Sequence
atgc intronic sequence ATGC exonic sequence...tagcattagtattaagtttaatatgttgaaatgatagttatgtagggaaattaattgttgtgctagtttttaagagctaattatagttttgtttacatagTCTGGACCTGATGAAAGAAGCATTCCTGGCAATACTATTGCTGTCCAAGCAGACATGCCATTTAGTGGTCTTACAACTTTTGGTACATCATTTTTGTCCA
Basic information
species | Glycine max |
transcript | GLYMA18G10150.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G10150.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 10
-tagcattagtattaagtt----taatatg-ttgaaatgatagttatgtagggaaatta--attgttgtgctagtttttaagagctaattatagttttgtttac----atagTCTGGACCTGATGAAAGAAGCATTCCTGGCAATACTATTGCTGTCCAAGCAGACATGCCATTTAGTGGTCTTACAACTTTTGGTACATCATTTTTGTCCA
||| | ||| || | ||| || || | | || | | | || || | || | || | | ||| ||| | | || |||||||||||||||||||| |||| ||||| || || ||||| || |||||||||||||||| |||||| | || ||||||| ||| ||||| | || |
gtaggttctatatggagatgtgtcaatttgctttgcctaacttttgtttgttctacctaacatatctccactgatcttcacttcccaatgatacatcctctcactactgcagTCTGGACCTGATGAAAGATGCATCCCTGGAAACACAATTGCCGTGCAAGCAGACATGCCATATAGTGGCTTGTCATCTTTTGGGACAGCATTTCTATCAA
upper sequence: GLYMA18G10150.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G065012_T02 (Zea mays), 3'ss of exon 10
-tagcattagtattaagtttaatatgttga--aatgatagtta----tgtagggaaattaattgttgtgctagtttttaagagctaattatag-----ttttgtttacatagTCTGGACCTGATGAAAGAAGCATTCCTGGCAATACTATTGCTGTCCAAGCAGACATGCCATTTAGTGGTCTTACAACTTTTGGTACATCATTTTTGTCCA
|| | || | | | || | | | ||| | | || | | | || | | | | | | | | | ||||| | |||||||||| || |||||| |||||||||| || || || || |||||||| |||||||||| ||||| || || | || || ||| ||||||||||||
gtaagttctgt-tcgactcctatgtctctatcaatcacacttgactccattcagtacgtatctttcccacgcatcctctcattcctacaacacctgctttttgccgccgcagTCTGGACCAGACGAAAGATGCATTCCTGGAAACACCATCGCCGTCCAAGCTGACATGCCATACAGTGGCCTGTCATCGTTCGGAACAGCATTTTTGTCCA
upper sequence: GLYMA18G10150.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 10
tagcattagtattaagtttaatatgttgaaatgatagttatgtagggaaattaattgttgtgctagtttttaagagctaatt---atagttt---tgt-ttacatagTCTGGACCTGATGAAAGAAGCATTCCTGGCAATACTATTGCTGTCCAAGCAGACATGCCATTTAGTGGTCTTACAACTTTTGGTACATCATTTTTGTCCA
||| | |||||| | | | || | ||| | | |||| | |||| || | ||| | | | || | | | ||| || ||| || || |||||||||||||||||||||||||||| || || || | || || |||||||| |||||||| |||||||||||||||||||| || | |||||||| |
---cat--attttaagtgtcaattatttagttgacaat--ggtagctagattacttcatttgcacctctcttgaaggtgacttctatatgttcaatgtgtttcacagTCTGGACCTGATGAAAGAAGCATTCCGGGGAACACAGTAGCAGTTCAAGCAGATATGCCATTCAGTGGTCTTACAACTTTTGGGACTGCCTTTTTGTCAA
upper sequence: GLYMA18G10150.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv19s0090g01130.t01 (Vitis vinifera), 3'ss of exon 10
--tagcattagtattaagtttaatatgttgaaatgatagt-tatgtagggaaatta-attgttgtgctagtttttaagagctaattatagttttgtttacatagTCTGGACCTGATGAAAGAAGCATTCCTGGCAATACTATTGCTGTCCAAGCAGACATGCCATTTAGTGGTCTTACAACTTTTGGTACATCATTTTTGTCCA
||| | || ||||| || | || |||| | | | ||| | | | || | | | || | ||||| | ||| || | |||||||||||||||||||||| |||||||| || || |||||||| |||||||||||||| | |||||||| ||||||||||| || ||||||||||||
ggcttttttactttttagtttgatttttttaaatttttttctctgtccatctttcccaatatttttttcatcttcactcactaatcctgcttt----tatacagTCTGGACCTGATGAAAGAAGTATTCCTGGAAACACAATTGCTGTTCAAGCAGACATGCCTTACAGTGGTCTGACAACTTTTGGAACGGCATTTTTGTCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaaattaattgttgtgctagtttttaagagctaattatagttttgtttacatagTCTGGACCTGATGAAAGAAGCATTCCTGGCAATACTATTGCTGTCCAAGCAGACATGCCATTTAGTGGTCTTACAACTTTTGGTACATCATTTTTGTCCA
agctaat putative branch site (score: 3)
ttttgttt putative PPT
taattatagttttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagcattagtattaagtttaatatgttgaaatgatagttatgtagggaaattaattgttgtgctagtttttaagagctaattatagttttgtttacatagTCTGGACCTGATGAAAGAAGCATTCCTGGCAATACTATTGCTGTCCAAGCAGACATGCCATTTAGTGGTCTTACAACTTTTGGTACATCATTTTTGTCCA
- - - - - - - - - - - -tgttgaa
- - - - - - - - - - - - - - - - - - - tatgtag
- - - - - - - - - - - - - - - - - - - - - - - gaaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtg