Sequence
atgc intronic sequence ATGC exonic sequencegtagttttagttatatagttatatatttatatatctcatacaaggccatttttttttttttttttttcagcgtacagttattactttgacttttgttcttgatgtatggtttttattaatttttagcttggtgggtgctttatcagGTGGTCTCAGATTGCAGCACAGTTACCAGGAAGAACAGACAATGAGATTAAGAACCTATGGAACTCGTGCCTGAAGAAGAAGCTGAGGCAAAGAGGCATT
Basic information
| species | Glycine max |
| transcript | GLYMA10G28250.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G28250.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0060g00240.t01 (Vitis vinifera), 3'ss of exon 2
gtagttttagttatatagttatatatttatatatctcatacaaggccatttttttttttttttttttcagcgtacagttattactttgacttttgttcttgatgtatggtttttattaatttttagcttggtgggtgctttatcagGTGGTCTCAGATTGCAGCACAGTTACCAGGAAGAACAGACAATGAGATTAAGAACCTATGGAACTCGTGCCTGAAGAAGAAGCTGAGGCAAAGAGGCATT
| ||| | | | || | | | | || |||||| | | | || | | || ||| | | || | || || ||||| ||||| ||||||||||| || ||||| |||||||| || ||||| || || || | |||||||| ||| | ||||||||||| || |||| ||||||
------------------------------------------------gtactttaaatcctgtcagcaacctcctacaagaaccc--acttttaatatagtagttttcctgttg--gattctgaagttttctgctgtttcatcagATGGTCGCAGATTGCAGCTCAATTACCGGGAAGAACGGATAATGAAATAAAAAATTTGTGGAACTCCTGCATTAAGAAGAAGCTTAGACAAAAAGGCATC
upper sequence: GLYMA10G28250.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 2
gtagttttagttatatagttatatatttatatatctcatacaaggccatttttttttttttttttttcagcgtacagttattactttgacttttgttcttgatgtatggtttttattaatttttagcttggtgggtgctttatcagGTGGTCTCAGATTGCAGCACAGTTACCAGGAAGAACAGACAATGAGATTAAGAACCTATGGAACTCGTGCCTGAAGAAGAAGCTGAGGCAAAGAGGCATT
| | || | | | || | | | | | || || || | | || | | || ||| |||||||||||||||||| | ||||||||||| | || ||||| || || || ||| | |||||||| || | ||||||||||| | | | |||||
----------------------------------------ctgagacacgataaggtcacatgttggtaataagctatcccccccccccccccccccctgctagttgggctaatgcagcaattgatccccttgcatgc------agGTGGTCTCAGATTGCAACTCAGTTACCAGGCCGCACCGACAACGAAATCAAAAACTTCTGGAACTCCTGTATCAAGAAGAAGCTTCGCAACATCGGCATC
upper sequence: GLYMA10G28250.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 2
gtagttttagttatatagttatatatttatatatctcatacaaggccatttttttttttttttttttcagcgtacagttattactttgacttttgttcttgatgtatggtttttattaatttttagcttggtgggtgctttatcagGTGGTCTCAGATTGCAGCACAGTTACCAGGAAGAACAGACAATGAGATTAAGAACCTATGGAACTCGTGCCTGAAGAAGAAGCTGAGGCAAAGAGGCATT
| | | | |||| | | | || || |||| | | || | | | ||| || ||| | | | | || ||||||| | || ||||| | ||| | || || |||||||||| |||||||| ||| | ||||||||||||||| ||||||||| | ||| || ||
---------------------------------------------------------gtgtgtgctcgagcgagctggaa----ttcga--tttggtgtggaaatgtagc----attggattgatgctgaattgtttccata-cagGTGGGCGCAAATTGCGACGCAGCTCCCGGGTCGAACAGACAACGAGATTAAAAACTTTTGGAACTCGTGCCTGCGGAAGAAGCTACGTCAAGTTGGTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgttcttgatgtatggtttttattaatttttagcttggtgggtgctttatcagGTGGTCTCAGATTGCAGCACAGTTACCAGGAAGAACAGACAATGAGATTAAGAACCTATGGAACTCGTGCCTGAAGAAGAAGCTGAGGCAAAGAGGCATT
tattaat putative branch site (score: 2)
ctttatc putative PPT
ttgatgtatggttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttttagttatatagttatatatttatatatctcatacaaggccatttttttttttttttttttcagcgtacagttattactttgacttttgttcttgatgtatggtttttattaatttttagcttggtgggtgctttatcagGTGGTCTCAGATTGCAGCACAGTTACCAGGAAGAACAGACAATGAGATTAAGAACCTATGGAACTCGTGCCTGAAGAAGAAGCTGAGGCAAAGAGGCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
