Sequence
atgc intronic sequence ATGC exonic sequence...ctaccaatgcagtgaaaatgctgtttgtatttagtgatatttattcattatatagattaagctaactgtggctaattgttttggacttgtcatttgctagACCTGCTTAACAATATGTGAGGGGCATGATGGGACTGAAACATCAAATGGAGATGTATTAATTTTTCCAGACATGATCAGATATAG
Basic information
species | Glycine max |
transcript | GLYMA08G44420.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G44420.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G020775_T01 (Zea mays), 3'ss of exon 1
ctaccaatgcagtgaaaatgctgtttgtatttagtgatatttattcatt-atatagattaagctaactgtggctaattgtt--ttggacttgtcatttgctagACCTGCTTAACAATATGTGAGGGGCATGATGGGACTGAAACATCAAATGGAGATGTATTAATTTTTCCAGACATGATCAGATATAG
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--agaaatgcttccgaaaaaggttgtaagtttggtagtatttgctgattcatctttcttccacata-tatatccaatggctgctatgttttaccatgtcacagATCAAATTGACCATCTGTGAAGGAGAAGATGGCACTGAATCATCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATATAA
upper sequence: GLYMA08G44420.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G000280_T01 (Zea mays), 3'ss of exon 1
ctaccaatgcagtgaaaatgctgtttgtatttagtgatatttattcattatatagattaagctaactg--tggctaat-tgttttggact-tgtcatttgctagACCTGCTTAACAATATGTGAGGGGCATGATGGGACTGAAACATCAAATGGAGATGTATTAATTTTTCCAGACATGATCAGATATAG
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----atatgctttcgaaaaagattgtaagctcgacagtttttttttctaattcatttttctttacatacatatccaatgcctgctatattctaccgtgtcacagATCAAATTCACCATCTGTGAAGGAGAAGATGGCACTGAATCATCAAATGGAGATGTGTTGATCTTTCCAGATATGATCAGATACAA
upper sequence: GLYMA08G44420.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G55900.1 (Arabidopsis thaliana), 3'ss of exon 1
ctaccaatgcag--tgaaaatgctgtttgtatttagtgatatttattcattatatagattaagctaactgtggctaattgttt-tggacttgtcatttgctagACCTGCTTAACAATATGTGAGGGGCATGATGGGACTGAAACATCAAATGGAGATGTATTAATTTTTCCAGACATGATCAGATATAG
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---acaatgtagcttcttattatcttgcacatcagttataaactatcttttgggtcttttagatgtctttctgatgtttttttatctatgcgttgaattgcagACTTTACTCACAATATGTGAGGGACATGATGGTTCAGAGACATCAAATGGGGATGTTCTGATATTTCCAGATATGATCAGATACAG
upper sequence: GLYMA08G44420.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G26620.1 (Arabidopsis thaliana), 3'ss of exon 1
---ctaccaatgcagtgaaaatgctgtttgtatttagtgatatttattcattatatagattaagctaactgtggctaattgttttggacttgtcatttgctagACCTGCTTAACAATATGTGAGGGGCATGATGGGACTGAAACATCAAATGGAGATGTATTAATTTTTCCAGACATGATCAGATATAG
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ggattgcttcttttcggatagtctcatgatgatgccttcatgattgtcttttgctttg--tgcctcatgtttttttttttttttttggcc-attgtttcgtagACTCGACTCACAATATGTGAGGGGCATGATGGAACAGAGACATCCAATGGTGATGTACTTATTTTTCCTGATATGATCAGATACAG
upper sequence: GLYMA08G44420.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0015g00750.t01 (Vitis vinifera), 3'ss of exon 1
ctaccaatgcagtgaaaatgctg--tttgtatttagtgatatttattcattatatagattaag--ctaactgtgg---ctaattgttttggacttgtcatttgctagACCTGCTTAACAATATGTGAGGGGCATGATGGGACTGAAACATCAAATGGAGATGTATTAATTTTTCCAGACATGATCAGATATAG
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------attcatgaatattgccagatctgcagtttatttttccttcctgttgtagtgactgagggttaatggtatgattttgccgttttctatttttc-ttctcaagACCCGCTTAACAATATGTGAAGGACATGATGGAACTGAGACATCAAATGGAGATGTATTAATATTTCCAGACATGATCAGATACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattatatagattaagctaactgtggctaattgttttggacttgtcatttgctagACCTGCTTAACAATATGTGAGGGGCATGATGGGACTGAAACATCAAATGGAGATGTATTAATTTTTCCAGACATGATCAGATATAG
tatagattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaccaatgcagtgaaaatgctgtttgtatttagtgatatttattcattatatagattaagctaactgtggctaattgttttggacttgtcatttgctagACCTGCTTAACAATATGTGAGGGGCATGATGGGACTGAAACATCAAATGGAGATGTATTAATTTTTCCAGACATGATCAGATATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
ctaccaa
- - - -tgcagtg
- - - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggcta