Sequence
atgc intronic sequence ATGC exonic sequence...ttctgtattctttcaacttatgttttagtgagagtgtgagactactacccatcttacaatatccaggatcatttactaaccttcaattttgtctcatcagGTCAAAGGTGAAGCTAATATATCATACATATGTTCACGGTTCTATCGAGCACCAGAACTCATATTTGGGGCCACAGAGTATACAAGTTCAATTGATATTT
Basic information
species | Glycine max |
transcript | GLYMA04G06760.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G06760.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 3'ss of exon 6
ttctgtattctttcaacttatgttttagtgagagtgtgagactactacccatcttacaatatccaggatcatttactaa---ccttcaattt--tgtctcatcagGTCAAAGGTGAAGCTAATATATCATACATATGTTCACGGTTCTATCGAGCACCAGAACTCATATTTGGGGCCACAGAGTATACAAGTTCAATTGATATTT
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ttacacctttttccaccttat--tccag---atgtttgctacaattgtacttttgataattttgatcttactgtcctaatatccattaatttactattccatcagGTCCCAGGTGAACCCAATATATCATATATATGCTCACGCTACTACCGAGCACCGGAGCTCATATTTGGTGCAACTGAATATACTACATCAATAGATATAT
upper sequence: GLYMA04G06760.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 6
ttctgtattctttcaacttatgttttagtgagagtgtgagactactacccatcttaca-atatccaggatc-----atttactaaccttcaattttgtctcatcagGTCAAAGGTGAAGCTAATATATCATACATATGTTCACGGTTCTATCGAGCACCAGAACTCATATTTGGGGCCACAGAGTATACAAGTTCAATTGATATTT
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----acttgactgtaattcatgtgtta-taataattggactct-ttacttgtataccgtaaatctttgatccacatgttaatcagttccttatgctgctttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATAT
upper sequence: GLYMA04G06760.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 5
ttctgtattctttcaacttatgttttagtgagagtgtgagactactacccatcttacaatatccaggatcatttactaaccttcaattttgtctcatcagGTCAAAGGTGAAGCTAATATATCATACATATGTTCACGGTTCTATCGAGCACCAGAACTCATATTTGGGGCCACAGAGTATACAAGTTCAATTGATATTT
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--gtaagactttgtgacatataaactcattcgact-tgtagcggttgtt-gttttctgtgatcttg--tcatttactgttgaaatttacttttgcttcagGTTAAAGGTGAAGCCAACATTTCTTACATCTGCTCACGATTCTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCT
upper sequence: GLYMA04G06760.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 3'ss of exon 6
ttctgtattctt-tcaacttatgttttagtgagagtgtgagactactacccatct-tacaatatccaggatcatttactaaccttcaattttgtct-catcagGTCAAAGGTGAAGCTAATATATCATACATATGTTCACGGTTCTATCGAGCACCAGAACTCATATTTGGGGCCACAGAGTATACAAGTTCAATTGATATTT
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tctttcatggtagtcagtactcagtaggaagaaagtctttgcttgttttttctttctatgatatctt---tcatgttttcaccatgaatccaattttcatcagGTTAAAGGTGAAGCAAACATATCATACATATGTTCTCGTTTCTACCGAGCACCTGAACTCATATTTGGGGCCACAGAGTATACAACCTCAATTGATATATMapped 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|26048883|gb|CA785336.1|CA785336EST: CTCTTACACACCAAGTGAAGCTATGTGACTTTGGAAGTGCAAAAGTTCTA GTCAAAGGTGAAGCTAATATATCATACATATGTTCACGGTTCTATCGAGCA
genomic: CTCTTACACACCAAGTGAAGCTATGTGACTTTGGAAGTGCAAAAGTTCTAgtatgttgac ... gtctcatcagGTCAAAGGTGAAGCTAATATATCATACATATGTTCACGGTTCTATCGAGCA
EST:
gi|213605463|gb|DB966956.1|DB966956EST: CTCTTACACACCAAGTGAAGCTATGTGACTTTGGAAGTGCAAAAGTTCTA GTCAAAGGTGAAGC
genomic: CTCTTACACACCAAGTGAAGCTATGTGACTTTGGAAGTGCAAAAGTTCTAgtatgttgac ... gtctcatcagGTCAAAGGTGAAGC
EST:
gi|209716661|gb|BW654294.1|BW654294EST: CTCTTACACACCAAGTGAAGCTATGTGACTTTGGAAGTGCAAAAGTTCTA GTCAAAGGTGAAGCTAATATATCATACATATGTTCACGGTTCTATCGAGCA
genomic: CTCTTACACACCAAGTGAAGCTATGTGACTTTGGAAGTGCAAAAGTTCTAgtatgttgac ... gtctcatcagGTCAAAGGTGAAGCTAATATATCATACATATGTTCACGGTTCTATCGAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacccatcttacaatatccaggatcatttactaaccttcaattttgtctcatcagGTCAAAGGTGAAGCTAATATATCATACATATGTTCACGGTTCTATCGAGCACCAGAACTCATATTTGGGGCCACAGAGTATACAAGTTCAATTGATATTT
tactaac putative branch site (score: 0)
ttttgtctc putative PPT
ttacaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctgtattctttcaacttatgttttagtgagagtgtgagactactacccatcttacaatatccaggatcatttactaaccttcaattttgtctcatcagGTCAAAGGTGAAGCTAATATATCATACATATGTTCACGGTTCTATCGAGCACCAGAACTCATATTTGGGGCCACAGAGTATACAAGTTCAATTGATATTT
- -tgtattc
- - - - - - - - - - - - - - - -gagtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - accttca