Sequence
atgc intronic sequence ATGC exonic sequencegtaagatgatgtattttacctgggggggggggattggttttctatgcattattaatgtgtctaatgcatgggaaaagtttctgtctctgttcaatttcattagGTGGGAAAAGTATGATGCTAAAGGCTGGACTGAGAAAGGGGCACATAAGTACGGTAGACTGAATGAACAATCATGGTGGGAAAAGTGGGGAGAGCATTAT
Basic information
species | Glycine max |
transcript | GLYMA04G02020.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G02020.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g04100.1 (Oryza sativa), 3'ss of exon 6
gtaagatgatgtattttacctgggggggggggattggttttctatgcattattaatgtgtctaatgcatgggaaaagtttctgtctctgttcaatttcattagGTGGGAAAAGTATGATGCTAAAGGCTGGACTGAGAAAGGGGCACATAAGTACGGTAGACTGAATGAACAATCATGGTGGGAAAAGTGGGGAGAGCATTAT
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--------gtgagagttatctcaggctttcgtttaggtttggt-tgcaattgttctgcaaaatatttgcttgaactgttgaagtgttcatgtttctttcctagGTGGGAGAAATATGATGCCAAAGGCTGGACAGAAAAAGGTGCTCATAAGTACGGAAGATTAAATGAACAATCCTGGTGGGAGAGGTGGGGTGAACATTAT
upper sequence: GLYMA04G02020.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G42430.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaagatgatgtattttacctgggggggggggattggttttctatgcattattaatgtgtctaatgcatgggaaaagtttctgtctctgttcaatt-------tcatt-----------agGTGGGAAAAGTATGATGCTAAAGGCTGGACTGAGAAAGGGGCACATAAGTACGGTAGACTGAATGAACAATCATGGTGGGAAAAGTGGGGAGAGCATTAT
||| | || | ||| | | ||| | | || || | | ||| | ||| | ||| ||| || | ||| | | | ||||| |||||||| ||||| ||||||||||| ||||| |||||||| ||||||||||| |||||||| ||||| || ||||||||||| |||||||| |||||||||
gtaggtcaata-acaacacc--agttgctaatattaccctgcagtgt-ttgct--tttgtttgatgtaaaggagaagcttattcttctactggactaaaactatcattcactgaaaatcagGTGGGAGAAGTACGATGCTAAAGGGTGGACAGAGAAAGGAGCACATAAGTATGGTAGACTTAATGAGCAGTCATGGTGGGAGAAGTGGGGGGAGCATTAT
upper sequence: GLYMA04G02020.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ21173 (Selaginella moellendorffii), 3'ss of exon 5
gtaagatgatgtattttacctgggggggggggattggttttctatgcattattaatgtgtctaatgcatgggaaaagtttctgtctctgttcaatttc--attagGTGGGAAAAGTATGATGCTAAAGGCTGGACTGAGAAAGGGGCACATAAGTACGGTAGACTGAATGAACAATCATGGTGGGAAAAGTGGGGAGAGCATTAT
|| || ||| | ||| || || | || | | | ||| | ||||||||||||||| |||| || |||||||| |||||||| || || ||||| || || || ||||| || || |||||||| |||||||| ||||| |||
------------------------------------------------gtaagaacacgtc----gtatgatcaagcttaatatcacatcttagttttggaccagGTGGGAAAAGTATAATGCCAAGGGCTGGACAGAGAAAGGTGCTCACAAGTATGGAAGGCTCAATGAGCAGTCCTGGTGGGAGAAGTGGGGCGAGCAATAT
upper sequence: GLYMA04G02020.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ19379 (Selaginella moellendorffii), 3'ss of exon 3
-------------------------------------------------------------------------------gtaagatgatgtattttacctgggggggggggattggttttctatgcattattaatgtgtctaatgcatgggaaaagtttctgtctctgttcaatttc--attagGTGGGAAAAGTATGATGCTAAAGGCTGGACTGAGAAAGGGGCACATAAGTACGGTAGACTGAATGAACAATCATGGTGGGAAAAGTGGGGAGAGCATTAT
| | | | | | |||| || | | | | | | ||| | | ||| || || | || | | ||| | ||||||||||||||| |||| || |||||||| |||||||| || || ||||| || || || ||||| || || |||||||| |||||||| || || |||
gtgaggagatattaagactgttgaaatccattttatgtgttttcttgcgcagtaacctggctcgaatcgaaaggacggcacagaaacaagcgaagcaagggaatggggaggccggatggtacgagaaatggtaa-gaacacgtcgtatgatcaagcttaatatcacatcgtagttttggaccagGTGGGAAAAGTATAATGCCAAGGGCTGGACAGAGAAAGGTGCTCACAAGTATGGAAGGCTCAATGAGCAGTCCTGGTGGGAGAAGTGGGGCGAACAATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattaatgtgtctaatgcatgggaaaagtttctgtctctgttcaatttcattagGTGGGAAAAGTATGATGCTAAAGGCTGGACTGAGAAAGGGGCACATAAGTACGGTAGACTGAATGAACAATCATGGTGGGAAAAGTGGGGAGAGCATTAT
tttcatt CT-rich tract
aatttcatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatgatgtattttacctgggggggggggattggttttctatgcattattaatgtgtctaatgcatgggaaaagtttctgtctctgttcaatttcattagGTGGGAAAAGTATGATGCTAAAGGCTGGACTGAGAAAGGGGCACATAAGTACGGTAGACTGAATGAACAATCATGGTGGGAAAAGTGGGGAGAGCATTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA