Sequence
atgc intronic sequence ATGC exonic sequence...taactacttactaattatttattggatatgatttatttctaaattttaaaacttatttgctccgtttgtgatttaacatcaattgtggttatcttattagGTTCGAGAAGAAAGTAAGATATGCCTCTCGCAAGGCTAGGGCTGATGTCAGAAAGCGTGTGAAGGGCCGATTTGTCAAAGCTGGTGATGTCTATGACTAT
Basic information
species | Glycine max |
transcript | GLYMA02G38870.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G38870.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g19444.2 (Oryza sativa), 3'ss of exon 4
-taactacttactaattatttattggatatgatttatttctaaattttaaaacttatttgctccgtttgtgatttaacatcaattgtgg-ttatcttattagGTTCGAGAAGAAAGTAAGATATGCCTCTCGCAAGGCTAGGGCTGATGTCAGAAAGCGTGTGAAGGGCCGATTTGTCAAAGCTGGTGATGTCTATGACTAT
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atgtcagtccactgat-gctaacatgctatatttctagcataccaattgcctcctttttga-cagctagctgattatcttttctcatggcttctcttgacagATTTGACAAGAAAATCAGGTATGCATCTCGCAAGGCTAGGGCAGATGTGAGAAAAAGAGTCAAGGGCCGGTTTGTTAAGGCTGGTGAAGCATACGACTAC
upper sequence: GLYMA02G38870.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G07650.2 (Arabidopsis thaliana), 3'ss of exon 4
taactacttactaattatttattggatatgatttatttctaaattttaaaacttatttgctccgtttgtgatttaacatcaattgtggttatctt--attagGTTCGAGAAGAAAGTAAGATATGCCTCTCGCAAGGCTAGGGCTGATGTCAGAAAGCGTGTGAAGGGCCGATTTGTCAAAGCTGGTGATGTCTATGACTAT
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---gtaagtagtagtctgaaactgcaaatacatgagcatca----ttgaagtgagtgcaggattttcctaatgtgactctggcttcttttttctggaaacagGTTTGATAAGAGAGTGAGGTATGCTTCCCGCAAAGCAAGAGCTGATGTGAGACGGCGTGTAAAGGGGCGATTTGTCAAAGCTGGTGAAGCTTATGATTAC
upper sequence: GLYMA02G38870.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0194g00070.t01 (Vitis vinifera), 3'ss of exon 4
---taactacttactaattatttattggatatgatttatttctaaattttaa-aacttatttgctccgtttgtgatttaacatcaattgtggttatcttattagGTTCGAGAAGAAAGTAAGATATGCCTCTCGCAAGGCTAGGGCTGATGTCAGAAAGCGTGTGAAGGGCCGATTTGTCAAAGCTGGTGATGTCTATGACTAT
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actaaaataagggtaggatttttatggaatttgattagaatgaaaattttcataactaaaaaataattttttttctttttcatcaat----gacttatgaacagATTTGAGAAGAAAATAAGATATGCCTCTCGCAAAGCAAGGGCAGATGTCAGGAAGCGTGTGAAGGGGCGATTTGTTAAGGCTGGCGATGCTTATGATTACMapped 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|19348272|gb|BM892804.1|BM892804EST: GAAGACCCGGAA GTTCGAGAAGAAAGTAAGATATGCCTCTCGCAAGGCTAGGGCTGATGTCAG
genomic: GAAGACCCGGAAgtaagttaat ... atcttattagGTTCGAGAAGAAAGTAAGATATGCCTCTCGCAAGGCTAGGGCTGATGTCAG
EST:
gi|8402537|gb|BE058171.1|BE058171EST: AACCGAAGCAATGCTGTCATGCGCTACAAGGNNNNNNNGAAGACCCGGAA GTTCGAGAAGAAAGTAAGATATGCCTCTCGCAAGGCTAGGGCTGATGTCAG
genomic: AACCGAAGCAATGCTGTCATGCGCTACAAGGAAAAAAAGAAGACCCGGAAgtaagttaat ... atcttattagGTTCGAGAAGAAAGTAAGATATGCCTCTCGCAAGGCTAGGGCTGATGTCAG
EST:
gi|19348099|gb|BM892631.1|BM892631EST: GAAGACCCGGAA GTTCGAGAAGAAAGTAAGATATGCCTCTCGCAAGGCTAGGGCTGATGTCAG
genomic: GAAGACCCGGAAgtaagttaat ... atcttattagGTTCGAGAAGAAAGTAAGATATGCCTCTCGCAAGGCTAGGGCTGATGTCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaaacttatttgctccgtttgtgatttaacatcaattgtggttatcttattagGTTCGAGAAGAAAGTAAGATATGCCTCTCGCAAGGCTAGGGCTGATGTCAGAAAGCGTGTGAAGGGCCGATTTGTCAAAGCTGGTGATGTCTATGACTAT
atttaac putative branch site (score: 3)
ttatctt putative PPT
atttaacatcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taactacttactaattatttattggatatgatttatttctaaattttaaaacttatttgctccgtttgtgatttaacatcaattgtggttatcttattagGTTCGAGAAGAAAGTAAGATATGCCTCTCGCAAGGCTAGGGCTGATGTCAGAAAGCGTGTGAAGGGCCGATTTGTCAAAGCTGGTGATGTCTATGACTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtggtt