Sequence
atgc intronic sequence ATGC exonic sequencegtatttcttcatttttttctaatattctctattttttgttttaattttggtcatgtatatttgctgtttaaacttgtgttcctagattttatatatatatatatattttgcacagATTGGCATTAAAGCAGAATGGAGAGCTCATCAAGGGCATCTTGTTCTTTTCTTGGGAAACAAGAATACTTCTCCTCTTGTCTCTGTTCAAGCTTTAATAT
Basic information
species | Glycine max |
transcript | GLYMA17G05410.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G092741_T01 (Zea mays), 3'ss of exon 5
gtatttcttcatttttttctaatattctctattttttgttttaattttggtcatgtatatttgctgtttaaacttgtgttcctagattttatatatatat-atatattttgcacagATTGGCATTAAAGCAGAATGGAGAGCTCATCAAGGGCATCTTGTTCTTTTCTTGGGAAACAAGAATACTTCTCCTCTTGTCTCTGTTCAAGCTTTAATAT
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---------------gtttgcataaattgtgttgcattgcatcacttcacataactgtatgttttatccgtcctcatgatgtgcatcttccttttcctattataccttgtgtctagATTGGTATGAAAGCAGAGTGGCGTGCCCATCATGGCCGTCTTGTTCTTTTCCTGGGTAACAAAAATACTTCAGCCCTTACGTCAGTGCGGGTGCTGATTT
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 20
lower sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 20
gtatttcttcatttttttctaatattctctattttttgttttaattttggtcatgtatatttgctgtttaaacttgtgttcctagattttatatatatatatatattttgcacagATTGGCATTAAAGCAGAATGGAGAGCTCATCAAGGGCATCTTGTTCTTTTCTTGGGAAACAAGAATACTTCTCCTCTTGTCTCTGTTCAAGCTTTAATAT
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------gtttgtttttttctagtttgtgcttttatttattcaagtatgcagcagacaagcct-ccgagctttcttatgttcccc-attttgttgat---tgtttgtattcctcagATTGGCATCAAAGCTGAATGGAGAGGACACCATGGTAGACTTGTTCTCTTCATGGGAAACAAGAATACTTCTCCACTTACATCAGTTCAAGCTCTGATAC
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 20
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 20
gtatttcttcatttttttctaatattctctattttttgttttaattttggtcatgtatatttgctgtttaaacttgtgttcctagattttatatatatatatatattttgcacagATTGGCATTAAAGCAGAATGGAGAGCTCATCAAGGGCATCTTGTTCTTTTCTTGGGAAACAAGAATACTTCTCCTCTTGTCTCTGTTCAAGCTTTAATAT
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------gtttgtttttttctagtttctgcttttatttattcaagtatgcagcagacaagcct-ccgagctttcttatgttccca--ttttgttgat---tgtttgtattcctcagATTGGCATCAAAGCTGAATGGAGAGGACACCATGGGAGACTTGTTCTCTTCATGGGAAACAAGAATACTTCTCCACTTACATCAGTTCAAGCTCTGATAC
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 20
----------------------------------------------------------gtatttcttcatttttttctaatattctctattttttgttttaattttggtcatgtatatttg--ctgtttaaacttgtgttcc---tagattttatatata-tata-tatattttgca----------cagATTGGCATTAAAGCAGAATGGAGAGCTCATCAAGGGCATCTTGTTCTTTTCTTGGGAAACAAGAATACTTCTCCTCTTGTCTCTGTTCAAGCTTTAATAT
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gttttaaatctttttttttaagtctttccttttgactgtaatttactctaacttaattgtcctttctggtgttttgctattatagcccacattt-atgttaatactagtta-gcatagttagattttttatttttttattttatgtaacttccatgagtcctatagtgaattttgtcaattaccttccagATTGGCATTAAAGCAGAGTGGCGAGCACATCATGGGCGTCTTGTCCTTTTCTTGGGAAACAAGAATACTTCTTCACTTGCTTCAGTTCAAGCTCTGATATMapped 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|14126214|gb|BG790652.1|BG790652EST: CTTTGTGCATGAAGGATAGTGGTGTTCTATATGAGGATCCTTATATTCAG ATTGGCATTAAAGCAGAATGGAGAGCTCATCAAGGGCATCTTGTTCTTTTC
genomic: CTTTGTGCATGAAGGATAGTGGTGTTCTATATGAGGATCCTTATATTCAGgtatttcttc ... ttttgcacagATTGGCATTAAAGCAGAATGGAGAGCTCATCAAGGGCATCTTGTTCTTTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgctgtttaaacttgtgttcctagattttatatatatatatatattttgcacagATTGGCATTAAAGCAGAATGGAGAGCTCATCAAGGGCATCTTGTTCTTTTCTTGGGAAACAAGAATACTTCTCCTCTTGTCTCTGTTCAAGCTTTAATAT
ttgtgttcctagattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttcttcatttttttctaatattctctattttttgttttaattttggtcatgtatatttgctgtttaaacttgtgttcctagattttatatatatatatatattttgcacagATTGGCATTAAAGCAGAATGGAGAGCTCATCAAGGGCATCTTGTTCTTTTCTTGGGAAACAAGAATACTTCTCCTCTTGTCTCTGTTCAAGCTTTAATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT