Sequence
atgc intronic sequence ATGC exonic sequence...cctttttgttttgaattaaaacagtactcagcatacattggtctatataaccaaagatatttatactgtcttacagtgactgataagatacattttccagTATTTTCTGTATCAGTTGTTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACT
Basic information
species | Glycine max |
transcript | GLYMA09G39190.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39190.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 3
------------------------------------------------------------------------cctttttgttttgaattaaaacagtactcagcatacattggtctatataaccaaagat------atttatactgtcttacagtgactgataagatacatt---ttccagTATTTTCTGTATCAGTTGTTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACT
|||| || |||| | || || ||| | | | | | || || ||||| || | | | | || | | || || || ||||| || ||||| |||||| ||||||| || |||||||| ||||| |||||||| ||||||||||||| ||||| ||||| ||| | || ||||| || |
gtttgttgcttccagcttgtgctttgctgaaacattttgcttgcagaaaatctagacagagatttccatgcaccttgttcctttggtcgctatatgttttcttcatcctatccatatttcagcttaacattctcttgtttatctggtttaataatcacaagtgacatgttttgcattgcagTACTTCCTGTACCAGTTGCTACGAGGGCTAAAATATGTGCACTCGGCAAATGTCTTGCACCGTGATCTGAAGCCAAGCAATTTGTTCCTTAATGCAAATT
upper sequence: GLYMA09G39190.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 3
cctttttgttttgaattaaaacagtactcagcatacattggtctatataaccaaagatatttatactgtcttacagtgactgataagatacattttccagTATTTTCTGTATCAGTTGTTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACT
| | | || || | ||| |||| | | | | | | |||| | | | | | | || ||||| || ||||||||||||||||||| || |||||||| |||||||||||| | ||||||| ||||| ||||| ||||| ||| | || ||||| || |
acaaagaactatattttggtacggagggagtaatatattgcttcacaacaatgatatattctataatctatatttctatgttccccctttttccttgcagTACTTCTTGTATCAGTTGTTACGAGGGCTAAAATATGTGCACTCAGCAAATATATTGCACCGCGATCTGAAGCCGAGCAATTTGTTCCTAAATGCAAATT
upper sequence: GLYMA09G39190.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G01560.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------cctttttgttttgaattaaaacagtactcagcatacattggtctatataaccaaagatatttatactgtcttacagtgactgataagatacattttccagTATTTTCTGTATCAGTTGTTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACT
|| ||||| | || || |||| || || | | | | | | | || || | | || || |||| |||| || |||||||||||||| ||||| ||||| ||||| || ||||| ||||| ||||| |||||| |||| || || |||||||| |||||||| ||||
gtacgcattaacctctcctgtgcttcttatagctcaagtatcttctgtttaggtcaaagtttataatcagaatctttttggttcgaaggctatgaagttggggtttgatgtataaccataaattttatgt-ttttgcagTTCTTCCTGTATCAGTTGTTGCGAGGCCTCAAGTATGTGCATTCAGCCAATGTACTGCATCGTGATTTAAAACCGAGTAACTTGCTCCTGAATGCAAACT
upper sequence: GLYMA09G39190.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G01370.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------------------------------cctttttgttttgaatta------aaacagtactcagca-tacattggtctatataaccaaagat---atttatactgtcttacagt---gactgataa---------gatacattttccagTATTTTCTGTATCAGTTGTTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACT
|| |||| || | | | | | || | | || || | || ||| ||| | || || ||| | | ||| || |||| |||| |||||||||||||||||| || || ||||||||||| || ||||| ||||| |||| || ||| | || |||||||| ||||| |||||||| || |
gtatgcatcaatctccatcttgcttatatctagcagctgaatcttctgtttctactttagaagcagctgttattgtgttagagcatctgatgagtattgcttgatactttataagtgagagctaataaggatttcgtttgttatgctttgaagttgtgtttagtaattagtttcgattatgttttgcagTTTTTTCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAATGTATTGCATCGAGATTTGAAACCTAGCAATTTGCTCCTGAATGCAAATT
upper sequence: GLYMA09G39190.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 3
cctttttgttttgaattaaaacagtactcagcatacattggtctatataaccaaagatatttatactgtcttacagtgactgataagatacattttc--cagTATTTTCTGTATCAGTTGTTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACT
|| | | ||| | | || | | ||| | || | ||| | | |||| | | || |||| | | | | || ||||| || ||||||||| ||||||||||||| ||||||||||||||||||||||| |||| |||||| | ||||| || || ||||| |||||||| || |
actgtgggatttttgtaagtgcaa-atataacat-cttttctgtatgatttctatgataccgaactgagatgtcaatgacactccaattctactctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAATGTCTTGCATCGTGATTTGAAGCCGAGTAATTTGCTTCTGAATGCAAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tataaccaaagatatttatactgtcttacagtgactgataagatacattttccagTATTTTCTGTATCAGTTGTTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACT
gactgat putative branch site (score: 3)
cattttcc putative PPT
aaagatatttatact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctttttgttttgaattaaaacagtactcagcatacattggtctatataaccaaagatatttatactgtcttacagtgactgataagatacattttccagTATTTTCTGTATCAGTTGTTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACT
- - - tgttttg
- - - - - - - - - - - - - - - gcataca
- - - - - - - - - - - - - - - - - - - - - - - - aaccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgactg