Sequence
atgc intronic sequence ATGC exonic sequence...tattctgtgaaacacactatattcagaatgtaggaagttgttgaatagaaagaacagaaatgattgatagctaagtaaatatatgctcttctatatgtagGTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAACAATGAGCTTTGGAGGAAACAATCGTGCACAGGTTTTCTTTAAGCAACATGGTTGGAAT
Basic information
species | Glycine max |
transcript | GLYMA08G36700.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G134045_T02 (Zea mays), 3'ss of exon 2
--tattctgtgaaacacactatattcagaatgtaggaagttgttgaatagaaagaacagaaatgattgatagctaagtaaatatatgctcttctatatgtagGTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAACAATGAGCTTTGGAGGAAACAATCGTGCACAGGTTTTCTTTAAGCAACATGGTTGGAAT
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tattttttgggaaatttaacatagttcactgacatttttactttatgcagttgcacatcgaatgactga-atcaatactgaaaaacag-ctacaatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAGCTGAAAATGATGGTCTATGGAGGAAACAACCGTGCACAAGCTTTCTTTAAGCAGCATGGTTGGACA
upper sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G094390_T01 (Zea mays), 3'ss of exon 2
tattctgtgaaacacactatattcagaatgtaggaagttgttgaatagaaa-gaacag-aaatga-ttgatagctaagtaaatatatgctcttctatatgtagGTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAACAATGAGCTTTGGAGGAAACAATCGTGCACAGGTTTTCTTTAAGCAACATGGTTGGAAT
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-atcctttggaaagtttaacatagttcactaacatttttactttatgcagttgcacactgaatgacttaatcaatactgaaaaaactgcta--caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTATGGCGGAAATAACCGTGCGCAAGCTTTCTTTAAGCAGCATGGTTGGACA
upper sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 2
lower sequence: AT4G17890.2 (Arabidopsis thaliana), 3'ss of exon 2
tattctgtgaaacacactatattcagaatgtaggaagttgttgaatagaaagaacagaa--atgattgatagc-----taagtaaatatatgctct-tctatatgtagGTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAACAATGAGCTTTGGAGGAAACAATCGTGCACAGGTTTTCTTTAAGCAACATGGTTGGAAT
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------ttgaaattagactcattcaaattatcg--attcattgactagataatattgaataatgccacattacgttctcaagatgctaccttttccgtttttgtatagATCAACGAATTTAGACTCTTGGAGCCCGGAGCAGCTCAGGACAATGATGTTTGGTGGTAACAACCGTGCTCAGGTTTTCTTCAAGCAACATGGATGGACT
upper sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G46750.1 (Arabidopsis thaliana), 3'ss of exon 2
tattctgtgaaacac--actatattcagaatgtaggaagttgttgaatagaaagaacagaaatgattgatagctaa-gtaaatatatgctcttctatatgtagGTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAACAATGAGCTTTGGAGGAAACAATCGTGCACAGGTTTTCTTTAAGCAACATGGTTGGAAT
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-gattaggaagatgttgacttattttttcctgttgaccact-ctatttatagcatttcatgttgttgtagatctattataagatcatattgtttt-tgtgcagGTCAACGAACTTAGACTCGTGGAGTCCTGAGCAGCTAAGAACAATGATGTTTGGAGGGAACAATCGAGCTCAGGTGTTTTTTAAGCAACATGGATGGAAT
upper sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 2
tattctgtgaaacacactatattcagaatgtaggaagttgttg--aatagaaagaacagaaatg----attgatagctaagtaaatatatgctcttctatatgtagGTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAACAATGAGCTTTGGAGGAAACAATCGTGCACAGGTTTTCTTTAAGCAACATGGTTGGAAT
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--atgtgtggagcatttccttttcatcctttctcctttttttttcaccctttttgatagttttgttttactaattgctgtgccaaaaattgatttgctcca----gGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTTTGGGGGAAACAACCGTGCACAGGCTTTCTTTAAGCAGCATGGATGGTCTMapped 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|207760906|gb|GD734957.1|GD734957EST: GATTGCTCCGCCGTACACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAG GTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAAC
genomic: GATTGCTCCGCCGTACACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGgcaagttttt ... ctatatgtagGTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAAC
EST:
gi|18735589|gb|BM528850.1|BM528850EST: GATTGCTCCGCCGTACACCGCAGTCTCGGCGTGCACTTCTTCTTCGTGAG GTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAACAATGAGCTT
genomic: GATTGCTCCGCCGTACACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGgcaagttttt ... ctatatgtagGTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAACAATGAGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagaaagaacagaaatgattgatagctaagtaaatatatgctcttctatatgtagGTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAACAATGAGCTTTGGAGGAAACAATCGTGCACAGGTTTTCTTTAAGCAACATGGTTGGAAT
gattgat putative branch site (score: 4)
tgctcttct putative PPT
taagtaaatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattctgtgaaacacactatattcagaatgtaggaagttgttgaatagaaagaacagaaatgattgatagctaagtaaatatatgctcttctatatgtagGTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAACAATGAGCTTTGGAGGAAACAATCGTGCACAGGTTTTCTTTAAGCAACATGGTTGGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA