Sequence
atgc intronic sequence ATGC exonic sequence...agtccaagaagttaaaaaatatttaatctttattttaaaaatttatgatccctaatttatccctgaaaagataagcaaagtaataattggtattctgcagGTTACTTTTATAGAAGCTTTAGATCAACTTATGCCTGGATTTGATCCTGAAATTAGCAAGTTGGCTCAGAGGGTCCTTATAAATCCCCGGAATATTGACT
Basic information
species | Glycine max |
transcript | GLYMA17G03560.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 5
agtccaagaagttaaaaaatatttaatctttattttaa-aaatttatgatccctaatttat-ccctgaaaagataagcaaagtaataattggtattctgcagGTTACTTTTATAGAAGCTTTAGATCAACTTATGCCTGGATTTGATCCTGAAATTAGCAAGTTGGCTCAGAGGGTCCTTATAAATCCCCGGAATATTGACT
| | | ||| ||| || | || || || || |||| | | | | | || | | | || ||||| |||||||||||| | |||||| | || || || |||||||| ||||||||||||||| || || || ||||| |||||||| || || |||||||| ||||
--tttcaacttacacaaatgattctattacagtagtattgtatcactgcatgctgatttttgttttcacatgccccctgaattgacagttttcattcttcagGTTACTTTTGTTGAAGCTCTTGACCAGCTAATGCCTGGTTTTGATCCTGAAATTGCAAAATTAGCCCAGAGAGTCCTTATCAACCCTCGGAATATAGACT
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 5
agtccaagaagttaaaaaatattta------atct-ttattttaaaaattt-atgatccctaatttatccctgaaaagataagcaaagtaataattggtattctgcagGTTACTTTTATAGAAGCTTTAGATCAACTTATGCCTGGATTTGATCCTGAAATTAGCAAGTTGGCTCAGAGGGTCCTTATAAATCCCCGGAATATTGACT
| | | || | ||| | |||| || | | ||| | || | | | || || | || || ||| || |||||| ||||||||||||| | |||||| | || || || |||||||||||||||||||||||| || || || ||||| || ||||| ||||| ||||| |||||||
-gctggatgaattctagaatgctccttagacatctgttgcctgatgaatatgattgttctcagttaattcacttgaatttactcaattcaa-aattgg------gcagGTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAAATTGCAAAATTAGCCCAGAGAGTTCTTATCAATCCTCGGAAAATTGACT
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 5
agtccaagaagttaaaaaatatttaatctttattttaaaaatttat--gatccctaatttatccctgaaaagataagcaaagtaataattggtattctgcagGTTACTTTTATAGAAGCTTTAGATCAACTTATGCCTGGATTTGATCCTGAAATTAGCAAGTTGGCTCAGAGGGTCCTTATAAATCCCCGGAATATTGACT
| | | || | | | | | |||| || ||| | | | | ||||| | | | | || || | || ||||||| |||||||||||||| | ||||| || |||||||||||||||||||| || || ||| | ||||||||||| | |||||||| | || |||||||
-ttttgtgtaaatagtagaaaataagattttaaggtaccaatctgttggtttttcgatttaaattgtagttactgatcgaaaacggaaacc-ttttgtgcagGTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTAGCTCAGAGGGTTTTGATAAATCCAAGAAAGATTGACT
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 5
agtccaagaagttaaaaaatatttaatctttattttaaaaatttatgatccctaatttatccctgaaaagataag---caaagtaataattggtattct--gcagGTTACTTTTATAGAAGCTTTAGATCAACTTATGCCTGGATTTGATCCTGAAATTAGCAAGTTGGCTCAGAGGGTCCTTATAAATCCCCGGAATATTGACT
| || | | ||| || ||| || || ||| |||| | ||| ||| || | || | || || | || | ||||| |||||||| || || | |||||||| |||||||||||||||||||| || || ||| ||||||| ||||| || |||||| | | || |||||||
---tcgagcaaatgggcgatagctatattttgctt--aaggtttgtgatgctctgcaactccaggaagtgaccaagctcaggggaactcttttttttttttacagGTAACTTTTATTGAGGCACTGGATCAACTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTGGCTCAAAGGGTTCTAATAAATACAAGAAAAATTGACT
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 5
agtccaagaagttaaaaaatatttaatctttattttaaaaatttatgatccctaatttatccctgaaaagataagcaaagtaataattggtattctgcagGTTACTTTTATAGAAGCTTTAGATCAACTTATGCCTGGATTTGATCCTGAAATTAGCAAGTTGGCTCAGAGGGTCCTTATAAATCCCCGGAATATTGACT
||| || | || | ||| | | | |||| | | | |||||| |||||| | |||||| | |||||||| ||||| || |||||||||||||| | ||| | ||||||||| | || || ||||| || || ||||| |
----------------------------------------gtttgcgagtttttcttctttcct-------ttttctacagaatacgcgatgt---gcagGTGACTTTTGTGGAAGCTCTGGATCAACTGATGCCAGGCTTTGATCCTGAAATCGGGAAGCTTGCTCAGAGGCTGCTGATCAATCCTCGAAAAATTGATT
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 5
agtccaagaagttaaaaaatatttaatctttattttaaaaatttatgatccctaatttatccctgaaaagataagcaaagtaataattggtattctgcagGTTACTTTTATAGAAGCTTTAGATCAACTTATGCCTGGATTTGATCCTGAAATTAGCAAGTTGGCTCAGAGGGTCCTTATAAATCCCCGGAATATTGACT
|| ||| || | | || ||| | | ||||||| |||||| | |||||| | |||||||| ||||| || |||||||||||||| | ||| | ||||||||| |||| || || || || || ||||| |
-------------------------------------------------gtttagtttttcttctttcctttttctatag----aatacgcgatgtgcagGTGACTTTTGTTGAAGCTCTGGATCAACTGATGCCAGGCTTTGATCCTGAAATCGGGAAGCTTGCTCAGAGGCTCCTGATCAACCCTCGAAAAATTGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatccctaatttatccctgaaaagataagcaaagtaataattggtattctgcagGTTACTTTTATAGAAGCTTTAGATCAACTTATGCCTGGATTTGATCCTGAAATTAGCAAGTTGGCTCAGAGGGTCCTTATAAATCCCCGGAATATTGACT
ccctaat putative branch site (score: 3)
taataattggtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtccaagaagttaaaaaatatttaatctttattttaaaaatttatgatccctaatttatccctgaaaagataagcaaagtaataattggtattctgcagGTTACTTTTATAGAAGCTTTAGATCAACTTATGCCTGGATTTGATCCTGAAATTAGCAAGTTGGCTCAGAGGGTCCTTATAAATCCCCGGAATATTGACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- -ccaagaa
- - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagata