Sequence
atgc intronic sequence ATGC exonic sequence...gtttttttccttaaatatccatgtttcttacagtcaagctgacaatggtggggttagtgattaattattcaaagatttcattctcttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
Basic information
species | Glycine max |
transcript | GLYMA04G38360.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g06300.1 (Oryza sativa), 3'ss of exon 12
gtttttttccttaaatatccatgtttcttacagtcaagctgacaatg---gtggggttagtga---ttaattattcaaagatttcattctcttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
| | || | | ||||| || | | | | || || | | || | | || || | |||| | ||| | ||||||||||| || | || ||||||||||| |||||||| |||||||| ||||| || |||||||||||||| ||||| |||
----agatgccaaattgccaatgttgattggtgactaattagcattgtgcattgcatttctcatctttgcttttctaaaggcagtaacaaggttttcaat--gcagTTTGAACCAGAATCTTCAAGTGCCATGGGTTTTGGCTTCAGATGTGGATTTCTCGGTCTTCTTCATATGGAGATTGTGCAG
upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G003157_T02 (Zea mays), 3'ss of exon 3
-gtttttttccttaaatatccatgtttcttacagtcaagctgacaatggtggggttagtgattaattattcaaagatttcattctcttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
| | | | || | | | | || | || ||| || || | || |||| | | | | | | ||||||||||| || | || ||||||||||| |||||||| ||||||||||| || || ||||| ||||||||||| ||||||
tgcatctgttctcatttggattctgtaatattggttattctttatgcattggtattt-tgtatgatacttcattttctctaaatccatgccattaatgcagTTTGAACCAGAATCTTCTAGTGCCATGGGGTTTGGCTTCAGATGTGGGTTCCTTGGTCTTCTCCATATGGAAATAGTTCAG
upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 12
--gtttttttccttaaa-tatccatgtttcttacagtcaagctgacaatggtggggttagtg-attaattattcaaagatttcattctcttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
|| | ||| | ||| ||| || ||| | | ||| | | | | | ||| || || | | ||| | ||| | | |||||||| ||||| || ||||||||||||||||||||||||||||| |||||| |||| ||||| || ||||||||||| |||
atgtatctttgttaaaaatattcacatttggtctaag-gagcgtata-cgttagcattaacatatctataggtt--tgtcctcaacttggtttttatcctgcagTTTGAGCCTGAAACTTCGAGTGCCATGGGATTTGGCTTTAGATGCGGGTTTTTGGGTCTTCTCCACATGGAAATTGTGCAG
upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv07s0031g03050.t01 (Vitis vinifera), 3'ss of exon 12
--gtttttttccttaaatatccatgtttcttacagtcaagctgacaatggtggggttagtgattaattattcaaagatttcattctcttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
|| ||| | |||| || || | | || || ||| ||| | ||| | | | | || ||| |||||||| ||||||||||| ||||||||||| ||||||||||| |||||||| |||| ||||| ||||||||||| |||||
ctattgtttggttgtaataagggcgtagttttaatggtatatgcagatcttgg--ttacttgctaaagaattgtgctcccttcttcaatgtccattttgcagTTTGAGCCTGAGACATCCAGTGCCATGGGCTTTGGCTTTAGGTGTGGGTTCTTGGGTCTTCTCCATATGGAAATCATTCAG
upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ20933 (Selaginella moellendorffii), 3'ss of exon 12
gtttttttccttaaatatccatgtttcttacagtcaagctgacaatggtggggttagtgattaattattcaaagatttcattctcttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
|| || | ||| | | | | | |||| || ||| |||| | | | | | ||||||||||| || | |||||||| ||||||||||| ||| ||||||| ||||| |||||| | || |||||||| || |||
--------------------------------gtatggcct-cgatgctaag--tcgccacctattaaacactgatgccattgtatctagaattctgcagTTTGAACCGGAAAGTTCGAGTGCAATGGGATTTGGATTTCGATGTGGATTTCTTGGCCTTTTGCACATGGAAATAGTACAG
upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ32321 (Selaginella moellendorffii), 3'ss of exon 12
gtttttttccttaaatatccatgtttcttacagtcaagctgacaatggtggggttagtgattaattattcaaagatttcattctcttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
|| || | ||| | | | | |||| || ||| |||| | | | | | ||||||||||| || | |||||||| ||||||||||| ||| ||||||| ||||| |||||| | || |||||||| || |||
--------------------------------gtatggcct-cgatgctaagcc--gccacctattaaacactgatgccattgtatctagaattctgcagTTTGAACCGGAAAGTTCGAGTGCAATGGGATTTGGATTTCGATGTGGATTTCTTGGCCTTTTGCACATGGAAATAGTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtggggttagtgattaattattcaaagatttcattctcttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
gattaat putative branch site (score: 3)
tttcattctcttttct putative PPT
attaattattcaaaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttttccttaaatatccatgtttcttacagtcaagctgacaatggtggggttagtgattaattattcaaagatttcattctcttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
- - - - - - - - - ccatgtt
- - - - - - - - - - - - - - - - - - -gctgaca
- - - - - - - - - - - - - - - - - - - - - - -tggtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - gttagtg