Sequence
atgc intronic sequence ATGC exonic sequencegtaaactttctatattcagtatggcattgtttcacagtttgattagttttattctgccaaatcacattgaaggttgcctaatctgaccatttctctatttttctttcatatgaaatttgttattcatcattattccctgtcgtattatttttgaaggcttgcataatctgacccttatgttttgtgtctgcttgtttagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG
Basic information
species | Glycine max |
transcript | GLYMA08G13560.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 5
gtaaactttctatattcagtatggcattgtttcacagtttgattagttttattctgccaaatcacattgaaggttgcctaatctgaccatttctctatttttctttcatatgaaatttgttattcatcattattccctgtcgtattatttttgaaggcttgc-ataatctgacccttatgttttgtgtctgcttgtttagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG
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---------------------------------------------------------------------------------------------gcacgatgccttgtgtgcaggccttggggc----cataagtcaataacata--attttgcattgtgtactatcaact-ataactagatgttattttctttattgcagTTCGGGAAGAAAACTCACCCTGAATGTGCTCGATTTTCACCTGATGGCCAGTACCTTGTATCATGCTCAGTGGATGGAATCATTGAG
upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 5
gtaaactttctatattcagtatggcattgtttcacagtttgattagttttattctgccaaatcacattgaaggttgcctaatctgaccatttctctatttttctttcatatgaaatttgttattcatcattattccctgtcgtattatttttgaaggcttgcataatctgacccttatgttttgtgtctgcttgtttagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG
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--------------------------------------------------------------------------tgctgaagacaga-atatttttaacatgctgtcaagtgagttttcttatctagcttttgatacta-------agttttataacattgca----ctgttcttgat-tcttgc------------agTTTGGGAAGAAAACTCATCCTGAATGTGCTCGATTTTCACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAA
upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaactttctatattcagtatggcattgtttcacagtttgattagttttattctgccaaatcacattgaaggttgcctaatctgaccatttctctatttttctttcatatgaaatttgttattcatcattattccctgtcgtattattt-ttgaaggcttgcataatct--gacccttatgttttgtgtc--tgcttgtttagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG
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-----------------------------------------------------------------gttcatattcac--actttaatagcttctttagcttagtggtctatga--tctgttgctcatgattattttgggttttctcatcagttgagttcttgtctaattttcatatctttttccttgtgctggtgctggtgcagTTTGGTAAAAAGAGTCATGCAGAATGCGCTAGATTCTCACCAGATGGACAGTTTCTTGCATCTTCTTCTGTGGATGGTTTTATCGAG
upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 6
gtaaactttctatattcagtatggcattgtttcacagtttgattagttttattctgccaaatcacattgaaggttgcctaatctgaccatttctctatttttctttcatatgaaatttgttattcatcattattccctgtcgtattatttttgaaggcttgcataatctgacccttatgttttgtgtctgcttg----tttagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG
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---------------------------------------------------------------------------------------------------gagctattatttgg---ttggtgtttagt-ttttcctttatgctattgggttcttcagttgttttgcttttcatctcatgtgttgtgctggtgttacactgcagTTTGGAACAAAAAGTCATGCAGAATATGCTCGGTTTTCTCCAGATGGGCAGTTTCTTGTGTCTTGCTCCGTGGATGGATTTATTGAGMapped 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|207732274|gb|GD705269.1|GD705269EST: AACAAGATGTGGATGACATGTATCCAACAACTCTTTCTCACACGATAAAG TTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAG
genomic: AACAAGATGTGGATGACATGTATCCAACAACTCTTTCTCACACGATAAAGgtaaactttc ... gcttgtttagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAG
EST:
gi|192300449|gb|FG987906.1|FG987906EST: AACAAGATGTGGATGACATGTATCCAACAACTCTTTCTCACACGATAAAG TTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAG
genomic: AACAAGATGTGGATGACATGTATCCAACAACTCTTTCTCACACGATAAAGgtaaactttc ... gcttgtttagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttttgaaggcttgcataatctgacccttatgttttgtgtctgcttgtttagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG
atctgac putative branch site (score: 3)
tctgctt putative PPT
ttatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaactttctatattcagtatggcattgtttcacagtttgattagttttattctgccaaatcacattgaaggttgcctaatctgaccatttctctatttttctttcatatgaaatttgttattcatcattattccctgtcgtattatttttgaaggcttgcataatctgacccttatgttttgtgtctgcttgtttagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG