Sequence
atgc intronic sequence ATGC exonic sequence...aatagatttgttctgaagtatgggctttttattcccccttaatgctgctgttaaatttttggtcaacataagatctattcaatggctgtttcttttttagGTGTTTGAGATCAATAATGATGCTAAAATGAAGAGAACAAGTCGCAGGCCACTACCCTCAGGACGCATCACAATACCTCATGCAGTTGGCTGGGCATCCT
Basic information
species | Glycine max |
transcript | GLYMA20G38710.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38710.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g34390.1 (Oryza sativa), 3'ss of exon 2
--------aatagatttgttctgaagtatgggctttttattcccccttaatgctgctgttaaatttttg-gtcaacataagatctattcaatggctgtttcttttttagGTGTTTGAGATCAATAATGATGCTAAAATGAAGAGAACAAGTCGCAGGCCACTACCCTCAGGACGCATCACAATACCTCATGCAGTTGGCTGGGCATCCT
| || | ||||| | | | | || | | |||| |||| | || || ||| | | ||| || | |||||||||||||||||| || ||||| ||||||||||| ||||| | || |||| ||||| ||||| ||||| | | ||||| | ||||| |
cctcgttaattatagttgttttcgttcagagaaaatgaatgttctgtacttgct----ttaagcatctgtatctgaatacagtttga--aataact---ttgtttttagGTGTTTGAGATAAAGAATGACGCTAAAATGAAAAGAACCATGCGACGGCCCCTACCATCAGGGCGCATTAGTCCTGCACATGCTGCCATGTGGGCTACTA
upper sequence: GLYMA20G38710.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G178859_T01 (Zea mays), 3'ss of exon 2
---aata-gatttgttctgaagtatgggctttttattcccccttaatgctgctgttaaatttttggtcaacataagatctattcaatggctgtttctt--ttttagGTGTTTGAGATCAATAATGATGCTAAAATGAAGAGAACAAGTCGCAGGCCACTACCCTCAGGACGCATCACAATACCTCATGCAGTTGGCTGGGCATCCT
|||| || | |||| | || ||| | | | ||| | ||||| | | | ||| | || | | | ||| ||||||||||||| || ||||||||||||||||| || |||| || |||| || || || || ||||| | | ||||| | ||||| |
ccaaatatgaataactctg---tttgaacttgctgtacttacttca-gctgcccc--aggccaaaacaactctgtattctttctgatcattaacacgtactttcagGTGTTTGAGATAAAAAATGATGCTAAAATGAAAAGGACAATGCGACGGCCCCTGCCATCTGGTCGCATTAGTCCTGCACATGCTGCGATGTGGGCTACAA
upper sequence: GLYMA20G38710.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0021g00430.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------------------------aatagatttgttctgaagtatgggctttttattcccccttaatgctgctgttaaatttttggtcaacataagatctattcaatggctgtttcttttttagGTGTTTGAGATCAATAATGATGCTAAAATGAAGAGAACAAGTCGCAGGCCACTACCCTCAGGACGCATCACAATACCTCATGCAGTTGGCTGGGCATCCT
| || ||| || || || | | | | ||| || || | | | || | ||| || || | || || ||||||||||||||| |||||||||||||||||||||||||||| | ||||||||||| || || ||| | | |||||||||||||| |||||| || |
gtttcttttgaactgcttattattattattattattttccaatcacaatcattttcatattacaagtactgtctatgtgtgtgtgcgcgcgcatgcgcatgcgtgcatgtgctaggctgcttg--aattttcagactaatctttgcattttgtattgttagGTGTTTGAGATAAATAATGATGCTAAAATGAAGAGAACAATGAGAAGGCCACTACCTTCTGGTCGCCTTAGTATACCTCATGCAGTCACCTGGGCTTCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctgttaaatttttggtcaacataagatctattcaatggctgtttcttttttagGTGTTTGAGATCAATAATGATGCTAAAATGAAGAGAACAAGTCGCAGGCCACTACCCTCAGGACGCATCACAATACCTCATGCAGTTGGCTGGGCATCCT
ctgtttctttttt CT-rich tract
ttaaattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatagatttgttctgaagtatgggctttttattcccccttaatgctgctgttaaatttttggtcaacataagatctattcaatggctgtttcttttttagGTGTTTGAGATCAATAATGATGCTAAAATGAAGAGAACAAGTCGCAGGCCACTACCCTCAGGACGCATCACAATACCTCATGCAGTTGGCTGGGCATCCT
- - - - - - - - - - - - - - - -ttccccc
- - - - - - - - - - - - - - - - - - - - -atgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctgt