Sequence
atgc intronic sequence ATGC exonic sequence...catcctagttctcattgttggttatcctagtgccaagttgtagatgtttgtagtgttgtttaattatactttacaatattaattatcaattttcttgcagGATGGAAGAATTAACTATGATGAGTTTGTAGCCATGATGAGGAAAGGCAACCCAGATATAACTCACATAACCCATAGACGTCGCAAATAACCCCTGCATT
Basic information
| species | Glycine max |
| transcript | GLYMA08G02300.1 |
| intron # | 8 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G02300.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g43410.1 (Oryza sativa), 3'ss of exon 7
----------------------------------------------------------------------------------------------catcct--agttctcattgttggttatcctagtgccaagttgtagatgtttgtagtgttgtttaattatactttacaatattaattatcaattttcttgcagGATGGAAGAATTAACTATGATGAGTTTGTAGCCATGATGAGGAAAGGCAACCCAGATATAACTCACA-TAACCCATAGACGTCGCAAATAACCCCTGCATT
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gtaagtatattccgtaacacatcttaaagcaagctctttgataacaaaatgtgcatgtcccaaccatcctacaaggagaatgccaaagatttccaatcctaaagtacctttcttaagtagaatttgagctcaaacacaggc---tgcgaggcccatttattacagtgc-taatttttccattttttgttttcacagGATGGAAGAATTAACTACCAGGAGTTTGTCGCCATGATGAGGAACAACAACCCTGAGATTGCTCCCAACCGGCGGCGCATGTTCTAACTT-CCTTTACAAT
upper sequence: GLYMA08G02300.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g50810.1 (Oryza sativa), 3'ss of exon 7
catcctagttctcattgttggttatcctagtgccaagttgtagatgtttgta---gtgttgtttaattatactttacaatattaattatcaattttct-tgcagGATGGAAGAATTAACTATGATGAGTTTGTAGCCATGATGAGGAAAGGCAACCCAGATATAACTC-ACATAACCCATAGACGTCGCAAATAACCCCTGCATT
| || | ||| | || ||| | | || | || | | || | | | || |||| | | | || || ||||||||||||||||||| | |||||||| |||||||||| ||| || ||| || || || | || | || || || ||| ||
----gaataactgaaaattgctgatgctattattcaaaagtgaacattaaaacgggaactgcatggatttcctactaaatactgtgtcctgacttactgcttagGATGGAAGAATTAACTACCAGGAGTTTGTTGCCATGATGAAGAACAACAGCCCTGAGATTGTTCCAAATCGACGGCGGATGTTTTAAGCCTTTCCTACAG-
upper sequence: GLYMA08G02300.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g50810.2 (Oryza sativa), 3'ss of exon 7
catcctagttctcattgttggttatcctagtgccaagttgtagatgtttgta---gtgttgtttaattatactttacaatattaattatcaattttct-tgcagGATGGAAGAATTAACTATGATGAGTTTGTAGCCATGATGAGGAAAGGCAACCCAGATATAACTC-ACATAACCCATAGACGTCGCAAATAACCCCTGCATT-------
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------------gaaaattgctgatgctattattcaaaagtgaacattaaaacgggaactgcatggatttcctactaaatactgtgtcctgacttactgcttaggatggaagAATTAACTACCAGGAGTTTGTTGCCATGATGAAGAACAACAGCCCTGAGATTGTTCCAAATCGACGGCGGATGTTTTAAGCCTTTCCTACAGTTATTGTG
upper sequence: GLYMA08G02300.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G856738_T01 (Zea mays), 3'ss of exon 6
catcctagttctcattgttggttatcctagtgccaagttgtagatgtttgtagtgttgtttaattatacttta--caatattaattatcaattttcttgcagGATGGAAGAATTAACTATGATGAGTTTGTAGCCATGATGAGGAAAGGCAACCCAGATATAACTC-ACATAACCCATAGACGTCGCAAATAACCCCTGCATT
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-aacataccgattataat-atttttgctggtgcatacataatgatgacttttcttttacaaaaagacatagtaatgagttcccatttctttacatatggcagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAATACCCCTGAGATTGTTCCAAACCGGAGACGCATGTTCTAACTGTCATGTACAA-
upper sequence: GLYMA08G02300.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G025387_T02 (Zea mays), 3'ss of exon 7
---catcctagttctcattgttggttatcctagtgccaagttgtagatgtttgtagtgttgtttaattatactttacaatattaattatcaatt-ttcttgc-agGATGGAAGAATTAACTATGATGAGTTTGTAGCCATGATGAGGAAAGGCAACCCAGATATAACTC-ACATAACCCATAGACGTCGCAAATAACCCCTGCATT
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cacaatctctacaaaccttgt-gatcaacct-gcatcaggaaaagagtgct---aactcaatttatcagagtgctaactttcccgttattttttcttattgccagGATGGAAGAATTAATTACCAGGAGTTTGTTGCCATGATGAGGAACAACAGCCCTGAGATTGTTCCAAATCGGAGGCGCATGTTCTAACTGTCATGGACAA-
upper sequence: GLYMA08G02300.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv02s0025g00690.t01 (Vitis vinifera), 3'ss of exon 7
--catcctagttctcattgttggttatcctagtgccaagttgtagatgtttgtagtgttgtttaattatactttacaatattaattatcaattt-tcttgcagGATGGAAGAATTAACTATGATGAGTTTGTAGCCATGATGAGGAAAGGCAACCCAGATATAACTCACATAACCCATAGACGTCGCAAATAA--CCCCTGCATT----
|| | ||||| | | || || | || | || | | || || | | | | | | | || || | || | ||| ||||||||||||| |||||||| ||||||| ||| |||||||||||||| ||||| ||| | | || || | |||||||| |||| | | |||
ctgatacatgttctgcacgctccttttcgagatataaa--tataaaagatt-tacgataaacagactgttccacaaataatgtgttccctgcttcttttgtagGATGGAAGAATCAACTATGAAGAGTTTGCAGCTATGATGAGGAAAGGAAACCCGGATTTGAT---CACAA---ACAGACGTCGGAAATGAGGTCATCCCATCGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgtagtgttgtttaattatactttacaatattaattatcaattttcttgcagGATGGAAGAATTAACTATGATGAGTTTGTAGCCATGATGAGGAAAGGCAACCCAGATATAACTCACATAACCCATAGACGTCGCAAATAACCCCTGCATT
tattaat putative branch site (score: 2)
ttttcttgc putative PPT
ttgtttaattatactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catcctagttctcattgttggttatcctagtgccaagttgtagatgtttgtagtgttgtttaattatactttacaatattaattatcaattttcttgcagGATGGAAGAATTAACTATGATGAGTTTGTAGCCATGATGAGGAAAGGCAACCCAGATATAACTCACATAACCCATAGACGTCGCAAATAACCCCTGCATT
- - - - - - - - gttggtt
- - - - - - - - - - - - - ctagtgc
- - - - - - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtt
