Sequence
atgc intronic sequence ATGC exonic sequence...actagtagtttgtattatacggtttcatttacttttgaacttcttgtttgtatagtttacttggtttcagagctatcctaattgtgggaaatatttgtagTTCCATTCAGGCATGGGGAGCGCATTGGTTTCAGTTACCTTGTCTCTCAAAAGTACACTGGGGATAGAGCTCTAGTAAAGGTTTTCCGGAATTTACAGAT
Basic information
species | Glycine max |
transcript | GLYMA01G16820.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G16820.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g50880.1 (Oryza sativa), 3'ss of exon 4
actagtagtttgtatt--atacggtttcattt--acttttgaact-tcttgtttgtatagtttacttggtttcagagctatcctaattgtgggaaatatttgtagTTCCATTCAGGCATGGGGAGCGCATTGGTTTCAGTTACCTTGTCTCTCAAAAGTACACTGGGGATAGAGCTCTAGTAAAGGTTTTCCGGAATTTACAGAT
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---tcttgtttacatttgaaaagttttgatgtcaacttcctaaccatttagaaaataaatctaatattgtcatattttctgacaaatcttgttgtgtaacc--agTTCCTTTCAGGCACGGCGAGCGCATTGGCTTCAGTTATCTTGTTTCCCAGAAATATACTGGCGAGAAGGCTCTAGTTAAAGTCCTGCGCAATTCGAAAGT
upper sequence: GLYMA01G16820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G868913_T01 (Zea mays), 3'ss of exon 1
actagtagtttgtattatacggtttcatttacttttgaacttcttgtttgtat-agttt----acttggtttcagag-ctatcctaattgtgggaaatatttgtagTTCCATTCAGGCATGGGGAGCGCATTGGTTTCAGTTACCTTGTCTCTCAAAAGTACACTGGGGATAGAGCTCTAGTAAAGGTTTTCCGGAATTTACAGAT
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----gcattct-taacaagaagccacatgaagattttaaatttaagagggaattagcctccagatttggtttttgaggctgtctttggtttgcttggtcatc-cagTTCCTTTCAGGCGTGGTGAGCGCATTGGATTCAGCTACCTTGTTTCTCAAAAGTATACAGGTGAGAAGGCACGTGTGAAAGTACTTCCCAACTCAAATGT
upper sequence: GLYMA01G16820.1 (Glycine max), 3'ss of exon 4
lower sequence: AC212112.4_FGT002 (Zea mays), 3'ss of exon 4
----actagtagtttgtattatacg--gtttcatttacttttgaacttcttgtttgtatagtttacttggtttcagagctatcctaattgtgggaaatatttgtagTTCCATTCAGGCATGGGGAGCGCATTGGTTTCAGTTACCTTGTCTCTCAAAAGTACACTGGGGATAGAGCTCTAGTAAAGGTTTTCCGGAATTTACAGAT
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ttgggtatggaagttatgttgaaagttgtgctaaatgtactagaaatggcaagcatctcatgctaatttgtttctta-ccatcttttttgttgg-----tcaacagTTCCTTTCAGGCATGGTGAGCGCATTGGCTTCAGTTATCTGGTTTCTCAGAAATATACTGGAGAGAAAGCTCTTGTTAAAGTTCTGCGTGATTCAAAAGT
upper sequence: GLYMA01G16820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G165969_T01 (Zea mays), 3'ss of exon 5
----actagtagtttgtattatacggtttcat-ttacttttgaacttcttgtttgtatagtttacttggtttcagagctatcctaattgtgggaaatatttgtagTTCCATTCAGGCATGGGGAGCGCATTGGTTTCAGTTACCTTGTCTCTCAAAAGTACACTGGGGATAGAGCTCTAGTAAAGGTTTTCCGGAATTTACAGAT
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ctttctcatccagttgaaacttaccttttcatgctactcagttatatccagtgaggaaaattgatttgatctctt-gctctctcactgcttggtcatcc----agTTCCTTTTAGGCATGGTGAACGCATTGGATTTACCTACCTTGTTTCTCAAAAGTACACTGGTGAGAAGGCACGCGTGAAAGTACTTCGCAACTCAAAAAT
upper sequence: GLYMA01G16820.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0066g01660.t01 (Vitis vinifera), 3'ss of exon 4
actagtagtttgtattatacggtttcatt----tacttttgaacttcttgtttgtatagtttacttggtttcagagctatcctaattgtgggaaatatttgtagTTCCATTCAGGCATGGGGAGCGCATTGGTTTCAGTTACCTTGTCTCTCAAAAGTACACTGGGGATAGAGCTCTAGTAAAGGTTTTCCGGAATTTACAGAT
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----atgacttccataatgaagaatcaagaaaatactgtcctaaaaaacaatgcaatggaaaaaatagcaactcactttttctgttttgggattaaaattgcagTTCCATTTAGGCATGGAGAGCGCATTGGTTTCAGTTACCTTGTTTCTCAAAAGTATACGGGGGATAATGCTGTAGTTAAAGTTCTCCGGAATTCACAGATMapped 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|15203292|gb|BI426060.1|BI426060EST: TGATGTAATTCTCAGCTTTGATGGGGTCAATATTTCGAATGATGGAACAG TTCCATTCAGGCATGGGGAGCGCATTGGTTTCAGTTACCTTGTCTCTCAAA
genomic: TGATGTAATTCTCAGCTTTGATGGGGTCAATATTTCGAATGATGGAACAGgtaatctacc ... atatttgtagTTCCATTCAGGCATGGGGAGCGCATTGGTTTCAGTTACCTTGTCTCTCAAA
EST:
gi|16348581|gb|BI974176.1|BI974176EST: AGCTTTGATGGGGTCAATATTTCGAATGATGGAACAG TTCCATTCAGGCATGGGGAGCGCATTGGTTTCAGTTACCTTGTCTCTCAAA
genomic: AGCTTTGATGGGGTCAATATTTCGAATGATGGAACAGgtaatctacc ... atatttgtagTTCCATTCAGGCATGGGGAGCGCATTGGTTTCAGTTACCTTGTCTCTCAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgtatagtttacttggtttcagagctatcctaattgtgggaaatatttgtagTTCCATTCAGGCATGGGGAGCGCATTGGTTTCAGTTACCTTGTCTCTCAAAAGTACACTGGGGATAGAGCTCTAGTAAAGGTTTTCCGGAATTTACAGAT
tcctaat putative branch site (score: 2)
aaatatttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actagtagtttgtattatacggtttcatttacttttgaacttcttgtttgtatagtttacttggtttcagagctatcctaattgtgggaaatatttgtagTTCCATTCAGGCATGGGGAGCGCATTGGTTTCAGTTACCTTGTCTCTCAAAAGTACACTGGGGATAGAGCTCTAGTAAAGGTTTTCCGGAATTTACAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtggg