Sequence
atgc intronic sequence ATGC exonic sequencegtagtttaagcatttgtttgttttgatgatgatatctgcaaatgttttgagtaacttgaacttccaatagttacataagttaggttgattttcttttcagacaacctttagactttgtattaattatttattatttttaccttttgtattattcatgaagGTTGCTTCCACTGTACTTTCCTCGGGATAAACATGAGGAGCAGGTTGCTTTGTCTAAACTTCCTGCAGATGTTGGGGATGAAAATGGTGAGACAATCTCA
Basic information
species | Glycine max |
transcript | GLYMA20G03330.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G03330.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g05660.1 (Oryza sativa), 3'ss of exon 6
gtagtttaagcatttgtttgttttgatgatgatatctgcaaatgttttgagtaacttgaacttccaatagttacataagttaggttgattttcttttcagacaacctttagactttgtattaattatttattatttttaccttttgtattattcatgaagGTTGCTTCCACTGTACTTTCCTCGGGATAAACATGAGGAGCAGGTTGCTTTGTCTAAACTTCCTGCAGATGTTGGGGATGAAAATGGTGAGACAATCTCA
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---------------------------------------------------------------------------gtacttagactaacacccacttatgctagc---taaatatgata--aatttcttataaaggttgacaacattgcattt--tgcagATTGCTTCCCCTATATTTCCCTCGGGACAAGAAAGAGGAAGAGATTGCTTCATTGAAACTTCCAGCTGATGTTGGGGATGAGAATGGTGAAACAATAATA
upper sequence: GLYMA20G03330.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G100707_T01 (Zea mays), 3'ss of exon 6
gtagtttaagcatttgtttgttttgatgatgatatctgcaaatgttttgagtaacttgaacttccaatagttacataagttaggttgattttcttttcagacaacctttagact-ttgtattaattatttattatttttaccttttgtattattcatgaagGTTGCTTCCACTGTACTTTCCTCGGGATAAACATGAGGAGCAGGTTGCTTTGTCTAAACTTCCTGCAGATGTTGGGGATGAAAATGGTGAGACAATCTCA
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-----------------------------------------------------------------------------------gtt--ctccacttgaagttcagtattagtttatcacaacaattttccaatataggttgataatgtttaattcctca-gGTTGCTTCCACTATATTTCCCTCGGGACAAGCAAGAAGAAGAGATAGCCGCATTGAAACTTCCAGCTGATGTTGGGGATGAGAATGGTGAGACAGTAATA
upper sequence: GLYMA20G03330.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G69340.1 (Arabidopsis thaliana), 3'ss of exon 7
gtagtttaagcatttgtttgttttgatgatgatatctgcaaatgttttgagtaacttgaacttccaatagt-tacataagttaggttgattttcttttcagacaacctttagactttgtattaattatttattatttttaccttttgtattattcatgaagGTTGCTTCCACTGTACTTTCCTCGGGATAAACATGAGGAGCAGGTTGCTTTGTCTAAACTTCCTGCAGATGTTGGGGATGAAAATGGTGAGACAATCTCA
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---------------------------------------------------catgtagaaatgctggcaatgtatataccataactt--cttatatttgagggg---tgcagaagcaatgccgaccattgctaa-----aaatttgactctctaaatgtagATTACTTCCACTTTACTTTCCTCGAGATGAACATGAGGAAGAGGTTGCCATATCAAAGCTCCCGGCTGATGTTGGAGATGAAAATGGTGAGACGGTTATA
upper sequence: GLYMA20G03330.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 6
gta-gtttaagcatttgtttgt-----tttgatgatgatatctgcaa-atgttttgagtaacttg--aacttccaatagttacataagttaggttgat----tttcttttcagacaacctttagactttgtattaattatttattatttttacc---ttttgtattattc--atgaagGTTGCTTCCACTGTACTTTCCTCGGGATAAACATGAGGAGCAGGTTGCTTTGTCTAAACTTCCTGCAGATGTTGGGGATGAAAATGGTGAGACAATCTCA
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gtatgtctgtattcttgtttgtgccattctgttgctgatctttatgccactttttgaattagttgctaggcaccttgtttcgcctatggcattgtgatgctattattttgtttctaattatgattttttgcccttaagttttgttggacttatcctattttgcctttttacaatgcagATTGCTTCCACTTTATTTTCCTCGGGATAAACATGAAGAGGAGGTGGCAATGTCAAAGCTTCCTGCAGATGTAGGGGATGAGAATGGTGAAACAATCATAMapped 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|208302400|gb|GE098345.1|GE098345EST: GCTGTTGTCTTTTGCACTGTGAGCACAACTGATACTGAGATATATAAAAG GTTGCTTCCACTGTACTTTCCTCGGGATAAACATGAGGAGCAGGTTGCTTT
genomic: GCTGTTGTCTTTTGCACTGTGAGCACAACTGATACTGAGATATATAAAAGgtagtttaag ... attcatgaagGTTGCTTCCACTGTACTTTCCTCGGGATAAACATGAGGAGCAGGTTGCTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttagactttgtattaattatttattatttttaccttttgtattattcatgaagGTTGCTTCCACTGTACTTTCCTCGGGATAAACATGAGGAGCAGGTTGCTTTGTCTAAACTTCCTGCAGATGTTGGGGATGAAAATGGTGAGACAATCTCA
tattaat putative branch site (score: 2)
tttgtattaattattt 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 |
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gtagtttaagcatttgtttgttttgatgatgatatctgcaaatgttttgagtaacttgaacttccaatagttacataagttaggttgattttcttttcagacaacctttagactttgtattaattatttattatttttaccttttgtattattcatgaagGTTGCTTCCACTGTACTTTCCTCGGGATAAACATGAGGAGCAGGTTGCTTTGTCTAAACTTCCTGCAGATGTTGGGGATGAAAATGGTGAGACAATCTCA
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