGATATGAATCGCCCAGATGCAGCCCCAAGAGAGATTGACAAATCTCCTG
upper sequence: GLYMA17G12770.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0016g04710.t01 (Vitis vinifera), 3'ss of exon 3
--------tacatctcttttgggagtaatggatatttgttctttatctgggttttgcctacaaatacttgcattttgaaattcactgatattttata-cctgggagcagGATACTCACCTTTTACTTACTGGGGGAGTTGAGAAAATTCTCCGAATCTATGATATGAATCGGCCTGATGCACCACCCAGAGAAGTGGATAAATCTCCTG
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tctttcctcattacactttaaaaggaaaaaaaaaaaaattccttttcctcattattgct-----tatttgtgct----aatggaccaatttttattaatctggatacagGATACACACTCTCTGCTTACTGGAGGAGTTGAGAAAATTCTTCGTATATTTGACTTGAATCGCCCAGATGCACCTCCTAGAGAAGTGGATAATTCTCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcctacaaatacttgcattttgaaattcactgatattttatacctgggagcagGATACTCACCTTTTACTTACTGGGGGAGTTGAGAAAATTCTCCGAATCTATGATATGAATCGGCCTGATGCACCACCCAGAGAAGTGGATAAATCTCCTG
cactgat putative branch site (score: 3)
actgatattttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacatctcttttgggagtaatggatatttgttctttatctgggttttgcctacaaatacttgcattttgaaattcactgatattttatacctgggagcagGATACTCACCTTTTACTTACTGGGGGAGTTGAGAAAATTCTCCGAATCTATGATATGAATCGGCCTGATGCACCACCCAGAGAAGTGGATAAATCTCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA