Sequence
atgc intronic sequence ATGC exonic sequence...ggactaaacatatttaagtcaccactctaaccagtactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTG
Basic information
species | Glycine max |
transcript | GLYMA08G24120.4 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G24120.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 11
ggactaaacatatttaagtcaccactctaaccagtactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTG
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-------------gtattttattacttagacacgcaaaatacttactttctgt--gcttataacatatat----aatggtcttgtgtaat-ggattgcagGTTGACATAGCAATCCCAGAGGTTTTTGTTGGTGGTTTACTTGGTTCAATGCTTATATTCCTGTTTAGTGCATGGGCTTGTTCTGCTGTTGGCAGAACTG
upper sequence: GLYMA08G24120.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 11
ggactaaacatatttaagtcaccactctaaccagtactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTG
|| | | | | || ||| | ||| | ||||| | || | | ||| ||| |||||||||||||| || || ||||| ||||||||||| || | ||| |||||||||| || | |||||||||||||| || | || ||||| ||||||
-----------------gtag--atttcgttatgcatcgttgctgtattc---tcgatgttgagacaacttctcatactcatcctcggataaaat--cagGTTGATATTGCTATCCCAGAAGTGTTCGTTGGTGGATTATTGGGTGCCATGCTTATTTTCCTCTTTAGTGCTTGGGCATGCGCGGCAGTTGGTCGAACTG
upper sequence: GLYMA08G24120.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 12
ggactaaacatatttaagtcaccactctaaccagtactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTG
|||| ||| | || | || | | | | | | | ||| | | | | | || | | | | || || |||||||||||||| || || ||||| ||| |||| ||||| ||||| ||||||||||||| | ||||| |||||||| ||| | || ||||| ||||||
-----gtacattttttactctttggtgtattctg---tttcctcttattccattccactcgcatactcatcctgattcttgtcctcacatctaa--acagGTTGATATTGCGATCCCAGAAGTCTTCATTGGAGGGTTATTAGGTGCCATGCTTATATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTG
upper sequence: GLYMA08G24120.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 11
ggactaaacatatttaagtcaccactctaaccagtactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTG
|| | ||| ||| | | | | || |||| | ||| || || || | ||| || || |||||||||||||| ||||| |||||||| |||||||||||| | || || |||||||| || | |||||||| ||||| |||||||| |||||| | ||||
---------gtaagtgga-cactactttgatc----tcttcatcgtgttt-----acattctctaactcactgcttttttatgtta--atcaccttacagGTTGATATTGCCATTCCAGAAGTTTTTGTTGGTGGGTTGTTGGGCTCTATGCTTATTTTCCTATTTAGTGCATGGGCATGTTCTGCAGTTGGCCGGACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtctcatcagatttcactggttcttctaagttgcaacttatgattgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTG
ttatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggactaaacatatttaagtcaccactctaaccagtactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- -ctaaaca
- - - - - - - - - tcaccac
- - - - - - - - - - - - - ctaacca
- - - - - - - - - - - - - - - - - - - - - - gtgtctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaact