Sequence
atgc intronic sequence ATGC exonic sequencegtatatttacttccttgctacggcttgctgcactggttaattgaatgggatcatattttaaagttggtatttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAG
Basic information
species | Glycine max |
transcript | GLYMA08G20070.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G20070.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os04g35420.1 (Oryza sativa), 3'ss of exon 14
gtatatttacttccttgctacggcttgctgcactggttaattgaatgggatcatattttaaagttg--gtatttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAG
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gtaacttgattttcatagtgtgcaca--tatatttgttgttt-attggtgcctcgtgctaattgtgcaggattgcagGTATTAATAAACCTGATGTCCGTTTTGTTATCCATCATTCCCTGCCCAAATCAATTGAAGGATATCATCAG
upper sequence: GLYMA08G20070.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G319573_T02 (Zea mays), 3'ss of exon 11
gtatattta-cttccttgctacggcttgctgcactggttaattgaatgggatcatattttaaagttggtatttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAG
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gtaacttaatctttcaaacacctgtgtataacatctatta-ttgggtgt--tccaatctaataggacaaactgtagGTATCAATAAACCTGATGTTCGCTTTGTTATTCATCATTCACTGCCCAAGTCAATTGAAGGATATCATCAG
upper sequence: GLYMA08G20070.1 (Glycine max), 3'ss of exon 17
lower sequence: AT1G10930.1 (Arabidopsis thaliana), 3'ss of exon 15
gtatatttacttccttgctacggcttgctgcactggttaattgaatgggatcatattttaaagttg-gtatttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAG
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--gtactggttt--ttgctaatgttgttttaattcattga--aaatgttgctgcccattaacattgcacatttcagGAATCAACAAGCCTGATGTCCGCTTTGTTATTCATCACTCGCTCCCAAAGTCTATAGAAGGCTATCATCAG
upper sequence: GLYMA08G20070.1 (Glycine max), 3'ss of exon 17
lower sequence: AT1G60930.1 (Arabidopsis thaliana), 3'ss of exon 15
gtatatttact--tccttgctacggcttgctgcactggttaattgaatgggatcatattttaaagttggtatttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAG
|| ||| | || || || | | | || || |||||| | ||| |||| ||||||||| || || || |||||||| || |||||||| |||||||| || ||||| || || |||||||||||||||
--gtaattaatggtctctgttatag----ccactttgattgattgaagtttgctgcctgctaacgttgatatttcagGAATCAATAAGCCTGATGTTCGTTTTGTAATTCATCATTCTCTACCAAAGTCCATAGAAGGCTATCATCAG
upper sequence: GLYMA08G20070.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv12s0035g00400.t01 (Vitis vinifera), 3'ss of exon 11
gtatatttacttccttgctacggcttgctgcactggttaattgaatgggatcatattttaa---agttggta------tttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAG
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----gtatcattgattattactattttcctgacttggtagctgatgacaaccatgtattgacatagtcactagactcattacagGTATCAACAAACCAGATGTCCGCTTTGTCATTCATCATTCTCTTCCAAAATCAATTGAAGGGTATCATCAGMapped 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|193549141|gb|FK505436.1|FK505436EST: GAGCAAAGATGAGATCAATATAATTTGTGCTACTGTGGCATTTGGAATGG GTATTAACAAACCTGATGTCCGCTTTGTAATCC
genomic: GAGCAAAGATGAGATCAATATAATTTGTGCTACTGTGGCATTTGGAATGGgtatatttac ... ggtatttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cggcttgctgcactggttaattgaatgggatcatattttaaagttggtatttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAG
ggttaat putative branch site (score: 4)
atcatattttaaagtt 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
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gtatatttacttccttgctacggcttgctgcactggttaattgaatgggatcatattttaaagttggtatttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG