Sequence
atgc intronic sequence ATGC exonic sequence...ctattttgtttttatttgatgttactgagcattactattttggctctgaaagctaaaagtttcccattcttattgtttggggatgtgatggctaatatagGGTTTCACATACCCTGTTAGAACTCAATTTTTGGAGGATATTCTGGAAATGTCGGGCTACAGATTGACTCCTGACAATCAAATTGATGACTATGGTCAAG
Basic information
species | Glycine max |
transcript | GLYMA09G18490.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G18490.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 2
ctattt-tgtttttatttgatgttactgagcattac-tattttggctctgaaagctaaaagtttcccattcttattgtttggggatgtg-atggctaatat-agGGTTTCACATACCCTGTTAGAACTCAATTTTTGGAGGATATTCTGGAAATGTCGGGCTACAGATTGACTCCTGACAATCAAATTGATGACTATGGTCAAG
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--atcagtagggttattc-ataagagagatcctaacctagcctagat-taaagcatcttattttattaggatggccctcattggttgcatacatctcatttcagGGTTTCACTTATCCTGTTCGGAGTCGATTTCTAGAAGATATTCTCGAAATTACTGGGCACAGATTAACTCCTTACAATCAAATTGATGACTATGGTCAAG
upper sequence: GLYMA09G18490.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 8
ctattttgtttttatttgatgttactgagcattactatt-ttggctctgaaagctaaaagtttcccattcttattgtttggggatgtgatggctaatatagGGTTTCACATACCCTGTTAGAACTCAATTTTTGGAGGATATTCTGGAAATGTCGGGCTACAGATTGACTCCTGACAATCAAATTGATGACTATGGTCAAG
| ||| ||||| | || || || || | | | || ||| || | || | || | | | | || | || |||||||| ||||| ||||| | | ||| ||| |||| |||||||| ||||| | || || | || ||||| |||||||||||||||||||||||||||
tgcaataaaatttgtttgaatgtcttgtgctttgctgtagcttcttgtgtaagttatatcttgacgtcctttcataaaaaacggttttatctc-aacttagGGTTTTACATATCCTGTCCGGAGTCATTTTCTGGAAGATATTCTTGAAATTACTGGGCACTGGTTAACTCCATACAATCAAATTGATGACTATGGTCAAG
upper sequence: GLYMA09G18490.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G01130.1 (Arabidopsis thaliana), 3'ss of exon 8
------------------------------ctattttgtttt----tatttgatgtt--actgagcattactatt--ttggctctgaaagctaaaagtttcccattcttattgtttggggatgtgatggctaatatagGGTTTCACATACCCTGTTAGAACTCAATTTTTGGAGGATATTCTGGAAATGTCGGGCTACAGATTGACTCCTGACAATCAAATTGATGACTATGGTCAAG
|| ||| ||||| || || ||||| | | |||| |||| ||| | ||| | | ||| | | ||| | | ||||||| || ||||| || ||| | | ||| || | |||||||||||||| ||| | | |||||||||||||| |||||||||||||||| ||||||||||
gtaagtaagaaacatatttgtttatcctctttagaacatttcaagatatttaatcttttgctgagt-tcaatattccttggatctatatgctctgattaaccccagtgaaactactaatattgtcttcttcactatagGGATTTACATATCCAGTTCGTAGTCATTTCCTAGAGGATATTCTGGAGATGACCCGGTACAGATTGACTCCATACAATCAAATTGATGATTATGGTCAAG
upper sequence: GLYMA09G18490.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0011g04360.t01 (Vitis vinifera), 3'ss of exon 8
ctattttgt--ttttatttgatgttactgagcattactattttggctctg-aaagctaaaagtttcccattcttattgtttggggatgtgatggctaatatagGGTTTCACATACCCTGTTAGAACTCAATTTTTGGAGGATATTCTGGAAATGTCGGGCTACAGATTGACTCCTGACAATCAAATTGATGACTATGGTCAAG
| || | ||||| | || || | ||| || | |||| | || | ||||| ||| |||| | | || |||||||| |||||||| ||||||| | || |||| |||||||||||||| | || |||||||||||||| |||||||| ||||||| |||||||| |
-cagttggaaattttagtcagagtggaggatgaaaactcccatgtaatggtggagctcatgtcttttttattttattttttt--aatgttttctgtgatgtagGGTTTTACATACCCAATTAGAACGTATTTCCTGGAAAATATTCTGGAAATGACAGGATACAGATTGACTCCGTACAATCAAGTTGATGATTATGGTCAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgaaagctaaaagtttcccattcttattgtttggggatgtgatggctaatatagGGTTTCACATACCCTGTTAGAACTCAATTTTTGGAGGATATTCTGGAAATGTCGGGCTACAGATTGACTCCTGACAATCAAATTGATGACTATGGTCAAG
ggctaat putative branch site (score: 3)
taaaagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctattttgtttttatttgatgttactgagcattactattttggctctgaaagctaaaagtttcccattcttattgtttggggatgtgatggctaatatagGGTTTCACATACCCTGTTAGAACTCAATTTTTGGAGGATATTCTGGAAATGTCGGGCTACAGATTGACTCCTGACAATCAAATTGATGACTATGGTCAAG
- - - - - - - - - - gttactg
- - - - - - - - - - - - - - gcattac
- - - - - - - - - - - - - - - - - - - - - -ctctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggggatg