Sequence
atgc intronic sequence ATGC exonic sequence...tccttcgtaggttgtatgtgaacgtgctgcatttgttgtatctaattttgatcatattttgtcatctcatacttatttagtcaattgtatgaatgtgcagATTCCATTCTTTTTCCTGAAATACCAATCGCACTCCGTTTGTCCAGCCATCTTCTACTTGGTGTGGTGAGGATATATTCTAGGAAGGTGAATTACCTTTT
Basic information
species | Glycine max |
transcript | GLYMA09G38310.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G38310.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g67250.2 (Oryza sativa), 3'ss of exon 1
tccttcgtaggttgtatgtgaacgtgctgcatttgttgtatcta--attttgatcatattttgtcatctcatacttatt--tagtcaattgtatgaatgtgcagATTCCATTCTTTTTCCTGAAATACCAATCGCACTCCGTTTGTCCAGCCATCTTCTACTTGGTGTGGTGAGGATATATTCTAGGAAGGTGAATTACCTTTT
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----atggaaatgttatgttttcctaacagtggtcatatatctgccatatgtctttttttttttcattttgagcttagtattaataatcatttttttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATCTTATGCTTGGTGTGGTCAGGATCTATTCTCGCAAGGTGAACTACCTATT
upper sequence: GLYMA09G38310.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G16270.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------------------------------------------tccttcgtaggttgtatgtgaacgtgctgcatttgttgtat--ctaattttgatcatattttgtcatctcatacttatttagtcaattgtatgaatgtgcagATTCCATTCTTTTTCCTGAAATACCAATCGCACTCCGTTTGTCCAGCCATCTTCTACTTGGTGTGGTGAGGATATATTCTAGGAAGGTGAATTACCTTTT
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gtgagtattttgctaccttttgcttttgtgtacaatacctctgattcaggtctcagttcgttgtgctcactagggttagcagaagctaaagtttccttctttttcagttgttatgtggctaaacaagttcatctaaaatatttcctaatataactaat---ttctttttctgagcagATTCTATTCTCTTTCCGGAAGCTCCGATTGCATTGCGATTGTCTAGTCATCTTCTGCTTGGTGTTGTGCGTATATATTCGAGAAAGGTGAATTACCTCTT
upper sequence: GLYMA09G38310.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0220g00080.t01 (Vitis vinifera), 3'ss of exon 1
----tccttcgtaggttgtatgtgaacgtgctgcatttgttgtatctaattttgatcatattttgtcatctcatacttatttagtcaattgtatgaatgtgcagATTCCATTCTTTTTCCTGAAATACCAATCGCACTCCGTTTGTCCAGCCATCTTCTACTTGGTGTGGTGAGGATATATTCTAGGAAGGTGAATTACCTTTT
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aacttcacttctgctttctttatta-tatatctcattaatttaa---aatgcacttcttactcatctaacatgtaccgttcaatttttttttctttctcaacagATTCAATTCTTTTTCCTGATGTACCAATTGCACTACGTTTGTCCAGCCATCTTCTGCTGGGTGTGGTGAGGATATATTCTAGAAAGGTTAATTACCTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgatcatattttgtcatctcatacttatttagtcaattgtatgaatgtgcagATTCCATTCTTTTTCCTGAAATACCAATCGCACTCCGTTTGTCCAGCCATCTTCTACTTGGTGTGGTGAGGATATATTCTAGGAAGGTGAATTACCTTTT
ttatttagtcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccttcgtaggttgtatgtgaacgtgctgcatttgttgtatctaattttgatcatattttgtcatctcatacttatttagtcaattgtatgaatgtgcagATTCCATTCTTTTTCCTGAAATACCAATCGCACTCCGTTTGTCCAGCCATCTTCTACTTGGTGTGGTGAGGATATATTCTAGGAAGGTGAATTACCTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - tgtatgt
- - - - - - - - - - aacgtgc
- - - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcatac