Sequence
atgc intronic sequence ATGC exonic sequence...cctgagcctatatggaatttgtaatcatgattttgaagattttgaagttagataagaaatcgtgaattgatttttctttttttctattttggattattagATGATTATCGGCTCTTCTGTGGGGATCTTGGTAACGAGGTGAATGATGATGTTCTCTCAAAAGCATTTTCACGGTTTCCTTCCTTTAACTTGGCACGA
Basic information
species | Glycine max |
transcript | GLYMA20G36570.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G36570.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G068255_T01 (Zea mays), 3'ss of exon 1
-cctgagcctatatggaatttgtaatcatgattttgaagattttgaagttagataagaaatcgtgaattgatttttctttttttctattttggattatt---agATGATTATCGGCTCTTCTGTGGGGATCTTGGTAACGAGGTGAATGATGATGTTCTCTCAAAAGCATTTTCACGGTTTCCTTCCTTTAACTTGGCACGA
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gtagcagccaacat--aacctattaatccagtttcctttgttttatgcttct--------cccttatttcatttccttgtgtttcaactcttaacaatttgcagACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGG
upper sequence: GLYMA20G36570.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G016106_T01 (Zea mays), 3'ss of exon 1
cctgagcctatatggaatttgtaatcatgattttgaagattttgaagttagataagaaatcgtgaattgatttttctttttttctattttggattatt---agATGATTATCGGCTCTTCTGTGGGGATCTTGGTAACGAGGTGAATGATGATGTTCTCTCAAAAGCATTTTCACGGTTTCCTTCCTTTAACTTGGCACGA
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---------gtagctaacata-acttattaattcagtttcctttgtgtttaatggatcacccttatttggtttgcttgtgtctcaactcctaacaatttgcagACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTATCCAAAGCATTCTCACGGTTTCCATCCTTCAACATGGCAAGG
upper sequence: GLYMA20G36570.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G04500.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------------------cctgagcctat---atggaatttgtaatcatgattttgaagattttgaa-gttagataagaaatcgtgaattgatttttctttttttctattttggattattagATGATTATCGGCTCTTCTGTGGGGATCTTGGTAACGAGGTGAATGATGATGTTCTCTCAAAAGCATTTTCACGGTTTCCTTCCTTTAACTTGGCACGA
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gtaagctctgctcgtctttttcttcttctttcccttgattttgctgattgttgttttagtttacgggatggtatcatagttgttcataggtaggattttagatgttttcttctctgttgttaaaatagatttcttatatctttctaacatttggcagATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAG
upper sequence: GLYMA20G36570.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0036g00630.t01 (Vitis vinifera), 3'ss of exon 2
cctgagcctatatggaatttgtaatcatgattttgaagattttgaagttagataagaaatcgtgaattgatttttctttttttcta------ttttggattatt--agATGATTATCGGCTCTTCTGTGGGGATCTTGGTAACGAGGTGAATGATGATGTTCTCTCAAAAGCATTTTCACGGTTTCCTTCCTTTAACTTGGCACGA
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--------ttcattgacattattcctatgatgctgtatatgttcctacccctcctttttgcctggatatgcttctctcatgcctggcagaactgttggcatcctgcagATGATTATCGTTTATTTTGTGGTGATCTTGGCAATGAGGTGAATGATGATGTTCTTTCAAAAGCATTTTCACGATTTCCTTCCTTCAATATGGCTAAA
upper sequence: GLYMA20G36570.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0018g01710.t01 (Vitis vinifera), 3'ss of exon 2
cctgagcctatatggaatttgtaatcatgattttgaagattttgaagttagataagaaatcgtgaattgatttttctttttttctattttgg-attat-tagATGATTATCGGCTCTTCTGTGGGGATCTTGGTAACGAGGTGAATGATGATGTTCTCTCAAAAGCATTTTCACGGTTTCCTTCCTTTAACTTGGCACGA
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--ttcattcacactgtttctatgatgctatttatgttcctacctctcctttttgcctggatatgcttctctcatgcttggaagaactgttggcattctgcagATGATTATCGTTTATTTTGTGGTGATCTTGGCAATGAGGTGAACGATGATGTTCTTTCAAAAGCATTTTCACGATTTCCTTCCTTCAATATGGCCAGAMapped 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|18040243|gb|BM308537.1|BM308537EST: GCTGCTGGCCAAGCTTGGGAAGGATC-TATCCCTGCGGAGTGGCCAGAAG ATGATTATCGGCTCTTCTGTGGGGATCTTGGT
genomic: GCTGCTGGCCAAGCTTGGGA-GGATCCTATCCTTGCGGAGTGGCCAGAAGgtattatgat ... ggattattagATGATTATCGGCTCTTCTGTGGGGATCTTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttagataagaaatcgtgaattgatttttctttttttctattttggattattagATGATTATCGGCTCTTCTGTGGGGATCTTGGTAACGAGGTGAATGATGATGTTCTCTCAAAAGCATTTTCACGGTTTCCTTCCTTTAACTTGGCACGA
aattgat putative branch site (score: 4)
tttttctttttttcta CT-rich tract
aattgatttttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctgagcctatatggaatttgtaatcatgattttgaagattttgaagttagataagaaatcgtgaattgatttttctttttttctattttggattattagATGATTATCGGCTCTTCTGTGGGGATCTTGGTAACGAGGTGAATGATGATGTTCTCTCAAAAGCATTTTCACGGTTTCCTTCCTTTAACTTGGCACGA
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