Sequence
atgc intronic sequence ATGC exonic sequence...attttgggctgagtaattttttatacgaataaaaaaatatattgacatctttatttagaagaataacatatactaattgtattgtgtatgaattgtgtagCTGGATGATTGGGTGTTGTGCCGAATCTACAAGAAGGGCAACACACAAAGGTCACATGAGAGGGACGATTCCATTGATGACATGATTGGAGAAGTACCTC
Basic information
species | Glycine max |
transcript | GLYMA12G22790.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G22790.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S140_93V6.1 (Physcomitrella patens), 3'ss of exon 2
--attttgggctgagtaattttttatacgaataaaaaaatatattgacatctttatttagaagaataacatatactaattgtattgtgtatgaattgtgt--agCTGGATGATTGGGTGTTGTGCCGAATCTACAAGAAGGGCA-ACACACAAAGGTCACATGAGAGGGACGATTCCATTGATGACATGATTGGAGAAGTACCTC
|| || | | ||||| | | || | | | | | || | |||| | || | | | || || | |||| || |||| || |||||||||||||||||||||| |||||||| ||| | | | | || || || | ||| || | | | | | |||
ggatggtgctgtcactaattctgtgcac-attccacacgtcaatcg-tatctgaaggc-gattgttcatg-gtgcttatgattttgtttacattctgtgcgcagTTGGATGATTGGGTGTTGTGCCGGATCTACAAAAAGAGTACAAATGCACAGCGTACTGGCAAGGAGCGTGATAGCTCTTCTTGCG-TCGAAGAG------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catctttatttagaagaataacatatactaattgtattgtgtatgaattgtgtagCTGGATGATTGGGTGTTGTGCCGAATCTACAAGAAGGGCAACACACAAAGGTCACATGAGAGGGACGATTCCATTGATGACATGATTGGAGAAGTACCTC
tactaat putative branch site (score: 1)
ttatttagaagaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attttgggctgagtaattttttatacgaataaaaaaatatattgacatctttatttagaagaataacatatactaattgtattgtgtatgaattgtgtagCTGGATGATTGGGTGTTGTGCCGAATCTACAAGAAGGGCAACACACAAAGGTCACATGAGAGGGACGATTCCATTGATGACATGATTGGAGAAGTACCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtatg