Sequence
atgc intronic sequence ATGC exonic sequence...ttgtaaaatttaatgaagcctagatctgtaatttatatgtttattcattatctagttactgtcatcataaactttaaacaactttgcttttcatctatagAGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
Basic information
species | Glycine max |
transcript | GLYMA05G03970.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os04g18030.3 (Oryza sativa), 3'ss of exon 14
--ttgtaaaatttaatgaagcctagatctgtaatttatatgtttattcattatctagttactgtcatcataaactttaaacaactttgcttttcatctat-agAGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
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gttaatggtattcaaagatttgttttatgttgaattaattatttctgt-tgataggatccttttctttttgtaatgtaaatg--cttgtgttatatttgtcagAAATGGTGGAGATTTATCAACCAAAGAGTTGCAAAAAATGGTTCAAGCTCTTCCGCAGTACAGTGATCAAATTGACAAGCTTGCGCTTCATGTTGAG
upper sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os02g25580.2 (Oryza sativa), 3'ss of exon 8
ttgtaaaatttaatgaagcctagatctgtaatt-tatatgtttattcattatctagttactgtcatcataaactttaaacaactttgcttttcatcta------tagAGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
||||| | | | || | | || || || ||| | | || | | | | ||||| | |||||| | || ||| | | || || || || | || || || ||||| ||||||||||| |||||||| ||||| || |||||||| ||||| || || ||||| |||
-------atttatttggacatgtatgttgagttgcatgagtccattttgtttgtaatgttcttgacttattattttaatggtcattgcttcatgtttaaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCTTCCACAGTACAGCGATCAAATTGAGAAGCTTTCTCTTCATGTTGAG
upper sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G012942_T01 (Zea mays), 3'ss of exon 12
ttgtaaaatttaatgaagcctagatctgtaat-ttatatgtttattcattatct-agttactgtcatcataaactttaaacaactttgcttttcatctatagAGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
| | | || | || | | ||| || || | | | | | | | | | | | | | | | | |||| | ||| | |||| || | || || | | | || || || ||||||||||| ||||||||||||||||| ||||||||||||||| |||| ||||| |||
--aaagggccaagcaatgctgttagctaaagtattagctgcttgatagctgtgtcaatggatctggttaacatttattcataggatctattttgagtgtcagATCTGGTGGAGAGTTATCTACCAAGCAGTTGCAGAAAATGGTTCAAGCTCTTCCACAATACAGTGATCAAATTGACAAGCTCACCCTTCATGTTGAG
upper sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 13
lower sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 12
-ttgtaaaatttaatgaagcctagatctgtaatttatatgtttattcattatctagttactgtcatcataaactttaaacaactttgctt-----ttcatctatagAGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
|| | | | | | | ||||| | |||| || || ||| | || ||| || ||| | ||| |||| || || | ||||| | | | ||| | || ||||| || || || ||||||||||||||| | ||||| |||||||||||||||||||||||||| ||||| ||||||
cttacattactctacg-----ttgatctatgtggtatactttatttggttagagaagtag-gtcttctctccttttgatcaattttgtttgactcttttttcttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG
upper sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 12
ttgtaaaatttaatgaagcctagatctgtaatttatatgtttattcattatctag-ttactgtcatcataaactttaaac-aactttgcttttcatctatagAGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
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--atgtatctttgtgatatctggttaatctttctacttgatgccagtgtattcagaccagtaatccaggatgtgttaacctaaatatttatctgttatgtagAGGTGGTGGTGAATTGTCTACAAGGGACTTGCAAAAGATGGTTCAAGCTTTGCCACAATATAGTGAGCAAATTGAGAAGCTTTCCCTCCATGTTGAGMapped 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|193370867|gb|FK334545.1|FK334545EST: ACCAACTTCATTTCAAAGAATAAAGCTGCACAAATCCAACATGGTTCAAG AGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACT
genomic: ACCAACTTCATTTCAAAGAATAAAGCTGCACAAATCCAACATGGTTCAAGgttagtctta ... tcatctatagAGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACT
EST:
gi|10844672|gb|BF067898.1|BF067898EST: ACCAACTTCATTTCAAAGAATAAAGCTGCACAAATCCAACATGGTTCAAG AGGTAGTGGTGAAATGTCCAAC-AGGGACCTTCCAAAAGATGGTTCAAGCA
genomic: ACCAACTTCATTTCAAAGAATAAAGCTGCACAAATCCAACATGGTTCAAGgttagtctta ... tcatctatagAGGTAGTGGTGAAATGT-CGACAAGGGA-CTTACAAAAGATGGTTCAAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattatctagttactgtcatcataaactttaaacaactttgcttttcatctatagAGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
ctttgcttttcatct CT-rich tract
atcataaactttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtaaaatttaatgaagcctagatctgtaatttatatgtttattcattatctagttactgtcatcataaactttaaacaactttgcttttcatctatagAGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - -aatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgtc