Sequence
atgc intronic sequence ATGC exonic sequence...cctccaaaccgaaggaggatacctgtgaggaaacaacaacaaaaatctattgctagtttgagttagatgaaattaatcaggatttttttttgtactacagGGTGCTCCTGAACGGTGGAGATTGGTCAGGGCTCATGGTACTGCTGTAGGACTTCCAACAGAAGATGACATGGGCAATAGTGAAGTTGGTCACAATGCCC
Basic information
species | Glycine max |
transcript | GLYMA18G45120.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g60190.1 (Oryza sativa), 3'ss of exon 2
--cctccaaaccgaaggaggatacctgtgaggaaacaacaacaaaaatctattgctagtttgagttagatgaaattaatcaggatttttttttgtactaca-gGGTGCTCCTGAACGGTGGAGATTGGTCAGGGCTCATGGTACTGCTGTAGGACTTCCAACAGAAGATGACATGGGCAATAGTGAAGTTGGTCACAATGCCC
|||| | || | || || | | || | | | | | | || | |||| ||||||| | | || | ||||||||| || |||||||||| || | ||||||||| || ||||| || ||||| | ||||||||||||||||| || ||||| ||||||||||| |
tgattccatgttgtgttgggttgcccttgtgctatgaatt-tacgcctttgcctgcactctagtttcagc--agttaactctattttttttgtacattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGTCTTCCTAGCGAAGATGACATGGGCAACAGCGAAGTGGGTCACAATGCTC
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 2
-cctccaaaccgaaggaggatacctgtgaggaaacaaca----acaaaaatctattgctagtttgagttagatgaaattaatcaggatttttttttgtactacagGGTGCTCCTGAACGGTGGAGATTGGTCAGGGCTCATGGTACTGCTGTAGGACTTCCAACAGAAGATGACATGGGCAATAGTGAAGTTGGTCACAATGCCC
| | | ||| | ||| | || | || | | || || | || || | ||| | | | | |||| |||| |||||||| |||||| | || | ||||||||| || ||||| || || ||| | || |||||||||||||| |||||||||||||||||||| |
tctttctcttgtaagaaagattgttctgtcagcataatttgttttgcaggtatactgtctatatgctttt-----acttacccttcagtgaaatatgtatattagGGCGCTCCTGAGAAATGGAGACTAGTGAAGGCTCATGGAACAGCTGTGGGCCTCCCATCTGATGATGACATGGGCAACAGTGAAGTTGGTCACAATGCAC
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G003385_T02 (Zea mays), 3'ss of exon 2
cctccaaaccgaaggaggatacctgtgaggaaacaacaacaaa-aatctattgctagtttgagttagatgaaattaatcaggatttttttttgtactacagGGTGCTCCTGAACGGTGGAGATTGGTCAGGGCTCATGGTACTGCTGTAGGACTTCCAACAGAAGATGACATGGGCAATAGTGAAGTTGGTCACAATGCCC
| | | || || | | ||| | || || || | || | | || || || ||| | | | | | | | ||||||||||||| |||||| | || | ||||||||| || ||||| || || ||| | || |||||||||||||| |||||||||||||||||||| |
ctttctcacggacgaaagattgttctgttctgtcagcataatttgatttgcaggtatactgtcttc-atgcactcacccttttgtgaaatacatgtattagGGTGCTCCTGAGAAATGGAGACTAGTGAAGGCTCATGGAACAGCTGTGGGTCTCCCATCTGATGATGACATGGGCAACAGTGAAGTTGGTCACAATGCAC
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 1
cctccaaaccgaaggaggatacctgtgaggaaacaacaacaaaaatctattgctagtttgagttagatgaaattaatcaggattttttt-ttgtactacagGGTGCTCCTGAACGGTGGAGATTGGTCAGGGCTCATGGTACTGCTGTAGGACTTCCAACAGAAGATGACATGGGCAATAGTGAAGTTGGTCACAATGCCC
| | || | ||||| ||| | || | | || | | | | | | | || || ||| |||| |||||||| |||| ||| ||| ||||| |||||||||||||||||||| | |||||||| ||||| || ||||| |||||||| ||||| |
----------------------------gtatgttacctccttaatct-ttgatttttgatgctttttggattcattgaacttactcttgtttctctatagGGAGCTCCTGATACTTGGACTTTGATCAAAGCTCACGGTACTGCTGTAGGACTTCCTAGTGAAGATGATATGGGAAACAGTGAGGTTGGTCATAATGCTC
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 1
cctccaaaccgaaggaggatacctgtgaggaaacaacaacaaaaatctattgctagtttgagttagatgaaattaatca---ggatttttttttgtactacagGGTGCTCCTGAACGGTGGAGATTGGTCAGGGCTCATGGTACTGCTGTAGGACTTCCAACAGAAGATGACATGGGCAATAGTGAAGTTGGTCACAATGCCC
| ||||| || || || | | || | || || | | | || | | ||| | |||| |||| ||||||||| ||||| ||||||||||| | ||||||||| | ||| ||||| |||||||| || |||||||||||||| ||||||||||| || ||||| |
ttcatgcattaaaggattat-tatgcttggtgcctgcctcacttacct--cattattgaaggctcaataatgtctgtcaattgttttttattttccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTC
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ14459 (Selaginella moellendorffii), 3'ss of exon 1
cctccaaaccgaaggaggatacctgtgaggaaacaacaacaaaaatctattgctagtttgagttagatgaaattaatcaggatttttttttgtactacagGGTGCTCCTGAACGGTGGAGATTGGTCAGGGCTCATGGTACTGCTGTAGGACTTCCAACAGAAGATGACATGGGCAATAGTGAAGTTGGTCACAATGCCC
|||| || | || | | ||| ||| | || ||||| | | || ||| || || ||||||||| | |||| ||| ||||| |||| || || |||||||| || ||||||||||| |||||||| ||||||||||||||
--------------------------------------gtaaaagcgctttttggatctggatctggatcgattgatcttg-ttgctttttttcttttagACTGCCCCCGATCGGTGGAGACTTGTCAAGGCGCATGGACCTGCCGTCGGCCTTCCAACCGAGGATGACATGGGAAATAGTGAGGTTGGTCACAATGCTT
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ26058 (Selaginella moellendorffii), 3'ss of exon 1
cctccaaaccgaaggaggatacctgtgaggaaacaacaacaaaaatctattgctagtttgagttagatgaaattaatcaggatttttttttgtactacagGGTGCTCCTGAACGGTGGAGATTGGTCAGGGCTCATGGTACTGCTGTAGGACTTCCAACAGAAGATGACATGGGCAATAGTGAAGTTGGTCACAATGCCC
|||| || | | | ||| ||| | || ||||| | | || || || || ||||||||| | |||| ||| ||||| |||| || || |||||||| || ||||||||||| |||||||| ||||||||||||||
--------------------------------------gtaaaagcgctttttggatccggatctcgatcgattgatcttg-ttgctttttttcttttagACCGCCCCCGATCGGTGGAGACTTGTCAAGGCGCATGGACCTGCCGTCGGCCTTCCAACCGAGGATGACATGGGAAATAGTGAGGTTGGTCACAATGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctattgctagtttgagttagatgaaattaatcaggatttttttttgtactacagGGTGCTCCTGAACGGTGGAGATTGGTCAGGGCTCATGGTACTGCTGTAGGACTTCCAACAGAAGATGACATGGGCAATAGTGAAGTTGGTCACAATGCCC
aattaat putative branch site (score: 3)
tttttttttgtact putative PPT
aaattaatcaggattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctccaaaccgaaggaggatacctgtgaggaaacaacaacaaaaatctattgctagtttgagttagatgaaattaatcaggatttttttttgtactacagGGTGCTCCTGAACGGTGGAGATTGGTCAGGGCTCATGGTACTGCTGTAGGACTTCCAACAGAAGATGACATGGGCAATAGTGAAGTTGGTCACAATGCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- -ccaaacc
- - - - - - - - - - -cctgtga
- - - - - - - - - - - - - - - - -caacaac
- - - - - - - - - - - - - - - - - - - - - - - ctattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaattaa