Sequence
atgc intronic sequence ATGC exonic sequencegtatatattctaaaaccaagtatctgatgattgcacatttggctttgctgcagctaaaattaatttttcttgttcagGGTGCTGTATATACGAGATGGCTGCTCATCGCCCTGCCTTTAAAGCTTTT
Basic information
species | Glycine max |
transcript | GLYMA11G18340.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 9
gtatata---ttctaaaaccaagtatctgatgattgcacatt----tggctttgctgcagctaaaattaatttttcttgttcagGGTGCTGTATATACGAGATGGCTGCTCATCGCCCTGCCTTTAAAGCTTTT
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gtaactgcctttttctcctcaggtcttctacaagttcatattactgcatatttatcttaatttaagttacgctttct-atatagGGTGCTGTATGTATGAGATGGCAGCTCATCGGCCTGCCTTCAAGGCTTTT
upper sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g64490.1 (Oryza sativa), 3'ss of exon 10
gtatatattctaaaaccaagtatctgatgattgcacatttggctttgctgcagctaaaattaatttttcttgttcagGGTGCTGTATATACGAGATGGCTGCTCATCGCCCTGCCTTTAAAGCTTTT
||| |||||| | | ||| || | | || ||| | || | || || ||| |||| || ||||| |||||||||||||||||||| |||||||| || || |||
gta-atattcccttgctcatatggatatgtttaaatgtgtgaatttct---aactgatatagatattta-----cagGATGTTGTATGTACGAGATGGCTGCTCATCGGCCTGCCTTCAAGGCATTT
upper sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 9
gtatatattctaaaaccaagtatctgatgattgcacatttggctttgct-gcagctaaaattaatttttcttgttcagGGTGCTGTATATACGAGATGGCTGCTCATCGCCCTGCCTTTAAAGCTTTT
|||| | || | | | | |||| || || || ||| | | |||||| || || || | ||||| |||||||| || ||||||||||||||||||||||| ||||| ||||||
gtatgtgttttcatagtgtctgg-tgatatttatggatctgcagttgtttgtggctaaattttgcattgct-gatcagGTTGCTGTATGTATGAGATGGCTGCTCATCGCCCTGCATTTAAGGCTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgatgattgcacatttggctttgctgcagctaaaattaatttttcttgttcagGGTGCTGTATATACGAGATGGCTGCTCATCGCCCTGCCTTTAAAGCTTTT
aattaat putative branch site (score: 3)
tttttcttgttc CT-rich tract
taaaattaatttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatattctaaaaccaagtatctgatgattgcacatttggctttgctgcagctaaaattaatttttcttgttcagGGTGCTGTATATACGAGATGGCTGCTCATCGCCCTGCCTTTAAAGCTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT