Sequence
atgc intronic sequence ATGC exonic sequencegtgagttctgaagttctttttggcttacatgtattaacttgtcactaataagcggtcagcctgtcacaattagtttatcaattatcattgaaaccagcatttcgttttccttttctgctggttttgtaatttgaactctctgcttcttcagCTGACAGAGAAATCATATGAACTTTCATTGAAGGGAAGTCCCTACTGGATGGCTCCTGAG
Basic information
species | Glycine max |
transcript | GLYMA04G03870.3 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G03870.3 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g55560.2 (Oryza sativa), 3'ss of exon 6
gtgagttctgaagttctttttggcttacatgtattaacttgtcactaataagcggtcagcctgtcacaattagtttatcaattatcattgaaaccagcatttcgttttccttttctgctggttttgtaatttgaactctctgcttcttcagCTGACAGAGAAATCATATGAACTTTCATTGAAGGGAAGTCCCTACTGGATGGCTCCTGAG
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--------------------------------------cgttgatgagtatatggttattctgt---gagtggacttt--atagtttttaggtttaaccttgc----tgcgtttctaattatttttccctttttatcttct----tttcagTTGAGTACTGCAGCTCCTAATCTTTCACTGAAGGGAACTCCATACTGGATGGCTCCTGAG
upper sequence: GLYMA04G03870.3 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G156800_T01 (Zea mays), 3'ss of exon 6
gtgagttctgaagttctttttggcttacatgtattaacttgtcactaata-agcggtcagcctgtcacaattagtttatcaattatcattgaaaccagcatttcgttttccttttctgctggttttgtaatttgaactctctgct-tcttcagCTGACAGAGAAATCATATGAACTTTCATTGAAGGGAAGTCCCTACTGGATGGCTCCTGAG
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---------------------------------------------caatatagcatttatttttgtcttgttgacatat--attgt--ttgtaatcctcatcg---tttcctttgtagttaatctt-tgttgcacactttcttcaattttcagTTGAGTACTGCAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAG
upper sequence: GLYMA04G03870.3 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G034877_T01 (Zea mays), 3'ss of exon 7
gtgagttctgaagttctttttggcttacatgtattaacttgtcactaata-agcggtcagcctgtcacaattagtttatcaattatcattgaaaccagcatttcgttttccttttctgctggttttgtaatttgaactctctgct-tcttcagCTGACAGAGAAATCATATGAACTTTCATTGAAGGGAAGTCCCTACTGGATGGCTCCTGAG
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---------------------------------------------caatataacattcatttttttcctgttgagatat--attgctggt--aatcctcat--cgttttctttgta-gttgatctt-tattgcacattttcttccattttcagTTGAGTGCTGCTGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAG
upper sequence: GLYMA04G03870.3 (Glycine max), 3'ss of exon 8
lower sequence: EFJ33606 (Selaginella moellendorffii), 3'ss of exon 5
gtgagttctgaagttctttttggcttacatgtattaacttgtcactaataagcggtcagcctgtcacaattagtttatcaattatcattgaaaccagcatttcgttttccttttctgctggttttgtaatttgaactctctgcttcttcagCTGACAGAGAAATCATATGAACTTTCATTGAAGGGAAGTCCCTACTGGATGGCTCCTGAG
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----------------------------------------gtaagtagcaagctgt-ggtttttctttttta-cttatccatccacgcttcagATATCTTCTAGTT---CACTTGTGCTATCTTTTAAA--GGAAGTCCCTACTGGAT-GGCTC-CTGAGGTAT-GTCCACGTTTTCTTTCTTCTAATACTTCTATGACAC----------
upper sequence: GLYMA04G03870.3 (Glycine max), 3'ss of exon 8
lower sequence: EFJ36960 (Selaginella moellendorffii), 3'ss of exon 5
gtgagttctgaagttctttttggcttacatgtattaacttgtcactaataagcggtcagcctgtcacaattagtttatcaattatcattgaaaccagcatttcgttttccttttctgctggttttgtaatttgaactctctgcttcttcagCTGACAGAGAAATCATATGAACTTTCATTGAAGGGAAGTCCCTACTGGATGGCTCCTGAG
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----------------------------------------gtaagtagcaagctgt--ggtttttgttgtttacttatccatccacgcttcagATATCTTCTAGTT---CACTTGTGCTATCTTTTAAA--GGAAGTCCCTACTGGAT-GGCTC-CTGAGGTAT-GTCCACGTTTTCTTTCTTCTAATACTTCTATGACAC----------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|151403455|gb|EV273265.1|EV273265EST: TCGATGCATCAGGCAGTGTTAAGCTTGCAGATTTTGGGGTGTCAAAAATT CTGACAGAGAAATCATATGAACTTTCATTGAAGGGAAGTCCCTACTGGATG
genomic: TCGATGCATCAGGCAGTGTTAAGCTTGCAGATTTTGGGGTGTCAAAAATTgtgagttctg ... gcttcttcagCTGACAGAGAAATCATATGAACTTTCATTGAAGGGAAGTCCCTACTGGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatttcgttttccttttctgctggttttgtaatttgaactctctgcttcttcagCTGACAGAGAAATCATATGAACTTTCATTGAAGGGAAGTCCCTACTGGATGGCTCCTGAG
ctctctgcttcttc CT-rich tract
ttttgtaatttgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttctgaagttctttttggcttacatgtattaacttgtcactaataagcggtcagcctgtcacaattagtttatcaattatcattgaaaccagcatttcgttttccttttctgctggttttgtaatttgaactctctgcttcttcagCTGACAGAGAAATCATATGAACTTTCATTGAAGGGAAGTCCCTACTGGATGGCTCCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG