Sequence
atgc intronic sequence ATGC exonic sequence...aaaaaaaactattgtattcgagaattttatttttcacacatgctgaactctgggatttgtgttgctatatctataaattaccatgctgtgttattttcagAATGCATTGCGGCAACAAAGATTTGTTCGAGAAGTCACAATACAGTACAATCTCTGCAATGAGCCTTG
Basic information
species | Glycine max |
transcript | GLYMA20G35720.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 8
--------------------------------------------aaaaaaaactattgtattc--gagaattttatttttcaca-catgctgaactctgggatttgtgttgctatatctataaattaccatgctgtgttattttcagAATGCATTGCGGCAACAAAGATTTGTTCGAGAAGTCACAATACAGTACAATCTCTGCAATGAGCCTTG
|| | | || | | | | |||| ||||| | |||| || | | | | | || || || ||| || | | | | | |||||||| || || ||||||||||||||||| ||||||||||||||||||||||||||||| ||||| ||
gtaattttctacctcctctttctgttatcaatgttttcatttcaaagacattttacttcactttgcaacatttagtttttgttatcatgagcaatctttg--tctatatt-ctgta-ctaaggtttttttcaatataatctatgcagAATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAATCTCTGCAACGAGCCATG
upper sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 8
-----------------------------------------------aaaaaaaactattgtattcgagaattttatttttcacacatgctgaactctgggatttgtgttgctatat-ctataaattaccatgctgtgttattttcagAATGCATTGCGGCAACAAAGATTTGTTCGAGAAGTCACAATACAGTACAATCTCTGCAATGAGCCTTG
|| | | ||| | | | | ||| | || || | ||| | || || ||| |||| | | ||| || ||||||||||||||||||||||||||||| || ||||| || |||||||||||||| ||||||||||| ||
gtatttttcttttgatttcctttatatctctctcacagttttattcccaactggatcaatgtttcttttagtctgttttaggtgccgtgacaaa---taaacttttcgccactctaaactaagaattttccaacacggtttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
upper sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G464000_T02 (Zea mays), 3'ss of exon 7
------------------------------aaaaaaaactattgtattcgagaat--tttatttttcacacatgctgaactc-tgggatttgtgttgc-tatatctataaattaccatgctgtgttatt-----ttcagAATGCATTGCGGCAACAAAGATTTGTTCGAGAAGTCACAATACAGTACAATCTCTGCAATGAGCCTTG
|| | | | | | || || ||||||| | |||| || || || | | |||| | | ||| | || | | || | ||| | |||||||||||||| |||||||||||||| || ||||| |||||||||||||| |||||||| ||||| ||
gtaattttctttcaatctttgtttttcctcaatgacttcactcctgattgataaatgtttatttatttcaca-gcagatttcataaaagcaatgtttcctctattcaaaactaagaattttccaatatggttgatgcagAATGCATTGCGACAACAAAGATTTGTCCGTGAAGTGACAATACAGTACAACCTCTGCAACGAGCCATG
upper sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G08450.3 (Arabidopsis thaliana), 3'ss of exon 8
------------------aaaaaaaactattgtattcg-------agaatttt--atttttcacacatgctgaactctgggatttgtgt---tgctatatctataaattacca-----tgctgtgttatttt-cagAATGCATTGCGGCAACAAAGATTTGTTCGAGAAGTCACAATACAGTACAATCTCTGCAATGAGCCTTG
||| | || | | || | || | | || | ||||||| | | ||| | |||||| | | || | | | | || | ||||||| ||||||||||||| ||||| ||||||||||||||||| ||||||||||||||||| |||||
gtattttccttccactttggaaatatctgctctcttaatcttcttacaactcttggattattacacatggcggcttgcatagttttctcatatttcatatctttcgaacactgacgacttatttactgttctgtagAATGCTCTGCGGCAACAAAGGTTTGTACGAGAAGTCACAATACAATACAATCTCTGCAATGAACCTTG
upper sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 7
--aaaaaaaactattgtattcgagaattttatttttcacacatgctgaactctgggatttgtgttgctatatctataaattaccatgctgtgttatt-ttcagAATGCATTGCGGCAACAAAGATTTGTTCGAGAAGTCACAATACAGTACAATCTCTGCAATGAGCCTTG
|| | | ||| |||| | || ||| | || || | || ||| || ||| || | ||| ||| || || |||||||||| |||||||||||||||||||| ||||||||||||||||||||||| | || ||||| |||||
gtaatcacatggattttatt-aatcatgttagtattgttttatctatttatttgttattataaatg--ataatcatcttctttgatggtgttttgttcttcagAATGCGTTGCGGCAACAAAGATTTGTACGAGAAGTCACAATACAGTACAACTTATGTAATGAACCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactctgggatttgtgttgctatatctataaattaccatgctgtgttattttcagAATGCATTGCGGCAACAAAGATTTGTTCGAGAAGTCACAATACAGTACAATCTCTGCAATGAGCCTTG
ttattttc CT-rich tract
tatatctataaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaaaaactattgtattcgagaattttatttttcacacatgctgaactctgggatttgtgttgctatatctataaattaccatgctgtgttattttcagAATGCATTGCGGCAACAAAGATTTGTTCGAGAAGTCACAATACAGTACAATCTCTGCAATGAGCCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
aaaaaaa
- - - - - - tgtattc
- - - - - - - - - - - - - - - - - cacacat
- - - - - - - - - - - - - - - - - - - - - ctgaact
- - - - - - - - - - - - - - - - - - - - - - - - - - ggatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgct