Sequence
atgc intronic sequence ATGC exonic sequencegtgagttgtttctctttcaggtctcttcctactagcagtcttagaagcgatagtgttttccgttagctcactaaataatgatgtattttctttagGTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCAAGAGATGTATGGTTTCACTATTCAATATACTCACCTTCCTTGCCTTCAA
Basic information
species | Glycine max |
transcript | GLYMA10G38770.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G079080_T01 (Zea mays), 3'ss of exon 6
-----gtgagt-tgtttctctttcaggtctcttcctactagcagtcttagaagcgatagtgttttccgttagctcactaaataatgatgtattttctttagGTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCAAGAGATGTATGGTTTCACTATTCAATATACTCACCTTCCTTGCCTTCAA
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tagcagtgaatacattcgacaaataaaatatgtgatggtgaaaggttgttgaacattgatgcctaa-atcagttgatcgttttttttcctgtttttcacagTTTCCCGATTGATGAACAAATGAATATGAAATCTGTCGTGGAATACTTCAAGGAAATGTATGGTTTCACCATTCAGCATCCTCATCTTCCCTGCCTTCAG
upper sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 7
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 5
-gtgagttgtttctctttcaggtctcttc--ctactagcagtcttagaagcgatagtgtt-ttccgttagctca-ctaaataatgatgtattttctttagGTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCAAGAGATGTATGGTTTCACTATTCAATATACTCACCTTCCTTGCCTTCAA
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tctaagtcaccttagcagtgaatacattcgacaattaaaagtatatgatgatcaagggttgttaaatcaccttagcctgatttttatctaattttcacagTTTCCCAATTGATGAACAAATGAATATGAAATCTGTCGTGGAGTACTTCAAGGAAATGTATGGTTTCACCATTCAGCATCCTCATCTTCCTTGCCTTCAG
upper sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgagttgtttctctttcaggtctcttcctactagcagtcttagaagcgatagtgttttccgttagctcactaaataatgatgtattttctttagGTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCAAGAGATGTATGGTTTCACTATTCAATATACTCACCTTCCTTGCCTTCAA
|||||| ||||| ||| | |||| || | | | | || | || | ||| | || | ||| ||||| |||||||| || |||||||||| |||||||| ||||| |||| || ||||||||||||||||| ||||| || || | || || | || || || |||
gtgagtattttcttttta---------cttact-----ctttgattactaaggcttgtttcattgag--attaatttctggtttatattctt-agGTTTCCAGTAGATGAGAACTGTACTATGAAGTCAGTTATTGAGTATTTCCAAGAGATGTATGGATTCACGATCCAGCACACGCATTTGCCATGTCTCCAA
upper sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 6
------gtgagttgtttctctttcaggtctcttcctactagcagtcttagaagcgatagtgttttccgttagctcactaaataatgatgtattttctttagGTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCAAGAGATGTATGGTTTCACTATTCAATATACTCACCTTCCTTGCCTTCAA
| || |||| | | ||| | | || | || || || | | || | |||| || | ||| | || || || |||||||||||||| || ||||| ||||| ||||| || |||||||||||||| |||||||| || || |||||| || | ||||||||||||||||||
agttaaagcaaaaattgctctattaactcttctttttcttctggaattttttgct-tataaatgcatgcaagttttctaattattcatggttcttgttcagTTTTCCTGTTGATGATAATTCAACCATGAAGTCAGTTGTGGAATACTTCCAAGAAATGTATGGCTTTACAATTCAACATGCACACCTTCCTTGCCTTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagaagcgatagtgttttccgttagctcactaaataatgatgtattttctttagGTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCAAGAGATGTATGGTTTCACTATTCAATATACTCACCTTCCTTGCCTTCAA
cactaaa putative branch site (score: 2)
tattttcttt putative PPT
taaataatgatgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttgtttctctttcaggtctcttcctactagcagtcttagaagcgatagtgttttccgttagctcactaaataatgatgtattttctttagGTTTCCTGTTGATGAGAACTCAACTATGAAATCAGTAGTTGAATACTTCCAAGAGATGTATGGTTTCACTATTCAATATACTCACCTTCCTTGCCTTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG