Sequence
atgc intronic sequence ATGC exonic sequence...gtcttgtttctattcttcaaattgtatatgggactggatcactaaatagctggatttttgaatggctgattgctttgtttgcatttgagatttggagcagATGCTGGGAGATGAGATTGGAAAAGGAGCTTATGGTCGAGTTTACAAAGGTTTGGACCTGGAGAATGGAGATTTTGTTGCCATTAAACAAGTTTCTTTGG
Basic information
species | Glycine max |
transcript | GLYMA12G03090.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G03090.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0011g02270.t01 (Vitis vinifera), 3'ss of exon 1
gtcttgtttctattcttcaaattgtatatgggactggatcactaaatagctggatttttgaatggc----tgattgctttgtttgcatttgagatttg-gagcagATGCTGGGAGATGAGATTGGAAAAGGAGCTTATGGTCGAGTTTACAAAGGTTTGGACCTGGAGAATGGAGATTTTGTTGCCATTAAACAAGTTTCTTTGG
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ttagttttttggcagttcaggtttgatt--agtttggttt--caagtcgtcggatctt-gagtgtcattttgatgtctgtatatgatttccatttttttgttcagATGCTTGGAGATGAGATCGGAAAAGGAGCATATGGTCGAGTTTACAAGGGTTTGGATTTGGAGAATGGAGACTTTGTTGCAATTAAACAAGTTTCTTTGG
upper sequence: GLYMA12G03090.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S99_12V6.1 (Physcomitrella patens), 3'ss of exon 1
gtcttgtttctattcttcaaattgtatatgggactggatcactaaatagctggatttttgaatg-gctgat-tgctttgtttgcatttga---gatttggagcagATGCTGGGAGATGAGATTGGAAAAGGAGCTTATGGTCGAGTTTACAAAGGTTTGGACCTGGAGAATGGAGATTTTGTTGCCATTAAACAAGTTTCTTTGG
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-----acatacgaactagcaacaatcgctggtatctggcttttccagagactcttacttgcatccagtgatgtaatatgatgtcatatggtttgatggttggcagTTGCTGGGAGATGAAATCGGTAAAGGGGCATATGGCCGAGTGTACAAGGGATTGGATTTGGACAATGGAGATTTTGTGGCGATCAAACAGGTTTCGCTGG
upper sequence: GLYMA12G03090.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S131_142V6.1 (Physcomitrella patens), 3'ss of exon 1
gtcttgtttctattcttcaaattgtatatgggactggatcactaaata-gctggatttttgaatggctgattg---ctttgtttgcatttgagatttggagcagATGCTGGGAGATGAGATTGGAAAAGGAGCTTATGGTCGAGTTTACAAAGGTTTGGACCTGGAGAATGGAGATTTTGTTGCCATTAAACAAGTTTCTTTGG
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----gggatatgttctcctgcttgtttttgagattctttggctcaatgtgtcagaatttagcttttctgctagtgtcttgactttgaccaattgtatttggcagATGCTTGGTGACGAAATTGGAAAAGGTGCATATGGGCGAGTGTACAAAGGGCTGGACTTGGAGAATGGCGACTTTGTGGCCATTAAACAGGTCTCATTGG
upper sequence: GLYMA12G03090.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ18166 (Selaginella moellendorffii), 3'ss of exon 1
-----gtcttgtttctattcttcaaattgtatatgggactggatcacta--aatagctggatttttgaa-tggctgattgctttgtttgcatttgagatttg-----gagcagATGCTGGGAGATGAGATTGGAAAAGGAGCTTATGGTCGAGTTTACAAAGGTTTGGACCTGGAGAATGGAGATTTTGTTGCCATTAAACAAGTTTCTTTGG
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gtgagtttttcattctcctttttttggtttagggagatcgtgatcattttcattatcttttgtatcgtgctgatcagtttttccttcttcttttgtatcgtgtaattaaacagATAATAGGAGATGAAATCGGGAAAGGTGCATATGGCAGAGTTTACAAAGGCTTGGACCTGGAAAATGGGGACTTTGTGGCAATTAAGCAGGTTTCTCTGG
upper sequence: GLYMA12G03090.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ14289 (Selaginella moellendorffii), 3'ss of exon 1
-----gtcttgtttctattcttcaaattgtatatgggactggatcacta--aatagctggatttttgaa-tggctgattgctttgtttgcatttgagatttg-----gagcagATGCTGGGAGATGAGATTGGAAAAGGAGCTTATGGTCGAGTTTACAAAGGTTTGGACCTGGAGAATGGAGATTTTGTTGCCATTAAACAAGTTTCTTTGG
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gtgagtttttcattctcctttttttggtttagggagatcgtgatcattttcattatcttttgtatcgtgctgatcagtttttccttcttcttttgtatcgtgtaatcaaacagATAATAGGAGATGAAATCGGGAAAGGTGCATATGGCAGAGTTTACAAAGGCTTGGACCTGGAAAATGGGGACTTTGTGGCAATTAAGCAGGTTTCTCTGGMapped 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|193448927|gb|FK414240.1|FK414240EST: AGACGACGTCGTCTGCTTTCACTAAATCGAAGACCCTCGACAATAAATAT ATGCTGGGAGATGA
genomic: AGACGACGTCGTCTGCTTTCACTAAATCGAAGACCCTCGACAATAAATATgtacgccatt ... tttggagcagATGCTGGGAGATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagctggatttttgaatggctgattgctttgtttgcatttgagatttggagcagATGCTGGGAGATGAGATTGGAAAAGGAGCTTATGGTCGAGTTTACAAAGGTTTGGACCTGGAGAATGGAGATTTTGTTGCCATTAAACAAGTTTCTTTGG
ggctgat putative branch site (score: 4)
atttttgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcttgtttctattcttcaaattgtatatgggactggatcactaaatagctggatttttgaatggctgattgctttgtttgcatttgagatttggagcagATGCTGGGAGATGAGATTGGAAAAGGAGCTTATGGTCGAGTTTACAAAGGTTTGGACCTGGAGAATGGAGATTTTGTTGCCATTAAACAAGTTTCTTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatttg