Sequence
atgc intronic sequence ATGC exonic sequence...atgtaattgatattcaaatataagcattattgttctagttatattattataagttggatatattatctacttgaggagttttagacttagctttttgtagAGGCACTGAAATATGGAGGATTGAGGATTTTCAGCCAGTTCCATTGCCCAGATCTGAATATGGGAAATTCTACATGGGAGATTCTTACATCATCTTGCAG
Basic information
species | Glycine max |
transcript | GLYMA19G32010.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 2
atgtaattgatattcaaatataagcattatt-gttctagttatattattata---agttggatata-------ttatctacttgaggagttttagacttagctttt-tgtagAGGCACTGAAATATGGAGGATTGAGGATTTTCAGCCAGTTCCATTGCCCAGATCTGAATATGGGAAATTCTACATGGGAGATTCTTACATCATCTTGCAG
||| | | || |||| || || ||| ||||| | || || || | | || | |||| || | ||| |||| | | ||| ||||| ||||||||||||||| | |||||| |||||||||| ||||| | | | || || || ||||| |||| |||||||| || || | | |||
--gta-tccttctttaaatgcctttatggtttgttttagttgtcttcttttagaaatctacgtacaagagtttctatccttttatgctgttagccccttaattaaaatatagTGGCACAGAAATATGGAGGATTCAAGATTTTAAGCCAGTTCCTTTGCCAAAAGCAGATTACGGTAAATTTTACAATGGAGATTCATATATAGTTCTCCAG
upper sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g24220.3 (Oryza sativa), 3'ss of exon 1
atgtaattgatattcaaatataagcattatt-gttctagttatattattata---agttggatata-------ttatctacttgaggagttttagacttagctttt-tgtagAGGCACTGAAATATGGAGGATTGAGGATTTTCAGCCAGTTCCATTGCCCAGATCTGAATATGGGAAATTCTACATGGGAGATTCTTACATCATCTTGCAG
||| | | || |||| || || ||| ||||| | || || || | | || | |||| || | ||| |||| | | ||| ||||| ||||||||||||||| | |||||| |||||||||| ||||| | | | || || |
--gta-tccttctttaaatgcctttatggtttgttttagttgtcttcttttagaaatctacgtacaagagtttctatccttttatgctgttagccccttaattaaaatatagTGGCACAGAAATATGGAGGATTCAAGATTTTAAGCCAGTTCCTTTGCCAAAAGCAGATTACG--------------------------------------
upper sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 1
atgtaattgatattcaaatataagcattattgttctagttat-------attattataagttggatatat-tatctacttgaggagttttagacttagctttttgtagAGGCACTGAAATATGGAGGATTGAGGATTTTCAGCCAGTTCCATTGCCCAGATCTGAATATGGGAAATTCTACATGGGAGATTCTTACATCATCTTGCAG
|| || | | |||||||||||| ||| | ||| | || | | | | ||| ||| || | ||||| | | |||||| ||||| ||||||||||| |||||| | |||||||||||||| ||||| | || || ||||| |||||||||| || || |||||||| || |||||
--------tgcatgcatgtgttcctgttattgttctagatattgaacaagctgctattgtcttaattgctatttttgcttctggaattgtgaacttaacatcttgtagTGGCACCGAAATATGGAGAATTGAGAACTTTCAGCCAGTTCCTTTGCCAAAGTCCGATTATGGTAAATTCTACACAGGGGACTCTTACATTGTCCTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attataagttggatatattatctacttgaggagttttagacttagctttttgtagAGGCACTGAAATATGGAGGATTGAGGATTTTCAGCCAGTTCCATTGCCCAGATCTGAATATGGGAAATTCTACATGGGAGATTCTTACATCATCTTGCAG
ctttttgt CT-rich tract
atatattatctactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgtaattgatattcaaatataagcattattgttctagttatattattataagttggatatattatctacttgaggagttttagacttagctttttgtagAGGCACTGAAATATGGAGGATTGAGGATTTTCAGCCAGTTCCATTGCCCAGATCTGAATATGGGAAATTCTACATGGGAGATTCTTACATCATCTTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - -aaatataa