Sequence
atgc intronic sequence ATGC exonic sequence...ggtggaattcctactcgtgtcgttcactgttgttgtggttgttattatattatcttctacctgacagattccaggaatgcatttttttgttaactggcagGGGGCATTGACCCTCACACCCACCTAGAGTTTGAGTTTATGGATACGGAAACTGTAGATGACTTCTTCAGTGGTCAGGCTGCAGCATTAGCTGGTGGGAC
Basic information
species | Glycine max |
transcript | GLYMA15G06100.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 6
ggtggaattcctactcgtgtcgttcactgttgttgtggttgttattatattatcttctacctgacagattccaggaatgcatttttttgttaactg----gcagGGGGCATTGACCCTCACACCCACCTAGAGTTTGAGTTTATGGATACGGAAACTGTAGATGACTTCTTCAGTGGTCAGGCTGCAGCATTAGCTGGTGGGAC------------------------------------------------------------------------------------
|| ||||| ||| || | | | | || | | | ||||||| | ||||| | | |||| || || || || |||| || |||||||||||||| ||||| ||| | || || |||| || | ||| | ||||| ||||| |||||||| ||||||||||| |||||||||||
-gta-aattcttacg-gttttgataaacattttggaattagttattacttgctcttcgggtttat--------------cattcttctggcaaatgtcacacaggtggaattgaccctcacactcacctggagatggaattcatgggaactgtaaccattgatgatttctttagtggtcatgctgcagCATTGGCTGGTGGGACAACAATGCACATTGACTTCGTCATTCCAGTGAATGGCAATTTAACTGCAGGTTTGGAATCCTACAAACAGAAGGCAGAAAAATC
upper sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g59340.3 (Oryza sativa), 3'ss of exon 6
ggtggaattcctactcgtgtcgttcactgttgttgtggttgttattatattatcttctacctgacagattccaggaatgcatttttttgttaactg----gcagGGGGCATTGACCCTCACACCCACCTAGAGTTTGAGTTTATGGATACGGAAACTGTAGATGACTTCTTCAGTGGTCAGGCTGCAGCATTAGCTGGTGGGAC
|| ||||| ||| || | | | | || | | | ||||||| | ||||| | | |||| || || || || |||| || |||||||||||||| ||||| ||| | || || |||| || | ||| | ||||| ||||| |||||||| ||||||||||| |||||||||||
-gta-aattcttacg-gttttgataaacattttggaattagttattacttgctcttcgggtttat--------------cattcttctggcaaatgtcacacagGTGGAATTGACCCTCACACTCACCTGGAGATGGAATTCATGGGAACTGTAACCATTGATGATTTCTTTAGTGGTCATGCTGCAGCATTGGCTGGTGGGAC
upper sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------ggtggaattcctactcgtgtcgttcactgttgttgtggttgtt--attatattatcttctacctgacagattccaggaatg-catttttttgttaact--------ggcagGGGGCATTGACCCTCACACCCACCTAGAGTTTGAGTTTATGGATACGGAAACTGTAGATGACTTCTTCAGTGGTCAGGCTGCAGCATTAGCTGGTGGGAC
|| || | | | | | | || ||||| || | | | || || ||||| | | | || | | ||| || | || | ||| || |||||||| ||||| ||||| | | || ||||||| ||| || ||| | ||||| ||||||||||||||||| || |||||||||||||| ||
gttaatcaattcatactagttga-tactttccaaaattttagccttttgttttgaatccttaactagtttcagttctaattaagaatggttagcattttcatcttactcttgtccctgatgtaaatagGAGGAATTGACCCCCACACGCACCTCGCCATGGAATTTATGGGTACCGAGACTATTGATGATTTCTTCAGTGGTCAGGCAGCGGCATTAGCTGGTGGAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatattatcttctacctgacagattccaggaatgcatttttttgttaactggcagGGGGCATTGACCCTCACACCCACCTAGAGTTTGAGTTTATGGATACGGAAACTGTAGATGACTTCTTCAGTGGTCAGGCTGCAGCATTAGCTGGTGGGAC
tgttaac putative branch site (score: 2)
tttttttgtt CT-rich tract
atttttttgttaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtggaattcctactcgtgtcgttcactgttgttgtggttgttattatattatcttctacctgacagattccaggaatgcatttttttgttaactggcagGGGGCATTGACCCTCACACCCACCTAGAGTTTGAGTTTATGGATACGGAAACTGTAGATGACTTCTTCAGTGGTCAGGCTGCAGCATTAGCTGGTGGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
ggtggaa
- - - - - - - - - - - - -actgttg
- - - - - - - - - - - - - - - - - gtggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgca