Sequence
atgc intronic sequence ATGC exonic sequence...atgccattctccttgggagtgtccataatttgttaatgcttcttttaatccttccaataaatctcgatgcaagttttacaatatctggtccattgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACAACAAATTAGTTG
Basic information
species | Glycine max |
transcript | GLYMA05G30630.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g38340.1 (Oryza sativa), 3'ss of exon 9
--------------------------------------------------------------------------------------------------atgccattctccttgggagtgtccata-atttgttaatgcttcttttaatccttccaataaatctcgatgcaagttttacaatatctggtccattgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCA-ACAACAAATTAGTTG
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gtattcaaacttctatttctatgtacagtagtaatgaacactcatatcacttgaaactagtgcatagcgtttacttttgcaagttgtttccaaagcttaaatttttttgttggaatatatccccatattcggggtttctttttcctttttccattttagaaattaaagctaattctg--gtagttttcccaac---cagGCTTGCCACACAAAAGCAGAGTATGAAGAGTATGGCGCAAGCATCTGCCGGACGAATCCTGTTTTCAAAGGGATGTACTAAACCACGGCGCAAAGCTTCT-
upper sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os08g03440.1 (Oryza sativa), 3'ss of exon 9
-------------------------------------------------------------------atgccat-tctccttgggagt--gtccataatttgtt-------aatgcttcttttaatccttcca-------ataaa-tctcgatgcaagttttacaatatctg---gtccattgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACAACAAATTAGTTG
|||||| | | ||| | | ||| ||||| || | ||||| || | | || ||||| | | | || | | | || || | | | ||| ||| || ||||||| |||||| |||||| ||||||||||||| |||||||| | | |||||||| || ||||| | ||| || |
gtgccttccactttacactctttgagtcttgacacctcattctgcaaatttaataatatgacatattctgccatataactttgttaataagtcaataatatgcttcaggtcaatgcaaaccatatgcactgcacacgtgaataaagtgataagatggaatctaaagtgtttgtatgttctcttt-cagAGTTGCCACACAAAGGAAGAATACGAGGAGCATGGAGCAAGCATCTGCCGGACCAGCACCGTTTTCAAAGGGATGTACTGAATTTTTTCCACCTGTCCAA
upper sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 8
lower sequence: AC205703.4_FGT002 (Zea mays), 3'ss of exon 9
--------------------------------------------------------------------------atgccatt-ctccttgggagtgtccataatttgttaatgcttcttttaatccttccaataaatct-cgatgcaagtt-ttacaata-tctggtccattgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACAACAAATTAGTTG--
|| ||| || || || | | || | || | | | | | || | | ||||| || ||| | | ||| || ||||||| || ||||||||||| || |||||||| || || ||||| ||||| || |||||||| ||||| || ||||| | | ||| | || ||
gtataccagctctcagtttatttgtgtacatacatatatagcattacaaaatttcttggaaagaaccagaacacctgaaatttctgaatgtgaacttgtctgcttggacaagttattacactaccttggtgaagtatgtgtgttgcaacttattatgggagttctttcctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGAACGAATCCTGTCTTCAAAGGGATGTACTGACTCAG--AGCGGTTCCCTGTG
upper sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 8
--atgccattctccttgggagtgtccataatttgttaatgcttcttttaatccttccaataaatctcgatgcaagttttacaatatctggtccattgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACAACA-AATTAGTTG
|||| | || || ||| | || |||| | ||| | || | | | | || |||| | || | | || | ||||| ||| || || | || |||||||| |||||||||||||| ||||| || ||||| || |||||||||||||||| || | | || || || ||
gtatgcaaa-ctagtttagagatccgctagtttg---aagctaaacctcatggcttgatcgtgttttgaaacaagatgtat----ttttgt---tgttgcagAGTTGCAGAACGAAAGAGGAGTATGAGGAATATGGAGCAAGCATATGCCGCACGAATCCGGTGTTCAAGGGAATGTATTGAAGCTGCTTCATAAATAATT-
upper sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv01s0137g00280.t01 (Vitis vinifera), 3'ss of exon 8
atgccattctccttgggagtgtccataatttgttaatgcttcttttaatccttcc--aat--aaatctcgatgcaagttttacaatatctggtccattgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAA-ATCAACAACAAATTAGTTG
|||| | ||| | | ||| | | | |||| | || | || | | | | | || | | | | | ||| |||| | || ||||||||||||||||| || || |||||||| || || |||||||| ||||| ||||||||||| |||||||| ||||||| | | || | || |
-ctgcattgttgttg--attccacatggtat-tccatgcatattatcatattacatgagtcgacattcttgtatgactatgaaaattcatggttctgtgcacagGCTTGTCATACAAAAGCTGAGTATGAGGAATACGGGGCAAGCATATGCCGAACAAATCCTGTCTTCAAGGGGATGTATTGATGTGAAGATTCTTTTGGGC- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatccttccaataaatctcgatgcaagttttacaatatctggtccattgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACAACAAATTAGTTG
ttttaat putative branch site (score: 3)
aagttttacaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgccattctccttgggagtgtccataatttgttaatgcttcttttaatccttccaataaatctcgatgcaagttttacaatatctggtccattgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACAACAAATTAGTTG
- - cattctc
- - - - - - - gggagtg
- - - - - - - - - - - - - - - - ttaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaagt