Sequence
atgc intronic sequence ATGC exonic sequence...aacaaaagaatgaacgatgttaatgctggactttttgtgtattgccattgtgcaatgggtgttgtctgtgtttgttgatgttgagtttattatcttttagGGCCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
Basic information
species | Glycine max |
transcript | GLYMA20G19980.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 3
aacaaaagaatgaacgatgttaatgctggactttttgtgta---ttgccattgtgcaatgggtgttgtc-tgtgt---ttgttgatgttgagtttattatcttttagGGCCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
||| ||| | | | ||||| || | || || | |||| ||| || || |||||| | | | | ||| || |||| || | |||||| ||||||||||| |||||||| |||||||| || || |||||||| |||||||| |||||||||||||||| | | |||||||
------gttatgtgagattgcttttttag-ttttttatggatctttaacagtacattttgggagttatcatgcaaacaatgttgagctcaatataactatgttgcagGGACGCACTGTTGTTATTGAGCAAAGCTTTGGTGCTCCTAAAGTTACAAAGGATGGAGTTACTGTTGCCAAGAGCATTGAATTCAGTAACAGGGTTAAGA
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 2
aacaaaagaatgaacgatgttaatgctggactttttgtgtattgccattgtgcaatgggtgttgtctgtgtttgttgatgttgagtttattatctttt------agGGCCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
| | | ||| |||| || | || | | |||| | | || | || | | ||| |||| |||||| || | |||| || ||||| || ||||||||||| |||||||| || ||||| || || ||||| || ||||| ||||||||||||||||| ||||||| ||| ||||
------gcactcactgattataatattgcttgatgtgctttactctgttgtagtactgttgcatttagtttgttttgtacttgaatttattgcctgctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 2
aacaaaagaatgaacgatgttaatgctggactttttgtgtattgccattgtgcaatgggtg--ttgtctgtgtttgttgatgttgagtttattatct------tttagGGCCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
| | | ||| ||| ||| ||||| | |||| | | || || ||| | | ||| |||| |||| || | ||||| || ||||| || ||||||||||| || ||||| || ||||| || || ||||| || |||||||| |||||||||||||| ||||||| ||| ||||
--------actcactgattccaatactgtttggtttgttttactttgttgtaatactgttgccttagttgtttgttttgtacttgaacttatcgcctgccttctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGA
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------------aacaaaagaatgaacgatgttaatgctggactttttgtgtattgcc-attgtgcaatgggtgttgtctgtgtttgttgatgttgagt--ttattatcttttagGGCCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
| | | | | | || ||| ||| | ||| || | | | | |||| | | | || || || | || || |||| ||||||||||||||||||||||||| ||||| |||||||| || |||||||| || |||||||| || || ||||| ||||| || ||| ||||||
gtactctttttcttctacacattttgatttgatttggacatgatttggccagaggttccttccttagcatgtgatttgggtgaccggttgattctgtatcgaatttggtctaagactttctgctttatgtgattctaattttgaagGGACGTAATGTTGTGATTGAGCAAAGTTGGGGTGCTCCTAAAGTGACAAAAGATGGTGTTACTGTTGCCAAAAGTATTGAGTTCAAAGACAAAATTAAGA
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------------------------------------------aacaaaagaatgaacgatg--ttaatgctggactttttgtgtattgccattgtgcaatgggtg--ttgtctgtgtt-tgttgatgttgagtttattatcttttagGGCCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
| ||| | || || ||| | | | |||| | | | || | | | || |||| | | ||| |||| | | | || ||||||| | |||| | || |||||| |||||| | |||||||| ||||| ||||| || |||||||| || ||||||||||||||||| | ||||||
gtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaactgtctaattcttggtattctagctttagatccgagattttactttgacttagagtcgtagttttagggggatttgataacatagtttacgaattaactgtaatgtcgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattgtgcaatgggtgttgtctgtgtttgttgatgttgagtttattatcttttagGGCCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
tgttgat putative branch site (score: 4)
ttatctttt putative PPT
agtttattatctttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacaaaagaatgaacgatgttaatgctggactttttgtgtattgccattgtgcaatgggtgttgtctgtgtttgttgatgttgagtttattatcttttagGGCCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- -aaaagaa
- - - - - - - - - - - -tgctgga
- - - - - - - - - - - - - - - - ttttgtg
- - - - - - - - - - - - - - - - - - - -tattgcc
- - - - - - - - - - - - - - - - - - - - - - - - tgtgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gggtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtctgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgatg