Sequence
atgc intronic sequence ATGC exonic sequencegtcagcaaattaatatttaactttattttctcactttctaattttaaaccatttttttttcatatattaattattttttccttgcagGATGACCCTAACAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
Basic information
species | Glycine max |
transcript | GLYMA10G39080.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os07g07974.1 (Oryza sativa), 3'ss of exon 6
gtcagcaaattaatatttaactttattttctcactttctaattttaaaccatttttttttcatatattaattatttt--ttccttgcagGATGACCCTAACAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
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gtaggcgctttt-tgctggatagtctgtacta--cttctagccctcatttccatttatgtggtgc-tgaaatacttcaataaattgcagGAAGATCCTAACAACACTCCAGCTTCAGCTCGACATAAGAGAGGATGCAATTGCAAGAAGTCAAGCTGTCTTAAGAAATACTGTGAATGCTATCAG
upper sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os12g41230.2 (Oryza sativa), 3'ss of exon 6
gtcagcaaattaatatttaactttatttt-ctcactttctaattttaaaccatttttttttcatatattaattattttttccttgcagGATGACCCTAACAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
| || | | |||| |||| || |||||| ||| || | | ||||||| || || | || |||||||| ||||||||||||| ||||| | || ||||||||||| || ||||| ||||| ||| || | || ||||| || ||||||||||||
----gtaag--agccactctctttgttttacttcctttctcctttgttacgtgctactgctcatata---atccttgctatattatagGATGACTCTAACAAAACTCCTGCTTCTTCTCGTCACAAAAGAGGCTGCAATTGTAAGAAGTCATCGTGTTTGAAAAAATACTGCGAATGTTATCAG
upper sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G366584_T01 (Zea mays), 3'ss of exon 5
gtcagcaaattaatatttaactttattttctcactttctaattttaaaccatttttttttcatatattaattattttttccttgcagGATGACCCTAACAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
|| || || ||| | | || | | | || | ||||| | ||| | | || | || || ||||||| ||||||||||||| ||||| || ||||| ||||||||||| ||||||| ||| || || || || ||||| || || || | ||||
gtaag--aactaagaa--gaacagatcctattagttgc--atttttatttttttcactattgctcatggcat-cccgctcattatagGATGATTCTAACAAAACTCCTGCTTCTGCTCGACATAAAAGAGGATGCAATTGCAGGAAGTCTTCTTGTCTTAAAAAATACTGCGAGTGCTTTCAG
upper sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G701689_T01 (Zea mays), 3'ss of exon 6
gtcagcaaattaatatttaactttattttctcactttctaattttaaaccatttttttttcatatattaattattttttccttgcagGATGACCCTAACAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
|| || | | || | | | ||| | |||| | | || | | | | || | |||| | || ||| |||| | | || |||||||| |||||||| || |||||||| ||||| ||||||||||| || || ||||| ||||| |||||||||| ||||
gtaagaga--cactaacttattgtatctgagtacttccc-----ttaatcttgtctgttgctaatatcatcatcttcaatattgtagGACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAG
upper sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G322090_T01 (Zea mays), 3'ss of exon 7
gtcagcaaattaatatttaactttattttctcactttctaattttaaaccatttttttttcatatattaattattttttccttgcagGATGACCCTAACAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
|| || | | || | | | || || | || || | || | | | | || | |||| | | || || |||| | || |||||||| |||||||| || |||||||| ||||| ||||||||||| || || ||||| ||||| |||||||||| ||||
gtaagaga--cactaacttattgtacttgagtatttcct-----ttaatcttgtctgttgctaatatcattgtcttcaatactgtagGACTTTTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCGTGTCTAAAAAAATACTGTGAATGTTTTCAG
upper sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 12
lower sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 5
gtcagcaaattaatatttaactttattttctcactttctaattttaaaccatttttttttcatatatta-attatttt--ttccttgcagGATGACCCTAACAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
| | | | || | | ||| | || | | | | | || || || | ||| | | |||| | | | |||||||| | | ||||||||||||||| || || || ||| | || || || ||||||||||||| ||| || |||||||| |||||||| ||||||
----gtaggattcttttccccgtcctttgattcctctgcatcatccatctatcttgcttgaagttataataatattgtaatgacacacagGATGATGCAAGCAAAACTCCAGCTTCTGCGCGCCATAAACGTGGCTGCAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
upper sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G22760.1 (Arabidopsis thaliana), 3'ss of exon 6
gtcagcaaatt-aatatttaactttattt-tctcactttctaattttaaaccatttttttttcatatattaattattttttccttgcagGATGACCCTAACAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
|| || | ||||||| |||| || || || || |||| |||| | |||| | | || | ||||| || | | ||||||||||||||||| ||||||||| |||| ||||| ||||||||||||| ||| || |||||||| |||||||| ||||||
gtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggc-tataaaattctgcattggttcacagGAGGATGCAAGTAAAACTCCAGCTTCAGCGCGACACAAACGAGGCTGTAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
upper sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 6
--gtcagcaaattaatatttaactttattttctcactttctaattttaaaccatttttttt-tcatatattaatt-----------attttttccttgca--gGATGACCCTAACAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
||| || | | |||||| | | | | | || | | | | || | |||||| || || |||||| |||||| | | ||||| || ||||| |||||||||||| | || || || ||||||||||||| ||| | |||||||| |||||||| ||||||
gtaagagctctctattccatctttttattccccccccccccccccctctctcactctctctgtcctccattaatctaagggatgacatcgttatcttgcacagGATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAACGTGGCTGCAACTGCAAGAAATCAAACTGTATGAAGAAATACTGTGAATGCTATCAG
upper sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 7
gtcagcaaattaatatttaactttattttctcactttctaattttaaaccatttttttttcatatattaattat--tttttccttgcagGATGACCCTAACAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
|| || | || | | || | || | || || || | | ||| | || | | |||| | |||| |||||||||||| |||| |||||||||||||||||||||||||||||||||||| || |||||||||||||| ||||||||||||||||| ||||| ||||||
gttaggacataattctt--gccttgtgtttatacaga--aaatctgaactgctagttaccc---tgttaagtgaggttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actttctaattttaaaccatttttttttcatatattaattattttttccttgcagGATGACCCTAACAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
tattaat putative branch site (score: 2)
ttattttttccttgc CT-rich tract
taattttaaaccattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagcaaattaatatttaactttattttctcactttctaattttaaaccatttttttttcatatattaattattttttccttgcagGATGACCCTAACAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGTAATTGCAAGAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA