Sequence
atgc intronic sequence ATGC exonic sequence...cactttttatggaagaatttaaaagatgaagttatatttaatttatgtcatctgtagctttcttatgcctagtgccaagagttttgttcttttgtttcagAGATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCATTGTTTTTCGGGG
Basic information
species | Glycine max |
transcript | GLYMA10G39540.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
cactttttatggaagaatttaaaagatgaagttatatttaatttatgtcatctgtagctttcttatgc---ctagtgccaagagttttgttcttttgtttcagAGATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCATTGTTTTTCGGGG
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---ttaaccccaaataagtctaggtttcatcttcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
upper sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 15
-------------------------------------------------cactttttatggaagaatttaaaagatgaagttatatttaatttatgtcatctgtagctttcttatgcctagtgccaagagttttgttcttttgtttcagAGATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCATTGTTTTTCGGGG
||||| | || | || || || | ||| | ||| | | | |||| || || || || |||| | | |||||||||| ||||| |||||||| ||||||||||| || || ||||| ||| | || |||| ||||| ||||| ||||| ||||| || | | || | ||
gtaagatctgtgtttgggtttaactagacttggttggataaataacttgtccttttgttcacagtaattcctcactgttattgtttttgtacattatcacttctcacactcttcca--taacgcaaa---ttctgtttctatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGG
upper sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
cactttttatggaagaatttaaaagatgaagttatatttaatttatgtcatctgtagctttcttat-gcctagtgcca-agagttttgttcttttgttt-cagAGATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCATTGTTTTTCGGGG
| | || || | | || | | || | | |||| || | | | | || || ||||| || ||| ||||| | |||||||||||||| ||||||||||| ||||||||||||||||| || |||| ||||| ||||||||||| || || || || | || | |||
---aatcaaatgacatccatatccaaaataattgggtgtgcctttgtgcttttgtattattgtcacagtttcgtaatgtggatctttgtgtttccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
upper sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 3
cactttttatggaagaatttaaaagatgaagttatatttaat-ttatgtcatctgtagctttctta-tgcctagtgccaagagttttgttcttttgtttcagAGATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCATTGTTTTTCGGGG
| | | || | || || | ||| | | | || || | || || | || | | ||| || |||| | || ||||||| | ||||||||||| || ||||||||||| ||||| || || ||||| || |||| ||||| || |||||||| ||||| || || | || | ||
taaactaggttcaacacttcaagatg-aaagatctgcatgatgctaagctatgtgcattggtcccagtctctaacaatgcacattctgttttctt-cttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAACCGTATCCTCGTGGAGAGATTTGTGTTAGGGGACCTATAATATTCTGTGG
upper sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 16
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 16
---cactttttatgga----agaatttaaaagatgaagttatatttaatttatgtcatctgtagctttcttatgcctagtgccaagagttttgttcttttgtttcagAGATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCATTGTTTTTCGGGG
||||||| || || | | | | ||| || | || | | ||| | ||| ||| | | | | | || | | ||||||| |||| ||||||||||| |||||||||||||||||||| | ||||||||| |||||||||| ||||| ||||| |||||||| || ||||| ||
gtgagctttttactgactctgcgatatgataagtagagtaatttggaactaaa--tatccat---tttaaattgctttgggatttaatatgcatttctatatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTATACATCAGCGGATCAGCCCCATCCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG
upper sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 16
cactttttatggaagaatttaaaagatga-agttatatttaatttatgtcatctgtagctttcttatgcctagtgccaagagttttgttcttttgtttcagAGATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCATTGTTTTTCGGGG
|| | | | | | | | || | ||| || || | || ||| | || || | ||| || | | ||||||| | || |||||||||||||| ||||||||||| |||||||| ||||||||| |||| ||||||||||| ||||| ||||||||||| |||||| ||
aacaagaaaaatgtggctcctgagtacaacaattttctttccattgtggtctgtgctgctctattttgggataaatttat-gttaatttgtcctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcatctgtagctttcttatgcctagtgccaagagttttgttcttttgtttcagAGATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCATTGTTTTTCGGGG
ttttgttcttttgttt CT-rich tract
tttcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cactttttatggaagaatttaaaagatgaagttatatttaatttatgtcatctgtagctttcttatgcctagtgccaagagttttgttcttttgtttcagAGATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCATTGTTTTTCGGGG
- - - - - - - - - - - - - - - - - - - - - - - - catctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctagtgc