Sequence
atgc intronic sequence ATGC exonic sequence...agctggtaataaacaaaagtgttatagtcaaccatcgggcatttatatcattttttaaatttttacctgacattgttggggcaaatacatttgtgtacagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGGAAATTCAGCAAACAGGAAGAGGAGACAAT
Basic information
species | Glycine max |
transcript | GLYMA20G29710.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G29710.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G25560.1 (Arabidopsis thaliana), 3'ss of exon 1
agctggtaataaacaaaagtgttatagtcaacc--atcgggcatttatatcattttttaaatttttacctgacattgttggggcaaatacatttgtgtacagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGGAAATTCAGCAAACAGGAAGAGGAGACAAT
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------------gtctctctttcatcttcttctttattagtttttagtttctcaaactgagtcaactttgataattgttgttgggatttaatttg---atagGGTTACAAAGGAATGGGAAGAGCTGCAGATTAAGATGGATTAATTACCTAAGACCAGGGTTAAAGAGGGATATGATTAGTGCAGAAGAAGAAGAGACTAT
upper sequence: GLYMA20G29710.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G48920.1 (Arabidopsis thaliana), 3'ss of exon 1
-agctggtaataaacaaaagtgttatagtcaaccatcgggcatttatatcatttttta---aatttttacctgacattgttggggcaaatacatttgtgtacagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGGAAATTCAGCAAACAGGAAGAGGAGACAAT
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agaaatatattttttcactttgtta-aataaatatttaggctctttcgatatttgtcatcgggtttttatgtaaactaattggttttcacata---atgtatagGATTGCAGAGGAATGGGAAGAGTTGTAGATTAAGGTGGGTTAATTATTTAAGACCTGGACTTAAGAAGTCTTTATTCACTAAACAAGAGGAAACTATACT
upper sequence: GLYMA20G29710.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G52260.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------agctggtaataaacaaaagtgttatagtcaacc---atcgggcattta--tatcattttttaaatttttacctgacattgt--tggggcaaatacatttgt-gtac-agGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGGAAATTCAGCAAACAGGAAGAGGAGACAAT
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gtttttttttaatctctaaaatcttatattagactctctttttttcttaaccctatatcctatattagactcttaattctcatcattgttgttaatcttatccttaactaagagtaattgttgtgccagGATTGCAAAGGAATGGGAAAAGCTGCAGATTAAGGTGGATTAATTACCTAAGACCAGGACTAAAGAGGGGGTCGTTTAGTGAAGAAGAAGAAGAGACCAT
upper sequence: GLYMA20G29710.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0050g00050.t01 (Vitis vinifera), 3'ss of exon 1
agctggtaataaacaaaagtgttata-gtcaaccatcgggcatttatatcattttttaa-atttttac-ctgacattgttggggcaaatacatttgtgtacagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGGAAATTCAGCAAACAGGAAGAGGAGACAAT
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-atgttcttttagtgccattgttgcatgttacataccatatgatcacatgttggtctagcattaatatgccttgattctttgaccttgtg-gtgcat-tgcagGTTTGCAAAGGAATGGAAAGAGCTGCAGATTAAGGTGGATTAACTACTTAAGACCAGGATTAAAACGCGGGATGTTTACGATCGAGGAGGAAGAGACGAT
upper sequence: GLYMA20G29710.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S189_29V6.1 (Physcomitrella patens), 3'ss of exon 1
------agctggtaataaacaaaagtgttatagtcaaccatcgggcatttatatcattttttaaatttttacctgacattgttggggcaaatacatttgtgta-cagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGGAAATTCAGCAAACAGGAAGAGGAGACAAT
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tttcctctttgctctaaaaaaagaaaagttcagataccccgttgacaccaatttagaataagagttgtgtcgctgacgctggtg-------tgccctggaacaacagGGTTACAGAGATGTGGAAAAAGCTGCAGGTTAAGGTGGATAAACTATCTGAGGCCAGACTTAAAGCGAGGGGTTTTCTCACCAGCAGAGGAGAATCTGATMapped 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|8283916|gb|BE021475.1|BE021475EST: CATCCTTAAACATGGTCATGGCTGTTGGAGTTCTGTCCCCATTAAGGCAG GCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAA
genomic: CATCCTTAAACATGGTCATGGCTGTTGGAGTTCTGTCCCCATTAAGGCAGgttggtttct ... ttgtgtacagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcattttttaaatttttacctgacattgttggggcaaatacatttgtgtacagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGGAAATTCAGCAAACAGGAAGAGGAGACAAT
acctgac putative branch site (score: 3)
ttttttaaatttttac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agctggtaataaacaaaagtgttatagtcaaccatcgggcatttatatcattttttaaatttttacctgacattgttggggcaaatacatttgtgtacagGCTTGCAAAGGAATGGAAAGAGCTGTAGATTAAGGTGGATTAACTATCTAAGGCCAGGATTAAAGAGAGGGAAATTCAGCAAACAGGAAGAGGAGACAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
-gctggta
- - - - - aaacaaa
- - - - - - - - - - - - - - caaccat
- - - - - - - - - - - - - - - - - - -ggcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttggg