Sequence
atgc intronic sequence ATGC exonic sequence...ccaattatttgaaaccagaagaagagaaagggaaattttgatcaaatgatcttattgttctaaagcaaggagaatggctaatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACAATAGTGACAGTGGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA
Basic information
species | Glycine max |
transcript | GLYMA17G17450.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G17450.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g10640.1 (Oryza sativa), 3'ss of exon 4
ccaattatttgaaaccagaagaagagaaagggaaattttgatcaaatgatcttat-tgttctaaagcaaggagaatggctaatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACAATAGTGACAGTGGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA
| ||| ||| || | | | | | || | || | ||| | | | | ||| || | | || ||| ||||||| || ||||||||||| || || || ||||| || || || |||||||| ||||| || || || |||||||| || ||||| ||||| |||||||| |
-aatttagttgtcttgagttgtactaccatccatttcatgccctcatagttctatgcactttttcactcccaaaatttctcactgtgctatctgtttgcagGTGGCAAAAGAAAGTGCTGACGTGATTATTCTTGACGACAACTTCTCCACTATAGTCACTGTTGCTAAATGGGGTCGGTCAGTGTACATTAATATTCAGA
upper sequence: GLYMA17G17450.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 4
ccaattatttgaaacca-gaagaagagaaagggaaattttga-tcaaatgatcttattgttctaaagcaaggagaatggctaatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACAATAGTGACAGTGGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA
| || |||| || || | | | || | || | | || || | || || |||| || | || | | |||| || ||||| ||||| || ||||| ||||| ||||| || ||||||||||| || || || || |||||||| || ||||||||||| || ||||| |
-tagatacccatgaccatgagtaacaatcaattacatgatatctcgagttat-ttgctatttactcccattttgaatttgactctttaacatgttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA
upper sequence: GLYMA17G17450.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 4
ccaattatttgaaaccagaagaagagaaagggaaattttgatcaaatgatcttattgttctaaagcaaggagaa-tggctaatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACAATAGTGACAGTGGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA
|| | | | |||||| | | | || | | |||||| | | || | ||| | |||| | | |||| || ||||| || || |||||||| ||||| || ||||| ||| ||| || || ||||| || |||||||||||||| ||||||||||| || || |
------------------gtgagtatatgataagattttg-ttatgtcatttgtgagagctaaagaatctaaaagtttctatctgtataaccttt---tagGTGGCGAAAGAGAGCGCTGATGTCATCATTCTCGACGATAACTTCAGCACGATCGTCACAGTTGCTAAATGGGGACGTTCTGTTTACATAAACATCCAGA
upper sequence: GLYMA17G17450.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0129g00110.t01 (Vitis vinifera), 3'ss of exon 3
ccaattatttgaaaccagaagaagagaaagggaaattttgatcaaatgatcttatt--gttctaaagcaaggagaat---ggctaatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACAATAGTGACAGTGGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA
|| | | || | ||||| | || || ||| | || | || ||| ||||| | | ||||| |||||||| ||||| ||||| ||||| |||||||||||||||||||||| | ||| ||||||||||||||||||||||| ||||||||||||||||
-----taaaagtcattgcttgatacaatctacaaattctcattgtttgcacttcctccattgtgaacagtaccaaattctaattaattctgcccatgaacttcagGTGGCTAAAGAGAGTGCTGATGTAATAATCTTGGATGATAATTTCTCCACAATTGCGACTGTGGCCAAATGGGGACGTTCAGTCTACATAAATATTCAAA
upper sequence: GLYMA17G17450.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 4
ccaattatttgaaaccagaagaagagaaagggaaattttgatcaaatgatcttattgttcta-aagcaaggagaatggctaatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACAATAGTGACAGTGGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA
|| || | | || | ||||| | || || ||| | | | || || |||||| | | ||||| |||||||| ||||| ||||| ||||| |||||||||||||||||||||| | ||| ||||||||||||||||||||||| ||||||||||||||||
-taaataaaagtcattgcttgatacaatctacaaattctcattgtttgcacttcctccattgtgaacagtaccaaattctaattctgcccatgaacttcagGTGGCTAAAGAGAGTGCTGATGTAATAATCTTGGATGATAATTTCTCCACAATTGCGACTGTGGCCAAATGGGGACGTTCAGTCTACATAAATATTCAAA
upper sequence: GLYMA17G17450.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S37_351V6.1 (Physcomitrella patens), 3'ss of exon 6
ccaattatttgaaaccagaagaagagaaagggaaattttgatcaaatgatcttattgttctaaagcaaggagaatggc--taatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACAATAGTGACAGTGGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA
||||| | ||| | | | || | | | ||| | | | | || | | | | || | | ||||||||||| |||||||||||||| | || ||||| ||||||||||| || || || |||||||| ||||| ||||| || || | ||| |||||||
ttgcttattctgtggt-gtagatatcttcccaactgtctagggaagttaaatctgggttgtgacccgtgctgatctacattgaacttattgtg-attctcagGTTGCTAAGGAAAGTGCAGATGTGGTTATACTGGACGATAATTTCTCTACCATTGTCGTTGTGGCCAAGTGGGGTCGTTCTGTGTATACAAACATTCAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgatcttattgttctaaagcaaggagaatggctaatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACAATAGTGACAGTGGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccaattatttgaaaccagaagaagagaaagggaaattttgatcaaatgatcttattgttctaaagcaaggagaatggctaatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACAATAGTGACAGTGGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA
- - - - -tgaaacc
- - - - - - - - - - -aagagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagcaag