Sequence
atgc intronic sequence ATGC exonic sequence...ctggcaaaaatgtcatttccatttgtagttcatcaaagttagtaaatttgtttttttaaaagtaaattatttttaattttttactaatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
Basic information
species | Glycine max |
transcript | GLYMA11G27410.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 6
ctggcaaaaatgtcatttccatttgtagttcatcaaa-gttagtaaatttgttt--ttttaaaagtaaattatttttaattttttactaatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
| | | || | |||| ||| | | | | || ||| || || ||| ||||| | ||| | || | | | || | |||| || || ||||| | ||||||||||| || |||||||| |||||||| || |||| ||||||||||||| | |||| ||| ||||||||||| |||
-tagtataataattatttgttattgcatcttaagattcatttgtatcactgcttattttgaaaagcagattttcttc--ctaaacatgtctacttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG
upper sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
---ctggcaaaaatgtcatttccatttgtagttcatcaaagttagtaaatttgtttttttaaaagtaaattatttttaattttttactaatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
|| || | ||||| | | | | || | | | | || || | | || || | | | | | ||||| || ||||||| | ||||| || || || || ||||| |||||||| || |||| |||||||||||| | || ||||||||||||||||| |||
catatgaagaatgaataatttctgtc---aatgtgttgaaatactttattatgcttcaaattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
upper sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
ctggcaaaaatgtcatttccatttgtagttcatcaaagttagtaaatttgtttttttaa---aagtaaat-tatttttaattttttactaatttttttatgt---agGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
|| || ||| | || | | ||| | | | ||| ||| ||| | ||||| | || ||||||| | || | | || | |||| || || ||||| ||||||| || || || ||||||||||||||||||||||| | |||||||||||| | || ||||||||||||||||| |||
--agctggaac--tattccagtt---aatccattgagatgtctttctttctttctttcagataagtatgcatgcagttctttttttaatcatctgctgatattctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
upper sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 6
ctggcaaaaatgtcatttccatttgtagttcatcaaagtta--gtaaatttgtttttttaaaagtaaattatttttaattttttactaatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
||| ||| | || | | | | ||| || | | | | ||| || ||| | | | || | | | ||| |||| || || ||||| | |||||||| |||||||||| ||| |||||||| || |||| |||||| || ||| | || | ||| |||||||||||||||
-tggtcaaatgcttatctgtttgaacaagtttctaaacttttcttcagtccttgtttccaacagttggatctccatctgaaaatatttactcccgtat-cagGTTGGCCTACCAGCTCGTGGTAAAACCTTCACTGCAGTTAAGCTTACAAGGTACCTTCGTTGGTTGGGCCATGAAACTAGACATTTCAATGTTGGGAAG
upper sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
-------ctggcaaaaat--gtcatttccatttgtagttcatcaaagttagtaaatttgtttttttaaaagtaaattatttttaattttttactaatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
| | || | || | |||||||||| | | | ||| || | | |||| |||||| | ||| || | | || ||| | | |||| || ||||||| ||||||||||||| |||||||||||||||||||||||||||| ||||| |||||| | |||||||||||||||||||| |||
gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaa---------caaatttatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
upper sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S215_89V6.1 (Physcomitrella patens), 3'ss of exon 7
----ctggcaaaaatgtcatttccatttgtagttcatcaaagttagtaaatttgtttttttaaaagtaaattatt--tttaattttttactaatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
| | | ||| ||| ||| | | || ||||| | |||| || | || ||| | || || ||| | ||| || | || || | || || || ||||||||||||||||| || |||||| | | |||||||||||| | ||||| |||||||||||||| |||
tgctttcctagtagtgt-attgttgagcgtataatgtgattgtggccaaattcacgctgttaagc-tacgctgggagttgaatgagtctctgatggtttca----gGTTGGGTTACCGGCTCGTGGAAAGACATTCACTGCAGCTAAACTGACCAGATATTTGCGGTGGTTAGGTCATGACACCAAGCACTTCAATGTTGGCAAG
upper sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ07288 (Selaginella moellendorffii), 3'ss of exon 2
ctggcaaaaatgtcatttccatttgtagttcatcaaagttagtaaatttgtttttttaaaagtaaattatttttaattttttact---aatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
|| | | ||| |||| | || || ||| || | ||||||| | ||||| || || |||||||||||||| | || || ||||||||||||| |||| | |||||| | || ||||||||||| ||||| ||
-------------------------------------------------------gtagattgtcgtcattcttaactcttatctttgaatcgggttctacagGTGGGCTTACCAGCAAGGGGGAAAACTTTCACTGCTGTCAAGCTAACAAGATATCTTCGTTGGCTTGGTCATGACACTAAACACTTCAACGTTGGAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgtttttttaaaagtaaattatttttaattttttactaatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
tactaat putative branch site (score: 1)
tttttttat CT-rich tract
tttttttaaaagtaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctggcaaaaatgtcatttccatttgtagttcatcaaagttagtaaatttgtttttttaaaagtaaattatttttaattttttactaatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG
- ggcaaaaa
- - - - - - - - - ccatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagtaa