Sequence
atgc intronic sequence ATGC exonic sequence...aagagaaagggaaatggtaacaataacgcacctcaatttgatcaaatgaccttaatcttctaaaacaaggagaatggctaatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACGATAGTGACAGTAGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA
Basic information
species | Glycine max |
transcript | GLYMA05G22420.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G22420.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g10640.1 (Oryza sativa), 3'ss of exon 4
aagagaaagggaaatggtaacaataacgcac-ctcaatttgatcaaatgaccttaatcttctaaaacaaggagaatggctaatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACGATAGTGACAGTAGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA
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aatttagttgtcttgagttgtactaccatccatttcatgccctcatagttctatgcactttttca-ctcccaaaatttctcactgtgctatctgtttgcagGTGGCAAAAGAAAGTGCTGACGTGATTATTCTTGACGACAACTTCTCCACTATAGTCACTGTTGCTAAATGGGGTCGGTCAGTGTACATTAATATTCAGA
upper sequence: GLYMA05G22420.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 4
aagagaaagggaaatggtaacaataacgcacctcaatttgatcaaatgaccttaatcttctaaaacaaggagaa-tggctaatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACGATAGTGACAGTAGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA
| | |||| | | | | | ||||| | | || | ||| | |||| | | |||| || ||||| || || |||||||| ||||| || ||||| ||| |||||| || ||||| || |||||||||||||| ||||||||||| || || |
-------------------gtgagtatatgataagattttgttatgtcatttgtgagagctaaagaatctaaaagtttctatctgtataaccttt---tagGTGGCGAAAGAGAGCGCTGATGTCATCATTCTCGACGATAACTTCAGCACGATCGTCACAGTTGCTAAATGGGGACGTTCTGTTTACATAAACATCCAGA
upper sequence: GLYMA05G22420.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0129g00110.t01 (Vitis vinifera), 3'ss of exon 3
aagagaaagggaaatggtaacaataacgcac---ctcaatttgatcaaatgaccttaatcttctaaaacaaggagaa-tggctaatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACGATAGTGACAGTAGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA
||| | | || | | || || || ||| | | ||| || | | | | | | ||||| | | ||||| |||||||| ||||| ||||| ||||| ||||||||||||||||||| || | ||| || |||||||||||||||||||| ||||||||||||||||
----taaaagtcattgcttgatacaatctacaaattctcattgtttgcacttcctccattgtgaacagtaccaaattctaattaattctgcccatgaacttcagGTGGCTAAAGAGAGTGCTGATGTAATAATCTTGGATGATAATTTCTCCACAATTGCGACTGTGGCCAAATGGGGACGTTCAGTCTACATAAATATTCAAA
upper sequence: GLYMA05G22420.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 4
aagagaaagggaaatggtaacaataacgcacctcaatttgatcaaatgaccttaatcttcta-aaacaaggagaatggctaatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACGATAGTGACAGTAGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA
| | ||| | | || | | || || | | | || || ||| || | |||| || |||||| | | ||||| |||||||| ||||| ||||| ||||| ||||||||||||||||||| || | ||| || |||||||||||||||||||| ||||||||||||||||
taaataaaagtcattgcttgatacaatctacaa-attctcattgtttgcacttcctccattgtgaacagtaccaaattctaattctgcccatgaacttcagGTGGCTAAAGAGAGTGCTGATGTAATAATCTTGGATGATAATTTCTCCACAATTGCGACTGTGGCCAAATGGGGACGTTCAGTCTACATAAATATTCAAA
upper sequence: GLYMA05G22420.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S37_351V6.1 (Physcomitrella patens), 3'ss of exon 6
aagagaaagggaaatggtaacaataacgcacct-caatttgatcaaatgaccttaatcttctaaaacaaggagaatggc--taatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACGATAGTGACAGTAGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA
| |||| ||| | || | | | || | | | || | | | | || | | | | || | | ||||||||||| |||||||||||||| | || ||||| ||||||||||| || || || || ||||| ||||| ||||| || || | ||| |||||||
--ttgcttattctgtggtgtagatatcttcccaactgtctagggaagttaaatctgggttgtgacccgtgctgatctacattgaacttattgtg-attctcagGTTGCTAAGGAAAGTGCAGATGTGGTTATACTGGACGATAATTTCTCTACCATTGTCGTTGTGGCCAAGTGGGGTCGTTCTGTGTATACAAACATTCAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgaccttaatcttctaaaacaaggagaatggctaatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACGATAGTGACAGTAGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA
taatttcataatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagagaaagggaaatggtaacaataacgcacctcaatttgatcaaatgaccttaatcttctaaaacaaggagaatggctaatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACGATAGTGACAGTAGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA
aagagaaa
- - - - - - - - - - - - - - cacctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaacaa