Sequence
atgc intronic sequence ATGC exonic sequence...gtttgagtttataatggaaacattatcaaagaaaaccttcagtaatgccaaatgctaaactaaaactatcatactaactcattctagcttcatttcgcagGTACATGGCTCCAGAGTATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTTCTTGAGCTTATAACTGGAAGGAAA
Basic information
species | Glycine max |
transcript | GLYMA02G04010.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G04010.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G70460.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------------------------gtttgagtttata---atggaaacattatcaaagaaaaccttcagtaatgc-caaatgctaaactaaaactatcatactaactcattc--tagcttcatttcgcagGTACATGGCTCCAGAGTATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTTCTTGAGCTTATAACTGGAAGGAAA
| ||||| || ||| ||| | | || | | || ||| | | || || | | || || | |||| || ||||||| |||| ||||| |||||| ||||||||| | || |||||||||||||||||||| ||||| ||||| || | ||||||||||| ||| | |||
gtaagattgatcacaaattctttattaaactactagatatgataaggatgaactagtttgcttgtatacaaaggttagaaggtattacttattgccatatattaataacatctgagaagtacctaagcctctattttgttggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGAAAGCTGACTGATAGATCAGATGTTTTCTCGTTTGGGGTTGTTCTCTTAGAGCTTATAACAGGACGCAAA
upper sequence: GLYMA02G04010.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G23540.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------------------gtttgagtttataatggaaacattatcaaagaaaaccttcagtaatg-------ccaaatgctaaactaaaactatcatactaactcattctagcttcatttcgcagGTACATGGCTCCAGAGTATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTTCTTGAGCTTATAACTGGAAGGAAA
| | | | | ||| ||| || | | | | | | | || |||| || || | ||| || ||| | || | |||||| | || || || |||||| ||||||||||||| || |||||||| ||||| ||||| || || ||||| || | |||||| |||||||| |||||
gtaagcaaacattcatcacaaactctactccaaaactggaccttattgatccaatgcctgatgaaaagtttgttatatatggcttgaggcaacaaattggatcaaacctgaatctttattgatcgtatggctgcatgacatgttttgtgttaagGTACCTAGCGCCGGAATATGCATCAAGTGGAAAATTGACTGATAGATCCGATGTATTCTCATTCGGGGTTGTTCTCTTAGAGCTTGTAACTGGACGGAAA
upper sequence: GLYMA02G04010.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G70450.1 (Arabidopsis thaliana), 3'ss of exon 4
---gtttgagtttataatggaaacattatcaaagaaaaccttcagtaatgccaaatgctaaactaaaactatcatactaactcattctagcttcatttcgcagGTACATGGCTCCAGAGTATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTTCTTGAGCTTATAACTGGAAGGAAA
| ||| || | ||| | | | ||| | | | || || | || | || |||| | | |||| || ||||||| |||| ||||| |||||| ||||||| || | || |||||||||||||||||||| ||||||||||| || | ||||||||||||||| | |||
taaatctga--ttgtgatgaactagtacgtatagagaggttaagaggttataaattgttgaaaagtacataagcctctaa-tgttataggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGACAACTTACTGATAGATCAGATGTTTTCTCGTTTGGAGTTGTTCTCTTAGAGCTTATAACTGGACGCAAA
upper sequence: GLYMA02G04010.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0127g00670.t01 (Vitis vinifera), 3'ss of exon 5
---gtttgagtttataatggaaacattatcaaagaaaaccttcagtaatgccaaatgctaaactaa-aactatcatactaactcattctagcttcatttcgcagGTACATGGCTCCAGAGTATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTTCTTGAGCTTATAACTGGAAGGAAA
|| || | || || |||| || | || | | |||||| || | | ||||||||| || || || || |||||||||||| |||||||||||| ||||||| ||||| || |||||||| ||||| ||||| || || || || ||| | ||||||||||| || | |||
aataagggaaagtaagaaagagctgcaattcaagatttccaactgttctcctaaatgcatctctggtgattgtcatactaat---gtccagtttggcttt-cagGTACATGGCACCAGAGTATGCATCAAGTGGGAAATTGACTGATAGATCTGATGTATTCTCATTCGGGGTGGTACTTTTAGAGCTTATAACAGGGCGTAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgccaaatgctaaactaaaactatcatactaactcattctagcttcatttcgcagGTACATGGCTCCAGAGTATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTTCTTGAGCTTATAACTGGAAGGAAA
tactaac putative branch site (score: 0)
cttcatttc putative PPT
taaactaaaactat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgagtttataatggaaacattatcaaagaaaaccttcagtaatgccaaatgctaaactaaaactatcatactaactcattctagcttcatttcgcagGTACATGGCTCCAGAGTATGCAACAAGTGGAAAATTAACAGATAGATCAGATGTTTTCTCTTTTGGAGTTGTCCTTCTTGAGCTTATAACTGGAAGGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - -ccttcag
- - - - - - - - - - - - - - - - - - - - - -aatgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - -gctaaac