Sequence
atgc intronic sequence ATGC exonic sequence...attcttgatcagtttttattgccgaactctgaattagtcagagccgtttccaacaagagggttaagacaaaaagaaataaccttttaacatacattgcagGTTGAAATTGAAGGCAGTCTATATGTACGCTGCTGGATTTTACTCATACTCCATTTTTGCTTTGATATTTTGGGAAACGAGGCGCTCCGACTTTGGAGTG
Basic information
species | Glycine max |
transcript | GLYMA08G36370.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G36370.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 2
attcttgatcagtttttattgccgaactctgaattagtcagagccgtttccaacaagagggttaagacaaaaagaaataaccttttaacatacattgcagGTTGAAATTGAAGGCAGTCTATATGTACGCTGCTGGATTTTACTCATACTCCATTTTTGCTTTGATATTTTGGGAAACGAGGCGCTCCGACTTTGGAGTG
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------------gtaatacgaattggtcctttattgcttcatgttcttactagttctcaggctggtgtatatctaacaattttccccttat---ctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG
upper sequence: GLYMA08G36370.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g20630.1 (Oryza sativa), 3'ss of exon 2
attcttgatcagtttttattgccgaactctgaattagtcagagccgtttccaacaagagggttaagacaaaaagaaataaccttt----taacatac---attgcagGTTGAAATTGAAGGCAGTCTATATGTACGCTGCTGGATTTTACTCATACTCCATTTTTGCTTTGATATTTTGGGAAACGAGGCGCTCCGACTTTGGAGTG
| ||| | | | | | || ||| || | || | ||| | ||| | ||| ||||||| | || | ||||| ||||| |||| ||||||||||||||| |||| ||||| || ||| | | || |||||||| ||||| || |||||||||||
-----------------------gtgagtggaaaaaaaataatctatacctgtgaaaaggtttctgtcacacagagtttttttttcctgttttctaccttattgcagACTCAAGCTTAAGGCTGTCTACATGTTTGCTGCTGGATTTTACACATATTCCATCTTCGCTCTTTTGTTCTGGGAAACAAGGCGGTCAGACTTTGGAGTC
upper sequence: GLYMA08G36370.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G170868_T01 (Zea mays), 3'ss of exon 2
attcttgatcagtttttattgccgaactctgaattagtcagagccgtttccaacaagagggttaagacaaaaagaaataaccttttaacatacattgcagGTTGAAATTGAAGGCAGTCTATATGTACGCTGCTGGATTTTACTCATACTCCATTTTTGCTTTGATATTTTGGGAAACGAGGCGCTCCGACTTTGGAGTG
| || | | | | | ||| | ||| | | | | | | | | | ||| || | | | | ||| |||||| | ||||| || |||||||| ||||||||||| ||| |||| ||||| ||||| | || ||||||||||| ||||| || ||||||||||||
---gtaattctgatccttccactgtacttt---ttaataaaaattctcactggttttcaatctgct-ctagatctaatgg--ttgtgcccttactctcagATTGAAACTTAAGGCTGTATATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTG
upper sequence: GLYMA08G36370.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G444643_T01 (Zea mays), 3'ss of exon 3
attcttgatcagtttttattgccgaactctgaattagtcagagccgtttccaacaagagggttaagacaaaaagaaa-taaccttttaacatacattg-cagGTTGAAATTGAAGGCAGTCTATATGTACGCTGCTGGATTTTACTCATACTCCATTTTTGCTTTGATATTTTGGGAAACGAGGCGCTCCGACTTTGGAGTG
| || |||| ||| | | || | | || || || | | | | | || ||| || || | | ||| |||||| | ||||| || |||||||| ||||||||||| ||| |||| ||||| ||||| | || ||||||||||| ||||| || ||||||||||||
--------gtaattcttatccttccactgt-actttttgatagaaattcttaat--gcttctcaggctggtataaatctaatggttgcacccttactctcagATTGAAACTTAAGGCTGTATATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTG
upper sequence: GLYMA08G36370.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0010g01110.t01 (Vitis vinifera), 3'ss of exon 2
------------------attcttgatcagttttta-ttgccgaactctgaatta---gtcag---agccgtttccaacaagagggttaagacaaa--------aagaaataacctt--ttaacatacattgca------gGTTGAAATTGAAGGCAGTCTATATGTACGCTGCTGGATTTTACTCATACTCCATTTTTGCTTTGATATTTTGGGAAACGAGGCGCTCCGACTTTGGAGTG
|| | | | || || | ||| || |||| || || || | | ||||| | | | | || | | ||| | | | | | ||| |||||| ||||||||||||||| | |||||||| || |||||| ||| |||||||||| ||||||||||| ||||||||||| ||||| || || |||||||||
gtaaggttttcacaagccatacattaaaagcttatggttgttaaattctggcttttgtgttagcttaactttttcctttagctgtgctttgaatagctcagcctatgaagtcagttgagtgatgatatattgcaaattcagGTTGAAATTGAAGGGTTTGTATATGTATTGTGGTGGATTCTACACATACTCCATATTTGCTTTGATTTTTTGGGAAACAAGGCGGTCTGATTTTGGAGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttccaacaagagggttaagacaaaaagaaataaccttttaacatacattgcagGTTGAAATTGAAGGCAGTCTATATGTACGCTGCTGGATTTTACTCATACTCCATTTTTGCTTTGATATTTTGGGAAACGAGGCGCTCCGACTTTGGAGTG
ttttaac putative branch site (score: 2)
acaaaaagaaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attcttgatcagtttttattgccgaactctgaattagtcagagccgtttccaacaagagggttaagacaaaaagaaataaccttttaacatacattgcagGTTGAAATTGAAGGCAGTCTATATGTACGCTGCTGGATTTTACTCATACTCCATTTTTGCTTTGATATTTTGGGAAACGAGGCGCTCCGACTTTGGAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - tattgcc
- - - - - - - - - - - - - ctctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaaa