Sequence
atgc intronic sequence ATGC exonic sequence...acctaacgaattgtatctaacttttgtctttatattttttctattttattggggcattcatttcaagaataaacatctatattttggtattaattcttagGCTGCTGGAATTCATGACTTGCCTGGACTTCCTGCTGGAGTGAAGTTTGATCCTACTGATCAGGAGATTCTTGAACATTTGGAAGCGAAGGTGCGCTCTG
Basic information
species | Glycine max |
transcript | GLYMA13G36980.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G36980.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g48850.1 (Oryza sativa), 3'ss of exon 1
---------------------------------------------------------------------------acctaacgaattgtatctaacttttgtctttatattttttctattttattggggcattcatttcaagaataaacatctatatt--ttggtattaattctt-----agGCTGCTGGAATTCATGACTTGCCTGGACTTCCTGCTGGAGTGAAGTTTGATCCTACTGATCAGGAGATTCTTGAACATTTGGAAGCGAAGGTGCGCTCTG
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gtatatatactgcgtgatcaagatcatgccttcttcttcttctttttttctgaatgcaacagccaacagctataaattcagcaagtgataactgatcatatatactgcgtagta-ctacattaattcttcttttggttgagatgcaaatcaacaaattaattaagatgaattattgcagGAGACGACGACGATCCAGGACCTGCCGGGGCTGCCGGCCGGAGTGAAGTTCGATCCGACGGACCAGGAGCTTCTTGAGCATTTGGAAGGGAAGGCGAGGC---
upper sequence: GLYMA13G36980.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G28500.1 (Arabidopsis thaliana), 3'ss of exon 1
acctaacgaattgtatctaacttttgtctttatattttttctattttattggggcattcatttcaagaataaacatctatattttg-gtattaattcttagGCT--GCTGGAATTCATGACTTGCCTGGACTTCCTGCTGGAGTGAAGTTTGATCCTACTGATCAGGAGATTCTTGAACATTTGGAAGCGAAGGTGCGCTCTG---
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-------------------gttcttgtttctct-ttctacctatatcaagtttaaactttagatgatattggatatttgaatataatatattaatatgtaatgtagGCTGGGATCCATGACTTGCCGGGACTTCCTGCTGGAGTAAAATTTGATCCGACGGATCAAGAGGTCTTGGAGCATCTTGAAGGCAAGGTAAGAGATGACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattggggcattcatttcaagaataaacatctatattttggtattaattcttagGCTGCTGGAATTCATGACTTGCCTGGACTTCCTGCTGGAGTGAAGTTTGATCCTACTGATCAGGAGATTCTTGAACATTTGGAAGCGAAGGTGCGCTCTG
tattaat putative branch site (score: 2)
ttctt CT-rich tract
aataaacatctatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acctaacgaattgtatctaacttttgtctttatattttttctattttattggggcattcatttcaagaataaacatctatattttggtattaattcttagGCTGCTGGAATTCATGACTTGCCTGGACTTCCTGCTGGAGTGAAGTTTGATCCTACTGATCAGGAGATTCTTGAACATTTGGAAGCGAAGGTGCGCTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - -attgggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaataaac