Sequence
atgc intronic sequence ATGC exonic sequencegtgtgttgtcttgttccctgtgtaattgtttgctattttcttttggaatgctagttttgtcagttattgcaaattcaaatgatgatatcctatagtcagaatggaccaatgattcttttattaataatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAGCACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
Basic information
species | Glycine max |
transcript | GLYMA06G01260.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G01260.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 6
gtgtgttgtcttgttccctgtgtaattgtttgctattttcttttggaatgctagttttgtcagttattgcaaattcaaatgatgatatcctatagtcagaatggaccaatgattcttttattaata-atacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAGCACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
| || || | | || || | | | | || | || | ||| | || || | ||||| || | |||||||||||| | |||||||| || || ||| |||| || |||| |||||| ||||| ||||| || || ||||| ||||| ||||| |
-----------------------------------------------gtactgtcttctactcaattcgctgataagcacagtactgtgttaattttcttgctaacttttttttcgtggttttatgtgttcagACCCTATATCAAATGTTTATTGTCAATGCTGGTCCGGGGTTTCGGCTCTTATGGAACACTGTGAAGTCCTTTCTGGACCCAAAAACCACTTCCAAGATAC
upper sequence: GLYMA06G01260.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
gtgtgttgtcttgttccctgtgtaattgtttgctattttcttttggaatgctagttttgtcagttattgcaaattcaaatgatgatatcctatagtcagaatggaccaatgattcttttattaataatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAGCACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
| || | | || || || || || || | | | | |||| | | || ||| || | |||||||| | ||||||||||||| | |||||||| || || || |||| | |||| |||||| ||||| ||||| ||||||||||| || | ||||| |
-----------------------------------------------gtatgagcctcatttttt-ttacactctcttttgttgtttttttgc--ttggaatatattg--ggttaatttgttgcatctccagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC
upper sequence: GLYMA06G01260.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G21520.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgtgttgtcttgttccctgtgtaattgtttgctattttcttttggaatgctagttttgtcagtta-ttgcaaattcaaatgat-gatatcctatagtcagaatggaccaatgattcttttattaataatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAGCACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
| | ||||| ||| | ||| ||| | ||| || || ||| | | || | | | | | || |||||||| ||||||||||||||| ||||| ||||||||||||||||| | |||| |||||||||| ||||| || || || ||| || |||| ||||
--------------------------------------------------------gtattagttaattggagcttctaatacttgatctcaggta-tcaaatgctaatcttggctttgtggtatttcatgcagACTCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTC
upper sequence: GLYMA06G01260.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 3'ss of exon 6
gtgtgttgtcttgttccctgtgtaattgtttgctattttcttttggaatgctagttttgtcagttattgcaaattcaaatgatgatatcctatagtcagaatggaccaatgattcttttattaataatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAGCACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
| | || ||| || || | || | |||| |||| | ||| |||| | | | | | ||| |||| | | ||| ||| | | | |||||||| ||||||||||||||||| |||||||| ||||| ||||||||| | |||| |||||| ||| ||||||| ||||||||||||||||| |||||||
-----------------gtattcaacctttttctgttgaca--tgataagctatagttgtaatccatttcaaaattgatataggtgactgaatatgtgccctggatcttgaactctctta--actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTCTGGAACACTGTAAAGACTTTTCTAGATCCCAAAACAACTTCCAAGATTC
upper sequence: GLYMA06G01260.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ17479 (Selaginella moellendorffii), 3'ss of exon 4
gtgtgttgtcttgttccctgtgtaattgtttgctattttcttttggaatgctagttttgtcagttattgcaaattcaaatgatgatatcctatagtcagaatggaccaatgattcttttattaataatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAGCACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
| | | ||| | |||| | | || | || || || ||||| | | |||||||||||||||||||| |||||||||| ||| |||||| ||| | | ||| | ||||| |||||| || | || ||
--------------------------------------------------------------------gtgagcctgctcgttga-actctatgcct----ttcttcctgagtttatgcgtttattatgcagACATTGCATCGTATGTTTATTATAAATGCTGGTCCTGGATTTAAGCTTGTGTGGAACACCATACGGGGATTTTTAGATCCGAAAACAGCTACCAAAATAT
upper sequence: GLYMA06G01260.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ28804 (Selaginella moellendorffii), 3'ss of exon 4
gtgtgttgtcttgttccctgtgtaattgtttgctattttcttttggaatgctagttttgtcagttattgcaaattcaaatgatgatatcctatagtcagaatggaccaatgattcttttattaataatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAGCACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
| | | ||| | |||| | | | || | || || || ||||| | | |||||||||||||||||||| |||||||||| ||| |||||| ||| | | ||| | ||||| |||||| || | || ||
--------------------------------------------------------------------gtcagcctgctcgttga-actctatgctt----ttcttcctgagtttatgcgtttattatgcagACATTGCATCGTATGTTTATTATAAATGCTGGTCCTGGATTTAAGCTTGTGTGGAACACCATACGGGGATTTTTAGATCCGAAAACAGCTACCAAAATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgatgatatcctatagtcagaatggaccaatgattcttttattaataatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAGCACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
tattaat putative branch site (score: 2)
aatgattcttttatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgttgtcttgttccctgtgtaattgtttgctattttcttttggaatgctagttttgtcagttattgcaaattcaaatgatgatatcctatagtcagaatggaccaatgattcttttattaataatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAGCACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA