Sequence
atgc intronic sequence ATGC exonic sequencegtatgcatacttttaacactgttttctttctatatggtatgttatttgcactagtataagacttttgaattgttgtattgtattgtagATGGAAGAAAGGATGACACTGTGCAACATGGTTATAGAAGCTGGAGGGAAAAACGGTATTGTTGCTGCTGATAGAACCACATACAAATACCTTGAG
Basic information
species | Glycine max |
transcript | GLYMA20G34160.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 7
gtatgcatacttttaacactgttttctttctatatggtatgttatttgcactagtataagacttttgaattgttgtatt-----gtattgtagATGGAAGAAAGGATGACACTGTGCAACATGGTTATAGAAGCTGGAGGGAAAAACGGTATTGTTGCTGCTGATAGAACCACATACAAATACCTTGAG
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------gtatgctccgtgctcataactagat---tgatcaattattttcatcttt-catggcttttaacctaatatttccgcaaacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAG
upper sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G010044_T02 (Zea mays), 3'ss of exon 7
gtatgcatacttttaacactgttttctttctatatggtatgttatttgcactagtataagacttttgaattgttgtattgtattgtagATGGAAGAAAGGATGACACTGTGCAACATGGTTATAGAAGCTGGAGGGAAAAACGGTATTGTTGCTGCTGATAGAACCACATACAAATACCTTGAG
| | || | | | || | | || | | | ||| || | |||| || | | || | | ||||||||||| | |||||||| |||||||||||||| |||||||| || || |||||| |||| |||||||| ||| |||| ||||||||||||
----gtgtgtttctggctcaagattatcttaattaattgccacact-gca-taaccttgaacttagtccttttcgcat-atttgctagATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
upper sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G133988_T01 (Zea mays), 3'ss of exon 2
gtatgcatacttttaacactgttttctttctatatggtatgttatttgcactagtataagacttttgaattgttgtattgtattgtagATGGAAGAAAGGATGACACTGTGCAACATGGTTATAGAAGCTGGAGGGAAAAACGGTATTGTTGCTGCTGATAGAACCACATACAAATACCTTGAG
| | || | | | || | | | | | ||||| || | |||| || | | || | | ||||||||||| | |||||||| |||||||||||||| |||||||| || || |||||| |||| |||||||| ||| |||| ||||||||||||
----gtgtgtttctggctcaagattatcttagttaattgccacacttgca-taaccttgaacttagtccttttcgcat-atttgctagATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
upper sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 8
gtatgcatacttttaacactgttttctttctatatggtatgttatttgcactagtataagacttttgaattgttgtattgtattgtagATGGAAGAAAGGATGACACTGTGCAACATGGTTATAGAAGCTGGAGGGAAAAACGGTATTGTTGCTGCTGATAGAACCACATACAAATACCTTGAG
||| | | | || || |||| | || || | || || |||| || | | | | |||||||||||| | |||||||| |||||||||||| | |||||||| || || |||||| | || |||||||| ||| |||| ||||||||||||
--gtgcgttccctgctcaagattatcttaattaat----tgccacaccacgtaacattgaacttagtccttttcacaaact-tgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
upper sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------------------------gtatgcatactttta-----acactgttttctttctatatggtatgttatt-tgcactagtataagacttttgaattgttgtattgtattgtagATGGAAGAAAGGATGACACTGTGCAACATGGTTATAGAAGCTGGAGGGAAAAACGGTATTGTTGCTGCTGATAGAACCACATACAAATACCTTGAG
| | | | || ||| | | || | || || ||||||| | | | || | | | | | | || | ||| | |||||||||||||| |||||| |||||||||||||| | |||||||| || || || ||| | | || ||||| || |||| || || |||||
gtaagaaatcattctatatttcctacattatgggtcccttctcttatagaaataaaaattaatagctgcatatgatgttatcattgatttataaatggttgcttgaatctt-ttttggctgctagATGGAAGAAAGAATGACATTGTGCAACATGGTTGTGGAAGCTGGGGGAAAGAATGGTGTCATCCCTCCTGATGCGACGACATTAAATTATGTTGAG
upper sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S227_66V6.1 (Physcomitrella patens), 3'ss of exon 8
----gtatgcatacttttaacactgttttctttctatatggtatgttatttgcactagta-taagacttttgaattgttgtattg------tat-tgtagATGGAAGAAAGGATGACACTGTGCAACATGGTTATAGAAGCTGGAGGGAAAAACGGTATTGTTGCTGCTGATAGAACCACATACAAATACCTTGAG----
|| || | || || | | || | || | || | | | | | | |||| | || || ||| || ||||||||||||| || ||||| |||||||||||||| | ||||||||||| || || || ||||| |||||||| || || || ||| | ||
aatcgttggctttattcgtactttctcgactgcacgaagagtttattttctagaggcttgctgggtctttctgactgctgcatttggaaattacatgtagATGGAAGACAGAATGACTCTGTGCAACATGGTCGTGGAAGCTGGAGGCAAGAATGGCGTTGTTCCTGCTGATGCCACAACCGCGAAGTACTTGGAAGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggtatgttatttgcactagtataagacttttgaattgttgtattgtattgtagATGGAAGAAAGGATGACACTGTGCAACATGGTTATAGAAGCTGGAGGGAAAAACGGTATTGTTGCTGCTGATAGAACCACATACAAATACCTTGAG
atgttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcatacttttaacactgttttctttctatatggtatgttatttgcactagtataagacttttgaattgttgtattgtattgtagATGGAAGAAAGGATGACACTGTGCAACATGGTTATAGAAGCTGGAGGGAAAAACGGTATTGTTGCTGCTGATAGAACCACATACAAATACCTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT