Sequence
atgc intronic sequence ATGC exonic sequencegtataacaacttacaacttttcttctctttcaaatgaaaaaaacatgggagagagcttcttaactcatttcatgatgaatttgcagGATTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGAGGCCTGATTTAAAGAGAGGCATGTTCTCACAGCAGGAGGAGGATCTTAT
Basic information
species | Glycine max |
transcript | GLYMA05G02550.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G02550.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g36460.1 (Oryza sativa), 3'ss of exon 1
-------------gtataacaact-tacaacttttcttctctttcaaatgaaaaaaacatgggagagagcttcttaactcatttcatgatga-atttgcagGATTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGAGGCCTGATTTAAAGAGAGGCATGTTCTCACAGCAGGAGGAGGATCTTAT
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tgtttatatcgtaatttagttgctatacctctctctttgtatctcactctctgacagtgtgtga-ataatataatgtgtgttgctgagttgctgtgtacagGATTGGAGAGGTGTGGCAAGAGTTGCAGGCTGAGATGGATCAACTACCTGAGGCCTGATCTCAAGAGAGGCAGCTTCTCCCAGCAGGAGGAGGAGCTCAT
upper sequence: GLYMA05G02550.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G064744_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------------------------------------------gtataacaacttacaacttttcttctctttca-----aatgaaaaaaacatg-ggagagagcttcttaactcatttcatgatgaatttgcagGA-TTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGAGGCCTGATTTAAAGAGAGGCATGTTCTCACAGCAGGAGGAGGATCTTAT
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gtacgagtacgacccatgatttgtaatgtaaaaagggttcgtcagaaataatatatataaacgctgcgttaatttgcttgatatttgatctcctgctagctgttgccttttgcattgtgatcgtcgatattatttagtcagagaatgttttttttttgtgtg-tgtgtaagtaagGCTTGGAGAGATGCGGCAAGAGCTGCAGGCTGAGATGGATCAACTACCTGCGGCCTGACCTCAAGAGGGGCAGCTTCTCCCAGCAGGAGGAGGATCTCAT
upper sequence: GLYMA05G02550.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g09080.t01 (Vitis vinifera), 3'ss of exon 1
gtataacaacttacaacttttcttctctttcaaatgaaaaaaacatgggagagagcttcttaactcatttcatgatgaa-tttgcagGATTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGAGGCCTGATTTAAAGAGAGGCATGTTCTCACAGCAGGAGGAGGATCTTAT
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-----gtaattaatttctcttcttcaccttcca-cattttcatctttcttggtagttggtaaattgttttgatggtgatctttgtagGTTTGCAGAGGTGCGGAAAGAGTTGCAGATTGAGATGGATTAACTATTTGAGACCCGACCTTAAGAGAGGAATGTTCTCTCAGCAAGAGGAGGATATCAT
upper sequence: GLYMA05G02550.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S189_29V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------gtataacaacttacaacttttctt--ctctttcaaatgaaaaaaacatgggagagagcttcttaactc-atttcatgatgaatttgcagGATTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGAGGCCTGATTTAAAGAGAGGCATGTTCTCACAGCAGGAGGAGGATCTTAT
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tttcctctttgctctaaaaaaagaaaagttcagataccccgttgacaccaatttagaataagagttgtgtcgctgacgctggtgtgccctggaacaacagGGTTACAGAGATGTGGAAAAAGCTGCAGGTTAAGGTGGATAAACTATCTGAGGCCAGACTTAAAGCGAGGGGTTTTCTCACCAGCAGAGGAGAATCTGAT
upper sequence: GLYMA05G02550.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 1
gtataacaacttacaacttttcttctctttcaaatgaaaaaaacatgggagagagcttcttaactcatttcatgatgaatttgcagGATTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGAGGCCTGATTTAAAGAGAGGCATGTTCTCACAGCAGGAGGAGGATCTTAT
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------------gtgagtatttgtacctc---aatttcaagttctcgtgag-----ctcacaattc--ttggtggcattgtcacagGCCTCCAAAGATGTGGGAAGAGCTGCAGGCTGAGATGGATCAACTATCTCCGGCCCGACTTGAAAAGGGGCCACTTTTCGCAACAGGAAGAAGAGTTGATMapped 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|19269734|gb|BM885990.1|BM885990EST: CATAACAAGATTTGGAGTCGGATGCTGGAGCTCGGTTCCCAAACTAGCTG GATTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGA
genomic: CATAACAAGATTTGGAGTCGGATGCTGGAGCTCGGTTCCCAAACTAGCTGgtataacaac ... gaatttgcagGATTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatgaaaaaaacatgggagagagcttcttaactcatttcatgatgaatttgcagGATTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGAGGCCTGATTTAAAGAGAGGCATGTTCTCACAGCAGGAGGAGGATCTTAT
tcttaac putative branch site (score: 2)
aaaaaaacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataacaacttacaacttttcttctctttcaaatgaaaaaaacatgggagagagcttcttaactcatttcatgatgaatttgcagGATTGCAAAGATGTGGAAAGAGTTGCAGGTTGAGATGGATAAACTATTTGAGGCCTGATTTAAAGAGAGGCATGTTCTCACAGCAGGAGGAGGATCTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT