Sequence
atgc intronic sequence ATGC exonic sequence...taacactttcttaagtcttgttcatgtcatgggatcatcttgttgaataagtgctgtgagtttttattcattaatattggcttgtttgaaatattcacagAGCTCAGTGTTAGCACTGGAGGAGTCAGCACTCGACACTGATCAGGTTGAGAACCTCATAAAGTTTTGTCCTACAAAAGAGGAGATGGAATTACTTAAG
Basic information
species | Glycine max |
transcript | GLYMA17G08230.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G08230.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G58160.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------taacactttcttaagtcttgttcatgtcatgggatcatcttgttgaataagtgctgtgagtttttat-----------tcattaata--ttggcttgtttgaaatattcacagAGCTCAGTGTTAGCACTGGAGGAGTCAGCACTCGACACTGATCAGGTTGAGAACCTCATAAAGTTTTGTCCTACAAAAGAGGAGATGGAATTACTTAAG
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gtaatataaagctagacaggtttaggttgtactgtaatcatagctttttaatctggtacaatgtctatgtgtcgctatgtctgccatgataattaaaagctaagtgtctctaaaatatt-acagAACTCAGTGCTTAACCTGGAGGAGTCGGCTCTTGATGCTGATCAGGTTGAGAACCTAATTAAGTTTTGCCCAACAAGAGAAGAGATGGAGTTACTAAAG
upper sequence: GLYMA17G08230.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g00160.t01 (Vitis vinifera), 3'ss of exon 6
-taacactttcttaagtcttgttcatgtcatgggatcatcttgttgaataagtgctgtgagtttttattcattaatattggcttgtttg--aaatattcacagAGCTCAGTGTTAGCACTGGAGGAGTCAGCACTCGACACTGATCAGGTTGAGAACCTCATAAAGTTTTGTCCTACAAAAGAGGAGATGGAATTACTTAAG
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tttgtagatg-tcagcttttaattgtcagacacatccgtcaagtagca-agattttgtgaccaattgtcc-ttaacaatcataaatttgtggaacatgaacagAATTCAGTGCTTGCTTTAGAGGATTCAGCTTTAGATGTTGATCAGGTTGATAACCTCATAAAGTTTTGTCCAACAAAAGACGAGATCGAGCTACTTAAG
upper sequence: GLYMA17G08230.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ14916 (Selaginella moellendorffii), 3'ss of exon 3
taacactttcttaagtcttgttcatgtcatgggatcatcttgttgaataagtgctgtgagtttttattcattaatattggcttgtttgaaatattcacagAGCTCAGTGTTAGCACTGGAGGAGTCAGCACTCGACACTGATCAGGTTGAGAACCTCATAAAGTTTTGTCCTACAAAAGAGGAGATGGAATTACTTAAG
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-----------------------------------------------------gtggctatctacattatgcaatgtggtttttacttgagCACTCAGAAAGC--------AATACTATGGGA--CAGTACTGGATGTAGATCAGGTTGATAATCTGATCAAGTTTTGTCCAACAAAGGAGGAGATGGAAACGCTCAAG
upper sequence: GLYMA17G08230.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ37653 (Selaginella moellendorffii), 3'ss of exon 6
taacactttcttaagtcttgttcatgtcatgggatcatcttgttgaataagtgctgtgagtttttattcattaatattggcttgtttgaaatattcacagAGCTCAGTGTTAGCACTGGAGGAGTCAGCACTCGACACTGATCAGGTTGAGAACCTCATAAAGTTTTGTCCTACAAAAGAGGAGATGGAATTACTTAAG
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----------------------------------------------gtaagttgctc---tctacattatgcaatgtggtttttacttgagcactcagAAAGC--AATACTAGCGTTGGATGGGGCAGTACTGGATGTAGATCAGGTTGATAATCTGATCAAGTTTTGTCCAACAAAGGAGGAGATGGAAACGCTCAAG
upper sequence: GLYMA17G08230.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ15040 (Selaginella moellendorffii), 3'ss of exon 6
taacactttcttaagtcttgttcatgtcatgggatcatcttgttgaataagtgctgtgagtttttattcattaatattggcttgtttgaaatattcacagAGCTCAGTGTTAGCACTGGAGGAGTCAGCACTCGACACTGATCAGGTTGAGAACCTCATAAAGTTTTGTCCTACAAAAGAGGAGATGGAATTACTTAAG
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----------------------------------------------gtaagttgctc---tctacattatgctatgtggtttttacttgagcactcagAAAGC--AATACTAGCGTTGGATGGGACAGTACTGGATGTAGATCAGGTTGATAATCTGATCAAGTTTTGTCCAACAAAGGAGGAGATGGAAACGCTCAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|16349026|gb|BI974621.1|BI974621EST: ATTGTGAAATCATGCTTTCAAAAGTGAAAGTGCCATTGCATGATTTAATG AGCTCAGTGTTAGCACTGGAGGAGTCAGCACTCGACACTGATCAGGTTGAG
genomic: ATTGTGAAATCATGCTTTCAAAAGTGAAAGTGCCATTGCATGATTTAATGgtaagattga ... atattcacagAGCTCAGTGTTAGCACTGGAGGAGTCAGCACTCGACACTGATCAGGTTGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aataagtgctgtgagtttttattcattaatattggcttgtttgaaatattcacagAGCTCAGTGTTAGCACTGGAGGAGTCAGCACTCGACACTGATCAGGTTGAGAACCTCATAAAGTTTTGTCCTACAAAAGAGGAGATGGAATTACTTAAG
cattaat putative branch site (score: 3)
tgagtttttattcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taacactttcttaagtcttgttcatgtcatgggatcatcttgttgaataagtgctgtgagtttttattcattaatattggcttgtttgaaatattcacagAGCTCAGTGTTAGCACTGGAGGAGTCAGCACTCGACACTGATCAGGTTGAGAACCTCATAAAGTTTTGTCCTACAAAAGAGGAGATGGAATTACTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- -cactttc
- - - - - - - - - - -tcatgtc
- - - - - - - - - - - - - - - - - - - cttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - gctgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgtt