Sequence
atgc intronic sequence ATGC exonic sequence...tgtgtatccatacaagttttgtgaatttagttatgcaaatattaaatagtttctcttagacctactaattttatgttgaaactttggcatgcattattagGTGGGTGTTATGTTGAAGGAGATTATTTAAGAAATGCATTTAGGTGGAAAGACACAGTTGGACCATGGGAAGAGAGACCAGGACACTATGGAGATGTATG
Basic information
species | Glycine max |
transcript | GLYMA03G00630.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G00630.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g03480.1 (Oryza sativa), 3'ss of exon 5
tgtgtatccatacaagttttgtgaatttagttatgcaaatattaaatagtttctcttagacctactaattttat-gttgaaactttggcatgcattattagGTGGGTGTTATGTTGAAGGAGATTATTTAAGAAATGCATTTAGGTGGAAAGACACAGTTGGACCATGGGAAGAGAGACCAGGACACTATGGAGATGTATG
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---------------gtatttcgaat---gttttccaactggcaatcaatttcggttg--ccctgtaatttaatcgctcgcatt---acat---ttggcagGGGGTTGCTTTGTCGAAGGCAATTGGTTAAAAAATGCATTCAGGTGGAAGGAAACTATTGGTCCATGGGAAGAGAGACCTGGACACTATGGAGATGTCTG
upper sequence: GLYMA03G00630.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os11g03734.1 (Oryza sativa), 3'ss of exon 5
tgtgtatccatacaagttttgtgaatttagttatgcaaatattaaatagtttctcttagacctactaattttat-gttgaaactttggcatgcattattagGTGGGTGTTATGTTGAAGGAGATTATTTAAGAAATGCATTTAGGTGGAAAGACACAGTTGGACCATGGGAAGAGAGACCAGGACACTATGGAGATGTATG
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---------------gtattatgatt---gttttccaactggtaatcaattttggttg--ccctgtaatttaatcgctggcatt---acat---ttggcagGGGGTTGCTTTGTTGAAGGCAATTGGTTAAAAAATGCGTTCAGGTGGAAGGAAACTATTGGTCCATGGGAAGAGAGACCTGGGCACTATGGAGATGTTTG
upper sequence: GLYMA03G00630.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G077299_T03 (Zea mays), 3'ss of exon 6
--------tgtgtatccataca-agttttgtgaatttagttatgcaa-atattaaatagtttctcttagacctactaattttatgttgaaactttggcatgcattat-------tagGTGGGTGTTATGTTGAAGGAGATTATTTAAGAAATGCATTTAGGTGGAAAGACACAGTTGGACCATGGGAAGAGAGACCAGGACACTATGGAGATGTATG
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gtatgctccgtgttttcttatttagaatcaggttcccaatgctaagatgtatatgatatattgcaatatattaatacatttaaggataatggactagattgcatgatgctattgtagGAGGCTGCTTTGTAGAAGGTGGCTGGTTAAGAAATGCCTTTAGGTGGAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTG
upper sequence: GLYMA03G00630.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 8
tgtgtatccatacaagttttgtgaatttagttatgcaaatattaaatagtttctcttagacctactaatttt-atgttgaaactttggcatgcattat-tagGTGGGTGTTATGTTGAAGGAGATTATTTAAGAAATGCATTTAGGTGGAAAGACACAGTTGGACCATGGGAAGAGAGACCAGGACACTATGGAGATGTATG
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catccattcata-atattttctgg-ttccatgacttcttccgaaggctcaggcatttggtcgaattaattcagataatatgttctctatttatattgcatagGTGGCTGTTTCGTTGAAGGTGATTGGTTAAGAAATGCATTTCGCTGGAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagtttctcttagacctactaattttatgttgaaactttggcatgcattattagGTGGGTGTTATGTTGAAGGAGATTATTTAAGAAATGCATTTAGGTGGAAAGACACAGTTGGACCATGGGAAGAGAGACCAGGACACTATGGAGATGTATG
tactaat putative branch site (score: 1)
taattttatgttgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgtatccatacaagttttgtgaatttagttatgcaaatattaaatagtttctcttagacctactaattttatgttgaaactttggcatgcattattagGTGGGTGTTATGTTGAAGGAGATTATTTAAGAAATGCATTTAGGTGGAAAGACACAGTTGGACCATGGGAAGAGAGACCAGGACACTATGGAGATGTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - -ccataca
- - - - - - - - ttttgtg
- - - - - - - - - - - - - - - -tatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttggc