Sequence
atgc intronic sequence ATGC exonic sequence...acatgtagcttttttttacattgaacaagtaatttatttaagtgtatattttgttttcttttcctatgtttatatgtttggctagatgtttgacttgcagGTGTAATGATGTTGCTGCTGTAGATATTAACATGGGTTGCCCGAAGTCATTTTCTGTGAGTGGTGGGATGGGTGCTGCTCTGTTGTCCAAACCAGAGCTT
Basic information
species | Glycine max |
transcript | GLYMA01G23820.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G23820.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g44890.1 (Oryza sativa), 3'ss of exon 3
acatgtagctt---ttttttacattgaacaagtaatttatttaagtgtatattttgttttcttttcctatgtttatatgtttggctagatgtttgactt--gcagGTGTAATGATGTTGCTGCTGTAGATATTAACATGGGTTGCCCGAAGTCATTTTCTGTGAGTGGTGGGATGGGTGCTGCTCTGTTGTCCAAACCAGAGCTT
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--ttgctgtttgaattgtttcaattaatcaaggaatcggatcaattgttttaaccgcccctgctttagatattt---tctttgatcacagtttcatccttaccagGTGTAACGATGTTGCTGCTATAGATATCAACATGGGTTGTCCCAAATCTTTCTCTCTTAGTGGTGGAATGGGAGCCGCATTACTCTCCAAACCTGAGCTT
upper sequence: GLYMA01G23820.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G468693_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------------acatgtagcttttttttaca------ttgaacaagtaatttatttaagtg-------tatatt---ttgttttcttttcctatgtttatatgtttggctagat-gtttga--cttgcagGTGTAATGATGTTGCTGCTGTAGATATTAACATGGGTTGCCCGAAGTCATTTTCTGTGAGTGGTGGGATGGGTGCTGCTCTGTTGTCCAAACCAGAGCTT
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gtgtaagctctacttctgagaccttttaggatataagtcctgaagtcggtaatataaattgtgtttataccaggtttggtaccgaaaattttccaattggtagcattagattagaccatatagttttgctttgcgtatttatttaaccatattgttttgtcctcatagGTGCCGTGATGTTTCTGCTATAGATATCAACATGGGTTGTCCAAAGTCTTTTTCACTTAGTGGAGGGATGGGTGCTGCATTACTCTCCAAACCTGAGCTT
upper sequence: GLYMA01G23820.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G468693_T02 (Zea mays), 3'ss of exon 3
-----------------------------------------------acatgtagcttttttttaca------ttgaacaagtaatttatttaagtg-------tatatt---ttgttttcttttcctatgtttatatgtttggctagat-gtttga--cttgcagGTGTAATGATGTTGCTGCTGTAGATATTAACATGGGTTGCCCGAAGTCATTTTCTGTGAGTGGTGGGATGGGTGCTGCTCTGTTGTCCAAACCAGAGCTT
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gtaagctctacttctgagaccttttaggatataagtcctgaagtcggtaatataaattgtgtttataccaggtttggtaccgaaaattttccaattggtagcattagattagaccatatagttttgctttgcgtatttatttaaccatattgttttgtcctcatagGTGCCGTGATGTTTCTGCTATAGATATCAACATGGGTTGTCCAAAGTCTTTTTCACTTAGTGGAGGGATGGGTGCTGCATTACTCTCCAAACCTGAGCTT
upper sequence: GLYMA01G23820.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s2201g00010.t01 (Vitis vinifera), 3'ss of exon 1
-------acatgtagcttttttttacattgaacaagtaatttatttaagtgtatattttgttttcttttcctatgtttatatgtttggctagatgtttgacttgcagGTGTAATGATGTTGCTGCTGTAGATATTAACATGGGTTGCCCGAAGTCATTTTCTGTGAGTGGTGGGATGGGTGCTGCTCTGTTGTCCAAACCAGAGCTT
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cacagtggcatatagattattatccctcagactgatgaa-------aaacctgatttttgccacctgcaatcttaactgaattactgacccagtatttttctttcagGTGTAAAGATGTTGCAGCGGTGGATATAAATATGGGTTGCCCCAAGTCATTCTCTATTAGTGGAGGCATGGGAGCTGCATTATTGACTAGACCTGAGCTTMapped 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|254316199|gb|GR827736.1|GR827736EST: CAAATAGGCACATCAGATGCTGTGAGGGCCCTAGCTACTGCTCAGTTAGT GTGTAATGATGTTGCTGCTGTAGATATTAACATGGGTTGCCCGAAGTCATT
genomic: CAAATAGGCACATCAGATGCTGTGAGGGCCCTAGCTACTGCTCAGTTAGTgtaagttaat ... tgacttgcagGTGTAATGATGTTGCTGCTGTAGATATTAACATGGGTTGCCCGAAGTCATT
EST:
gi|21600377|gb|BQ610708.1|BQ610708EST: ACTGCTCAGTTAGT GTGTAATGATGTTGCTGCTGTAGATATTAACATGGGTTGCCCGAAGTCATT
genomic: ACTGCTCAGTTAGTgtaagttaat ... tgacttgcagGTGTAATGATGTTGCTGCTGTAGATATTAACATGGGTTGCCCGAAGTCATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattttgttttcttttcctatgtttatatgtttggctagatgtttgacttgcagGTGTAATGATGTTGCTGCTGTAGATATTAACATGGGTTGCCCGAAGTCATTTTCTGTGAGTGGTGGGATGGGTGCTGCTCTGTTGTCCAAACCAGAGCTT
gtttgac putative branch site (score: 4)
tatgtttatatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acatgtagcttttttttacattgaacaagtaatttatttaagtgtatattttgttttcttttcctatgtttatatgtttggctagatgtttgacttgcagGTGTAATGATGTTGCTGCTGTAGATATTAACATGGGTTGCCCGAAGTCATTTTCTGTGAGTGGTGGGATGGGTGCTGCTCTGTTGTCCAAACCAGAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
acatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgtttg