Sequence
atgc intronic sequence ATGC exonic sequence...ttttgaagtttataatggaaactttatcagggaaaaccttcagtaatgccaaatgctaaactaaactaccacacttactcattctagcttcatttcgcagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTCCTTGAGCTTATAACTGGAAGGAAA
Basic information
species | Glycine max |
transcript | GLYMA01G03690.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G03690.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G10620.1 (Arabidopsis thaliana), 3'ss of exon 5
ttttgaagtttataatggaaactttatcagggaaaaccttcagtaatgccaaat-gctaaactaaactaccacacttactcattctagcttcatttcgcagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTCCTTGAGCTTATAACTGGAAGGAAA
|| || | | | | | || | |||| | | | | || | | || || |||| | || || ||||||| | || ||||||||||| |||| ||||| |||| |||||||||||||| || || ||||||||||| || || || || || || || | |||
-----------gtactgtcacttctcttatttgtttttttta-taataaaatgttacgatacgatattaacaacattacataacataatgcaat---gcagGTATCTAGCACCAGAATATGCGTCAAGCGGAAAGCTAACGGATAGATCAGATGTGTTTTCATTTGGAGTTGTGCTTCTCGAACTCATCACCGGTCGCAAA
upper sequence: GLYMA01G03690.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G70460.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------------------------------------------ttttgaagtttataatggaaactttatcagggaaaaccttcagtaatgc-caaatgctaaacta-aactaccacacttactcattc--tagcttcatttcgcagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTCCTTGAGCTTATAACTGGAAGGAAA
| | || || | ||| ||| ||| | || | | || ||| | | || |||| | || || | |||| || ||||||| |||| |||||||||||| ||||||||| | || |||||||||||||||||||| ||||| ||||| ||| | ||||||||||| ||| | |||
gtaagattgatcacaaattctttattaaactactagatatgataaggatgaactagtttgcttgta-tacaaaggttagaaggtattacttattgccatatattaataacatctgagaagtacctaagcctctattttgttggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGAAAGCTGACTGATAGATCAGATGTTTTCTCGTTTGGGGTTGTTCTCTTAGAGCTTATAACAGGACGCAAA
upper sequence: GLYMA01G03690.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G23540.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------------------ttttga---agtttataatggaaactttatcagggaaaaccttcagtaatg-------ccaaatgctaaactaaact-accacacttactcattctagcttcatttcgcagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTCCTTGAGCTTATAACTGGAAGGAAA
| |||| | | | ||| ||| ||| | | | | | | || |||| || || | | | | | ||| | || | |||||| | || || ||||||||| ||||||||||||| || |||||||| ||||| ||||| || || ||||| ||| | |||||| |||||||| |||||
gtaagcaaacattcatcacaaactctactccaaaactggaccttattgatccaatgcctgatgaaaagtttgttatatatggcttgaggcaacaaattggatcaaacctgaatctttattgatcgtatggctgcatgacatgttttgtgttaagGTACCTAGCGCCGGAATATGCATCAAGTGGAAAATTGACTGATAGATCCGATGTATTCTCATTCGGGGTTGTTCTCTTAGAGCTTGTAACTGGACGGAAA
upper sequence: GLYMA01G03690.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G70450.1 (Arabidopsis thaliana), 3'ss of exon 4
ttttgaagtttataatggaaactttat---cagggaaaaccttcagtaatgccaaatgctaaactaaactaccacacttactcattctagcttcatttcgcagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTCCTTGAGCTTATAACTGGAAGGAAA
| || | || || | | | | || | | | || || | || || | || | | |||| || ||||||| |||| |||||||||||| ||||||| || | || |||||||||||||||||||| ||||||||||| ||| | ||||||||||||||| | |||
---taaatctgattgtgatgaactagtacgtatagagaggttaagaggttataaattgttgaaaagtacataagcctctaatgttataggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGACAACTTACTGATAGATCAGATGTTTTCTCGTTTGGAGTTGTTCTCTTAGAGCTTATAACTGGACGCAAA
upper sequence: GLYMA01G03690.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0127g00670.t01 (Vitis vinifera), 3'ss of exon 5
--ttttgaagtttataatggaaactttatcagggaaaaccttcagtaatgccaaatgctaaactaa--actaccacacttactcattctagcttcatttcgcagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTCCTTGAGCTTATAACTGGAAGGAAA
| | | || | || || || || | || | | |||||| || | | || ||| | || || || || |||||||||||| ||||| |||||| ||||||| ||||| || |||||||| ||||| ||||| || || || || || | ||||||||||| || | |||
aataagggaaagtaagaaagagctgcaattcaagatttccaactgttctcctaaatgcatctctggtgattgtcatactaat---gtccagtttggcttt-cagGTACATGGCACCAGAGTATGCATCAAGTGGGAAATTGACTGATAGATCTGATGTATTCTCATTCGGGGTGGTACTTTTAGAGCTTATAACAGGGCGTAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgccaaatgctaaactaaactaccacacttactcattctagcttcatttcgcagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTCCTTGAGCTTATAACTGGAAGGAAA
cacttac putative branch site (score: 2)
cttcatttc putative PPT
taaactaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttgaagtttataatggaaactttatcagggaaaaccttcagtaatgccaaatgctaaactaaactaccacacttactcattctagcttcatttcgcagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTCCTTGAGCTTATAACTGGAAGGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - -accttca
- - - - - - - - - - - - - - - - - - - - - - aatgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - gctaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccacact