Sequence
atgc intronic sequence ATGC exonic sequence...atctggttgcatgcagctatcagtagaggcattttagagaagtagcttgcgcttctcacttagtgtgtatatcttgtgcattgtatttcctgtattgcagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
Basic information
species | Glycine max |
transcript | GLYMA11G10180.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G10180.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g38970.1 (Oryza sativa), 3'ss of exon 3
atctggttgcatgcagctatcagtagaggcattttagagaagtagcttgcgcttctcacttagtgtgtatatcttgtgcattgtatttcctgtattgcagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
| || ||| || | || || | || |||| | || | | ||| || || |||| |||| || || | | | | | |||||| ||||| ||||||||||| || ||||||||||| |||||||||||||| || ||||| |||||||||
gtatg-ttg-atctatct-tctggggatgcatcattcagta--aactta---tttgatttttgtgt-tataactcttgttatacaaaat-tatttggcagGTTCGCAAATTCAGTAAACACTGCAGAAGTTGTGACAAATGTGTTGATGGATTTGATCATCATTGTCGG
upper sequence: GLYMA11G10180.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g44230.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------atct-ggttgcatgcagctatcagtagaggcattttagagaagtagctt-----gcgcttctcacttagtgtgtatatcttgtgcattgtatttcctgtattg-cagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
||| ||| || ||| | | || | | || ||| || | || | || ||| ||| | | ||| ||||| ||||| |||||||||||||| |||||||||||||||||||| ||||| || ||||| || ||||||
gtaagcttgtatatgtgctcaacgttggaactgcataatgatttttgtctcagtttcaggcaaaatatatcatttattttcctctgtaataactttgtaaaagcgaaaacttctgttgtcagatgttgctaattacaaaggcaaaattttcagGTTCGCAAATTCAGTAAACATTGCAGAAGTTGTGATAAATGTGTGGATGGTTTTGATCATCACTGTCGG
upper sequence: GLYMA11G10180.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G149442_T01 (Zea mays), 3'ss of exon 3
----atctggttgcatgcagctatcagtagaggcatttt------agagaagtagcttgcgct---tctcacttagtgtgtatatcttgtgcatt--gtatttcctgtattgcagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
| ||| | | || | || ||||| | || || || ||| | | |||| ||| | || | | | || ||||| ||||| ||||||||||| || ||||||||||| || ||||| ||||| || ||||| || ||||||
gtacgttctgttcaacgttgcaaccatgtagcatatttttttcctaagtcagcaggttatatcctgtcttaacttgtgttgtcatcacttccaattaagaaagatgatttttcagGTTCGCAAATTCAGTAAACACTGCAGAAGTTGTGACAAGTGTGTGGATGGATTTGATCATCACTGTCGG
upper sequence: GLYMA11G10180.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G22180.1 (Arabidopsis thaliana), 3'ss of exon 3
atctggttgcatgcagctatcagtagaggcattttagagaagtagcttgcgcttctcacttagtgtgtatatct--tgtgcattgtatttcctgtatt--gcagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
| | | | | | || |||| | || |||||| | | | | || || || | |||| | | ||| | | || ||||| ||||||||||| || |||||| ||||||||||||||||||||||| | || ||||||||||| |
-tttcttggtctttatcttc---tagaatctgctttaagaagtctttagggaaagcaatttggttcagattttagatgtgtactcaattatgtatgtttcacagGTACGCAAGTTCAGCAAGCATTGTCGAAGTTGTGATAAATGTGTTGATTGTTTTGATCACCATTGCAAG
upper sequence: GLYMA11G10180.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0017g01770.t01 (Vitis vinifera), 3'ss of exon 3
-atctggttgc-atgcagctatcagtagaggcattttagagaagtagcttgcgcttctcacttagtgtgtatatcttgtgcattgtatttcctgtattgcagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
| ||||| ||| || || | | ||| ||| | || | ||| | | | | | || | |||| | |||||||| ||||| ||||| ||||| |||||||||||||| |||||||| ||||| || |||||||||||||||
actttggttatgatgtagacatgcccacatgcagcttatggtc-taaca-atatttccttttgggctttttttatttaccaagaaaatttttcatgttgcagGTACGCAAATTCAGCAAACACTGTAGAAGTTGTGACAAATGTGTGGATGGATTTGATCACCATTGTCGG
upper sequence: GLYMA11G10180.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S96_102V6.1 (Physcomitrella patens), 3'ss of exon 3
atctggttgcat--gcagctatcagtagaggcattt-tagagaagtagcttgcgcttctcacttagtgtgtatatcttgtgcattgtattt---cctgtattgcagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
|||| || | | || || || | | || || | | || ||| | ||| || | | ||| ||| | | ||| |||| || |||| |||||||||||| ||||| || || ||||||||||||||||| || ||||||||||||
-----gttgtattggtcaatgcttgtgaggggatctctctagcagcaaaatttcttttgtactaaaattgtg-atagtaaaaactgtgtttgttctcgatttgtagGTTCGGAAGTACAGTAAACATTGCAGAAGCTGCGACAAATGTGTTGATGGCTTTGACCACCATTGTCGG
upper sequence: GLYMA11G10180.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S118_83V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------------------atctggttgcatgcagctatcagtagaggcat-tttagagaagtagcttgcgcttctcacttagtgtgtat-atcttgtgcattgtatttcctgtattgcagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
|||| | | |||| | | || || | ||||||| | | | | | |||| || | ||||| | | ||||| ||||| | |||||| |||||||| || || |||||||| |||||||||||||| ||||||||||||
gtaatttgttctaaggattttattattattattattattattattattattattttaaatttatttctagacttctaaaatcttggttagcattatgatcaattgctccaagctttaatccatagcttgtaaatttgtcaagctaaaagtgatctgttgtttcgtatt----ggacgacagGTTCGCAAATACAGTAAGCATTGTAGGAGCTGCGATAAATGCGTTGATGGCTTCGACCACCATTGTCGG
upper sequence: GLYMA11G10180.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ36891 (Selaginella moellendorffii), 3'ss of exon 3
atctggttgcatgcagctatcagtagaggcattttagagaagtagcttgcgcttctcactt-agtgtgtatatcttg-tgcattgtatttcctgtatt----gcagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
| ||| | | | | | ||| ||| | ||| | | ||| | ||| |||||| | |||||||| ||||||||| |||| |||||||| ||||||||||| |||||||||||||||||
--------------------------------------------gtttgagttctttccgtgagtatgtcgacattgatttgataagtttggtttatctcacgcagGTTCATAAGTTCAGCAAACATTGTCGAAGCTGTGATAAGTGTGTTGATGGATTCGATCACCATTGTCGT
upper sequence: GLYMA11G10180.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ29393 (Selaginella moellendorffii), 3'ss of exon 3
atctggttgcatgcagctatcagtagaggcattttagagaagtagcttgcgcttctcacttagtgtgtatatcttgtgcattgtatttcctgtattgcagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
||| | || | || ||||| || | | | || || | |||||||||||||||| || ||||| || || ||||| || || ||||| |||||||| ||||| |||||
-----------------------------------------gtaatcgtcaggacttagcta-tgtgtgcatggcatttaccattgtttctacct---agGTGCGCAAGTTCAGCAAGCATTGCAGGAGCTGTGACAAGTGCGTTGACGGCTTCGACCACCACTGTCGC
upper sequence: GLYMA11G10180.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ33542 (Selaginella moellendorffii), 3'ss of exon 3
atctggttgcatgcagctatcagtagaggcattttagagaagtagcttgcgcttctcactt-agtgtgtatatcttg-tgcattgtatttcctgtatt----gcagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
| ||| | | | | | ||| ||| | ||| | | ||| | ||| |||||| | |||||||| || |||||| |||| |||||||| ||||||||||| |||||||||||||||||
--------------------------------------------gtttgagttctttccgtgagtatgtcgacattgatttgataagtttggtttatctcacgcagGTTCATAAGTTCAGCAAGCATTGTCGAAGCTGTGATAAGTGTGTTGATGGATTCGATCACCATTGTCGT
upper sequence: GLYMA11G10180.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ12139 (Selaginella moellendorffii), 3'ss of exon 3
atctggttgcatgcagctatcagtagaggcattttagagaagtagcttgcgcttctcacttagtgtgtatatcttgtgcattgtatttcctgtattgcagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
||| | | | | ||||| || | | | || || | |||||||||||||||| || ||||| || || ||||| || || ||||| |||||||| ||||| |||||
-----------------------------------------gtaatcgtcaggacgagc--aatgtgtgcatggcatttaccattgtttctacct---agGTGCGCAAGTTCAGCAAGCATTGCAGGAGCTGTGACAAGTGCGTTGACGGCTTCGACCACCACTGTCGCMapped 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|208330707|gb|GE126380.1|GE126380EST: AGCAGGGTGGTGGTGAAGATGCTTTGTTCTGCACTTTNTGCAATGCTGAG GTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGAT
genomic: AGCAGGGTGGTGGTGAAGATGCTTTGTTCTGCACTTTGTGCAATGCTGAGgtattgcatt ... tgtattgcagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGAT
EST:
gi|208311934|gb|GE106944.1|GE106944EST: AGCAGGGTGGTGGTGAAGATGCTTTGTTCTGCACTTTGTGCAATGCTGAG GTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTG
genomic: AGCAGGGTGGTGGTGAAGATGCTTTGTTCTGCACTTTGTGCAATGCTGAGgtattgcatt ... tgtattgcagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgcgcttctcacttagtgtgtatatcttgtgcattgtatttcctgtattgcagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
ttctcac putative branch site (score: 2)
tatttcct putative PPT
attgtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atctggttgcatgcagctatcagtagaggcattttagagaagtagcttgcgcttctcacttagtgtgtatatcttgtgcattgtatttcctgtattgcagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
-tctggtt
- - - - gcatgca
- - - - - - - - - - - - - -ggcattt
- - - - - - - - - - - - - - - - - - - - - - gcttgcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgtgc