Sequence
atgc intronic sequence ATGC exonic sequence...ttcctctaaaatgttctaatgattgtttctttaagatgcttatatattatatctttggtaagaagtatgctctattttaactcttaactttgtggtgcagATGAAGACAGGATGTGTAGCTCTAGTATTATGTTTAAACATTAGTGTCGATCCACCAGATGTAATAAAGATATCCCCTTGTGCCAGAATGGAGTGCTGGA
Basic information
species | Glycine max |
transcript | GLYMA09G41510.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 1
ttcctctaaaatgttctaatgattgtttctttaagatgcttatatattat-atctttggtaagaagtatgctctattttaactcttaactttgtggtgcagATGAAGACAGGATGTGTAGCTCTAGTATTATGTTTAAACATTAGTGTCGATCCACCAGATGTAATAAAGATATCCCCTTGTGCCAGAATGGAGTGCTGGA
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ctatatacttctatttgtatttctgttctttttattttcgggtgtactgttggatgttattgcttttatgctatttactaa-tagtgttttggtagtgcagATGAAAACTGGCTGTGTGGCACTTGTGTTGTGTTTAAACATTAGTGTTGATCCGCCGGATGTGATCAAAATCTCCCCTTGTGCAAGAAAGGAGTGCTGGA
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G048067_T02 (Zea mays), 3'ss of exon 1
-ttcctct-aaaatgttctaatgattgtttctttaagatgcttatatattatatctttggtaagaagtatgctctattttaactcttaactttgtggtgcagATGAAGACAGGATGTGTAGCTCTAGTATTATGTTTAAACATTAGTGTCGATCCACCAGATGTAATAAAGATATCCCCTTGTGCCAGAATGGAGTGCTGGA
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cttcttcttaatataataccgtgggtggt-ctttcccctaccggccgagttt-ttttggattgtttacatgatctttactaacaatggattttgtagtgcagATGAAGACAGGATGTGTTGCACTTGTATTATGTTTAAACATAAGTGTGGATCCACCTGATGTAATTAAAATTTCCCCTTGTGCAAGAATGGAGTGCTGGA
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 1
ttcctctaaaatgttctaatgattgtttctttaagatgcttatatattatatctttggtaagaagtatgctctattttaactcttaactttgtggt--gcagATGAAGACAGGATGTGTAGCTCTAGTATTATGTTTAAACATTAGTGTCGATCCACCAGATGTAATAAAGATATCCCCTTGTGCCAGAATGGAGTGCTGGA
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-tctcgtcggaagctaaatcaggtgttcattggatctgatagc-taggggagttcttgcaagtctcatattctttgttaacttttcttcttcttctttgcagATGAAAACAGGATGTGTAGCTTTAGTTCTGTGTTTAAACATTACTGTTGATCCGCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGA
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 1
ttcctctaaaatgttctaatgattgtttctttaagatgcttatatatta--tatctttggtaag-aagtatgctctattttaactcttaactttgtggtgcagATGAAGACAGGATGTGTAGCTCTAGTATTATGTTTAAACATTAGTGTCGATCCACCAGATGTAATAAAGATATCCCCTTGTGCCAGAATGGAGTGCTGGA
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--cctgtaatccgatctggtcaatcattgtgcttgatgcttacaaattcattattgtacgtatttaggtctgctttggtttaactcccgagttt-taatgcagATGAAGACAGGATGTGTAGCTCTTGTTTTATGTTTAAACATTAGTGTTGATCCACCTGATGTAATTAAGATATCTCCTTGTGCCAGAATGGAGTGCTGGAMapped 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|193661655|gb|FK605185.1|FK605185EST: CCGGCCCCTCCGACAGCGGCCTCGTCTCCAAGTGGCGACCTAAGGACAGA ATGAAGACAGGATGTGTAGCTCTAGTATTATGTTTAAACATTAGTGTCGAT
genomic: CCGGCCCCTCCGACAGCGGCCTCGTCTCCAAGTGGCGACCTAAGGACAGAgtaagaactt ... tgtggtgcagATGAAGACAGGATGTGTAGCTCTAGTATTATGTTTAAACATTAGTGTCGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatatctttggtaagaagtatgctctattttaactcttaactttgtggtgcagATGAAGACAGGATGTGTAGCTCTAGTATTATGTTTAAACATTAGTGTCGATCCACCAGATGTAATAAAGATATCCCCTTGTGCCAGAATGGAGTGCTGGA
tcttaac putative branch site (score: 2)
tattttaactcttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcctctaaaatgttctaatgattgtttctttaagatgcttatatattatatctttggtaagaagtatgctctattttaactcttaactttgtggtgcagATGAAGACAGGATGTGTAGCTCTAGTATTATGTTTAAACATTAGTGTCGATCCACCAGATGTAATAAAGATATCCCCTTGTGCCAGAATGGAGTGCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - gatgctt