Sequence
atgc intronic sequence ATGC exonic sequencegtgaggtttatattgtaaattgtaattgagatgcttgcttaaatgacttaaagtcttgttgatttagtgctagggttaactaatgtgcctcttcctatgagggtcattgcagATAAGGAAAAACAAGTTGATATACCAGGACAAGCCAAGGCTAAAAACAGCATTAGAAATGTTGAGAATCAGCATGAGCCTTGAAGACAGCTTATATAAG
Basic information
species | Glycine max |
transcript | GLYMA03G37290.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G37290.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g21310.1 (Oryza sativa), 3'ss of exon 2
gtgaggtttatattgtaaattgtaattgagatgcttgcttaaatgacttaaagtc-ttgttgatttagtgctagggttaactaatgtgcctcttcctatgagggtcattgcagATAAGGAAAAACAAGTTGATATACCAGGACAAGCCAAGGCTAAAAACAGCATTAGAAATGTTGAGAATCAGCATGAGCCTTGAAGACAGCTTATATAAG
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-----------atttctgaacat--ttgatacagtggtccaacagatttgttgtcgttgagcatataaactcagtttggtgtgttctttgccatgccatgccaaatttaacagATCAGGAAGAACAAGCTGATATACCAGGACAAGCCGAGGCTCAAGACCGCACTTGAGATGCTCAGGACCAGCATGTACGTAGAGGACAGCTTGTCCAAG
upper sequence: GLYMA03G37290.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g29974.1 (Oryza sativa), 3'ss of exon 6
------------------------------------------gtgaggtttatattg---taaattgtaa----ttgagatgcttgcttaaatgactta-----aagtcttgttgatttagtgctagggt-taactaatgtgcctcttcctatgagggtcattg--cagATAAGGAAAAACAAGTTGATATACCAGGACAAGCCAAGGCTAAAAACAGCATTAGAAATGTTGAGAATCAGCATGAGCCTTGAAGACAGCTTATATAAG
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gttcaaacgtttgagcaattcaccaatttgtattgtcagaatgcaagattcagacctaatcatgctgcgagatcttgtgtgttttgagcaaagaatgtaggaaaaagagagagagagagagagagagattctgttttctgaaactgttttcttgtgaacaattgagcagATCAGGAAGAACAAGCTGATCTACCAGGACAAGCCCAGGCTGAAGACGGCGCTGGAGCTGCTGCGAACCAGCATCAGCGTCGAGCAAAGCTTGTCACAG
upper sequence: GLYMA03G37290.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g29974.2 (Oryza sativa), 3'ss of exon 6
------------------------------------------gtgaggtttatattg---taaattgtaa----ttgagatgcttgcttaaatgactta-----aagtcttgttgatttagtgctagggt-taactaatgtgcctcttcctatgagggtcattg--cagATAAGGAAAAACAAGTTGATATACCAGGACAAGCCAAGGCTAAAAACAGCATTAGAAATGTTGAGAATCAGCATGAGCCTTGAAGACAGCTTAT-ATAAG
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gttcaaacgtttgagcaattcaccaatttgtattgtcagaatgcaagattcagacctaatcatgctgcgagatcttgtgtgttttgagcaaagaatgtaggaaaaagagagagagagagagagagagattctgttttctgaaactgttttcttgtgaacaattgagcagATCAGGAAGAACAAGCTGATCTACCAGGACAAGCCCAGGCTGAAGACGGCGCTGGAGCTGCTGCGAACCAGCATCAGCGTCGAGCAAAGCTTGTCACAGG
upper sequence: GLYMA03G37290.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G62860.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgaggtttatattgtaaattgtaattgagatgcttgcttaaatgacttaaagtcttgttgatttagtgctagggttaactaatgtgcctcttcctatgagggtcattgcagATAAGGAAAAACAAGTTGATATACCAGGACAAGCCAAGGCTAAAAACAGCATTAGAAATGTTGAGAATCAGCATGAGCCTTGAAGACAGCTTATATAAG-
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--------------------------------------gtatattaatcgaatcagtcaacacataactaaaaagtgtactaataaaaaacttggttcctaa---aatgtagATAAGGAACAACAAGCTGATATATCAAGACAAGCCAAGACTTAAAACCGCACTTGAAATGCTTAGAACGAGCATGGACCTTGAAGACACTCTCCACGAGA
upper sequence: GLYMA03G37290.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g00510.t01 (Vitis vinifera), 3'ss of exon 6
gtgaggtttatattgtaaattgtaattgagatgcttgcttaaatgacttaaagtcttgttgatttagtgctagggttaactaatgtgcctcttcctat-gagggtcat-tgcagATAAGGAAAAACAAGTTGATATACCAGGACAAGCCAAGGCTAAAAACAGCATTAGAAATGTTGAGAATCAGCATGAGCCTTGAAGACAGCTTATATAAG
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-----------gtgatgatatatatctgttttccaacttctagtcccatata-tttctctcatgtaaacgtgggattctgaacagcattgctttctgtcgttaataatgcgcagATAAGAAACAATAAGTTGATATACCAAGACAAGCCGAGGCTGAAGACAGCGCTGGAAATGCTCAGAACCAGCATGAGCCTCGAGGACTCATTACATGAGMapped 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|17519393|gb|BM188435.1|BM188435EST: CAAAGGATGTCATCGATTCAGCCTTTAAAGACCCTGCTAAACGAGAGAGG ATAAGGAAAAACAAGTTGATATACCAGGACAAGCCAAGGCTAAAAACAGCA
genomic: CAAAGGATGTCATCGATTCAGCCTTTAAAGACCCTGCTAAACGAGAGAGGgtgaggttta ... gtcattgcagATAAGGAAAAACAAGTTGATATACCAGGACAAGCCAAGGCTAAAAACAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgatttagtgctagggttaactaatgtgcctcttcctatgagggtcattgcagATAAGGAAAAACAAGTTGATATACCAGGACAAGCCAAGGCTAAAAACAGCATTAGAAATGTTGAGAATCAGCATGAGCCTTGAAGACAGCTTATATAAG
aactaat putative branch site (score: 2)
ttaactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggtttatattgtaaattgtaattgagatgcttgcttaaatgacttaaagtcttgttgatttagtgctagggttaactaatgtgcctcttcctatgagggtcattgcagATAAGGAAAAACAAGTTGATATACCAGGACAAGCCAAGGCTAAAAACAGCATTAGAAATGTTGAGAATCAGCATGAGCCTTGAAGACAGCTTATATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA