Sequence
atgc intronic sequence ATGC exonic sequence...aattagatgctttaagtgatggttatattcgaggatatctcaataatcaggaccaaaaaaagctctcttttaatcttgaatattttacaaattcttgcagTTGATTGGAAATACACCAATGGTGTACCTCAATAAGGTTACAGAAGGTTGTGTGGCTAACATTGCTGCGAAACTCGAGTCTATGGAACCTTGCCGAAGTG
Basic information
species | Glycine max |
transcript | GLYMA19G29740.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G29740.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G133359_T01 (Zea mays), 3'ss of exon 1
aattagatgctttaagtgatggttatattcgaggatatctcaataatcaggaccaaaaaaagctctcttttaatcttga----atat-tttacaaattcttg-cagTTGATTGGAAATACACCAATGGTGTACCTCAATAAGGTTACAGAAGGTTGTGTGGCTAACATTGCTGCGAAACTCGAGTCTATGGAACCTTGCCGAAGTG
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---tagcaactgta--taggggata-gctggcaaaaatccttttctttagcgtttcagtatgcccaatcacgtctctgataaaatgtgtttatgtgctgttaacagCTCATTGGAAAAACACCAATGGTGTATCTCAATAGAGTTGCTGACGGATGTGTGGCTAATATCGCTGCAAAGCTCGAGTACATGGGACCTTGCCGAAGTG
upper sequence: GLYMA19G29740.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G03630.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------aattagatgct-ttaag-tgatggttatatt--cgaggatatctcaataatca--ggaccaaaaaaagctctcttttaatcttgaatattttacaaattcttgcagTTGATTGGAAATACACCAATGGTGTACCTCAATAAGGTTACAGAAGGTTGTGTGGCTAACATTGCTGCGAAACTCGAGTCTATGGAACCTTGCCGAAGTG
| | | || | |||| | ||| || | || | ||| | ||| | || | | | | | |||| | | || || | |||||||||||| ||||||||||| || ||||||| || ||||| |||||| ||||| |||||||||| || ||||| || ||||| || || |||| |
gtgagttcaaaggattcaaattttactaagcttatgagtaaagagacgtttttttcttattaaagattagattatgtgatgaagtttgataatttaggattcgaactttgtttgtatagTTGATTGGAAGCACACCAATGGTCTATCTCAATAGAGTCACAGATGGTTGTTTGGCTGACATTGCTGCCAAGCTCGAATCAATGGAGCCCTGTAGAAGCG
upper sequence: GLYMA19G29740.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0056g00820.t01 (Vitis vinifera), 3'ss of exon 1
-------aattagatgctttaagtgatggttatattcgaggat-atctcaataatcaggaccaaaaaaagctctcttttaatcttgaatattttacaaattcttgcagTTGATTGGAAATACACCAATGGTGTACCTCAATAAGGTTACAGAAGGTTGTGTGGCTAACATTGCTGCGAAACTCGAGTCTATGGAACCTTGCCGAAGTG
|||| | | |||| | || | | | | || | || | | | |||| | | | || |||| | | ||| | | ||||||| || | ||||||||| | || ||||| ||||| ||| |||| |||||||| || |||||||| |||||||| ||||||||||||||||||||||
tactgtaaattgaagtataaaagtttttctttcaatagttttttatttttatttttatgtttgaaaaca----ttgactgat-ttgagcagct---aaaatgatatagTTGATCGGGAGAACACCAATGATTTATCTCAACAAGGTAACACAAGGCTGTGTGGCAAATATTGCTGCTAAACTCGAATCTATGGAACCTTGCCGAAGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcaggaccaaaaaaagctctcttttaatcttgaatattttacaaattcttgcagTTGATTGGAAATACACCAATGGTGTACCTCAATAAGGTTACAGAAGGTTGTGTGGCTAACATTGCTGCGAAACTCGAGTCTATGGAACCTTGCCGAAGTG
ttttaat putative branch site (score: 3)
ttcttgc putative PPT
ttttaatcttgaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattagatgctttaagtgatggttatattcgaggatatctcaataatcaggaccaaaaaaagctctcttttaatcttgaatattttacaaattcttgcagTTGATTGGAAATACACCAATGGTGTACCTCAATAAGGTTACAGAAGGTTGTGTGGCTAACATTGCTGCGAAACTCGAGTCTATGGAACCTTGCCGAAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - -gatgctt
- - - - - - - -gtgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa