Sequence
atgc intronic sequence ATGC exonic sequence...tgaatgttgacaatttatctgcaataatcttttatagctgttggattttctttttgtatatatttttattaatcgtatgttacttatgatgctttgcagtTAAAGAAGCTCTGTGTCACCCATACTTGGCACCTCTTCATGATATTAATGAGGAACCTGTTTGCGTTAGACCTTTCAGTTTTGATTTTGAGCAACCATCT
Basic information
species | Glycine max |
transcript | GLYMA18G47140.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 5
tgaatgttgacaatttatctgcaataatcttttatagctgttggattttctttttgtatatatttttattaatcgtatgttacttatgatgctttgcagtTAAAGAAGCTCTGTGTCACCCATACTTGGCACCTCTTCATGATATTAATGAGGAACCTGTTTGCGTTAGACCTTTCAGTTTTGATTTTGAGCAACCATCT
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------------------gtacattgac--tttacaccaact--actccacttttgttgcctttactgtaaattgaacattattttt----ccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATGAAGAACCCACCTGCCCAGCACCTTTCAGCTTTGATTTTGAGCAACCATC-
upper sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g06060.1 (Oryza sativa), 3'ss of exon 5
-------------------------------------------------------------------------------tgaatgttgacaatttatctgcaataatcttt-tatagctgttggattttct----ttttgtatatatttttattaatcgtatgttacttatgatgctttgcagtTAAAGAAGCTCTGTGTCACCCATACTTGGCACCTCTTCATGATATTAATGAGGAACCTGTTTGCGTTAGACCTTTCAGTTTTGATTTTGAGCAACCATCT
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gtaattttgcagccttgcataatcttgctagattgcaaaatgacatattctgctacctgatacataagctgaaatgcttcttgtcattataactaagtttaaatgacattcatgtacacactaattaatctcagatcctgacaataacatgagatactaaccttgacttctgtggcattgcagTTGATGAAGCTCTGTGCCATCCATACTTGGCATCCCTTCATGAGATATATGATGAACCAGTCTGCCCAGCGCCTTTCAGCTTCGATTTCGAGCAGCCGTC-
upper sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 5
tgaatgttgacaatttatctgcaataatcttttatagctgttggattttctttttgtatatatttttattaatcgtatgttacttatgatgctttgcagtTAAAGAAGCTCTGTGTCACCCATACTTGGCACCTCTTCATGATATTAATGAGGAACCTGTTTGCGTTAGACCTTTCAGTTTTGATTTTGAGCAACCATCT
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--------------------gtacctgccttc-atgcaagtc--actttattagtggtggcttaactataaactcaaagaccttttttttcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATGATGAACCTACCTGCCCTGCACCTTTCAGCTTTGATTTTGAGCAACCATC-
upper sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 5
tgaatgttgacaatttatctgcaataatcttttatagctgttggattttctttttgta----tatatttttattaatcgtatgttacttatgatgctttgcagtTAAAGAAGCTCTGTGTCACCCATACTTGGCACCTCTTCATGATATTAATGAGGAACCTGTTTGCGTTAGACCTTTCAGTTTTGATTTTGAGCAACCATCT
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--gttggttttagatctttgggaaaaatttcttaaattatactattcttattattggagttctatgtgcttatttat-gctcattttttccttttgtttgcagTTGAAGGGGCACTGTCTCATCCATACTTGGCACCTCTTCATGATATCAATGAGGAGCCCGTTTGTCCAAGGCCTTTTGTTTTTGATTTCGAGCAACCATC-Mapped 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|22933316|gb|BU550455.1|BU550455EST: GATTTGTTAGAGAAGATGCTTGTCTTTGATCCAAATAGGCGCATTACAGT TAAAGAAGCTCTGTGTCACCCATACTTGGCACCTCTTCATGATATTAATGA
genomic: GATTTGTTAGAGAAGATGCTTGTCTTTGATCCAAATAGGCGCATTACAGGtaaaatgaca ... gctttgcagtTAAAGAAGCTCTGTGTCACCCATACTTGGCACCTCTTCATGATATTAATGA
EST:
gi|254335273|gb|GR846770.1|GR846770EST: GATTTGTTAGAGAAGATGCTTGTCTTTGATCCAAATAGGCGCATTACAGT TAAAGGAGCTCTGTGTCACCCATACTTGGCAC-TCTTCATGATATTAATGA
genomic: GATTTGTTAGAGAAGATGCTTGTCTTTGATCCAAATAGGCGCATTACAGGtaaaatgaca ... gctttgcagtTAAAGAAGCTCTGTGTCACCCATACTTGGCACCTCTTCATGATATTAATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctttttgtatatatttttattaatcgtatgttacttatgatgctttgcagtTAAAGAAGCTCTGTGTCACCCATACTTGGCACCTCTTCATGATATTAATGAGGAACCTGTTTGCGTTAGACCTTTCAGTTTTGATTTTGAGCAACCATCT
tattaat putative branch site (score: 2)
tttttgtatatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaatgttgacaatttatctgcaataatcttttatagctgttggattttctttttgtatatatttttattaatcgtatgttacttatgatgctttgcagtTAAAGAAGCTCTGTGTCACCCATACTTGGCACCTCTTCATGATATTAATGAGGAACCTGTTTGCGTTAGACCTTTCAGTTTTGATTTTGAGCAACCATCT
- - tgttgac
- - - - - - - - atctgca
- - - - - - - - - - - - - - - - - - gctgttg