Sequence
atgc intronic sequence ATGC exonic sequence...atgctgagtttccaactgcttgtaagttgtaatctgtaattaaaagcatttactctaacaaaaagatagtgtttccccgagttatcttcataattggcagGTTGGCTGGTTTAGTTTTGATCCTGAGGTCCATATTGAAAGAGAGCAGATGTGCTGCTACCTAACTCGTACTACAAGTACAACTCATCAGATAATACAAG
Basic information
species | Glycine max |
transcript | GLYMA08G00380.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G00380.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g72980.1 (Oryza sativa), 3'ss of exon 5
---atgctgagtttccaactgcttgtaagttgtaatctgtaattaaaagcatttactctaacaaaaagatagtgtttccccgagttatcttcataattggcagGTTGGCTGGTTTAGTTTTGATCCTGAGGTCCATATTGAAAGAGAGCAGATGTGCTGCTACCTAACTCGTACTACAAGTACAACTCATCAGATAATACAAG
| ||| | | ||| | | | | | || | || || ||| || | || | | | | | || | ||| | ||||||||||||||||||||||||||||| |||||||||| || || || ||||||||||| |||| | ||||||| || ||||| || | ||
gcgtttatgaatctatgacttatcagctgcttaagtttgcagttcaag---tttgctttgaccatatatgtaaatgttcaaaagatggtttctctttaaacagGTTGGCTGGTTTAGTTTTGATCCTGAATTCCATATTGAGAGGGACCAAATGTGCTGCTATTTAACAAGGACTACAAAAGAGACACATCAAATTGTTAGAG
upper sequence: GLYMA08G00380.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G481548_T01 (Zea mays), 3'ss of exon 5
atgctgagtttccaact-gcttgtaagttgtaatctgtaattaaaagca-tttactctaacaaaaagatagtgtttccccgagttatcttcataattggcagGTTGGCTGGTTTAGTTTTGATCCTGAGGTCCATATTGAAAGAGAGCAGATGTGCTGCTACCTAACTCGTACTACAAGTACAACTCATCAGATAATACAAG
|| | | || | | | | | | || | || || | ||| | | ||| | | | | | | | | ||||| || |||||||||||||||||||| | || | || ||||| |||||||||||||| ||||| || ||||||| || || || || | |
--ttagaatgtagggcttgtcaggatggttaagcttgaagttcaagttacttttgtgttacacatttttggggggataaaaggatggttcctcttgaaacagGTAGGTTGGTTTAGTTTTGATCCTGAATTTCACGTCGAGAGAGAACAGATGTGCTGCTATCTAACACGAACTACAAAAGAGACGCACCAAATTGTTATCG
upper sequence: GLYMA08G00380.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G13440.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------------------------------------------------------------atgctgagtttccaactgcttgtaagttgtaatctgtaattaaaagcatttactctaacaaaa-agatagtgttt-----ccccgagttatc-ttcataattggcagGTTGGCTGGTTTAGTTTTGATCCTGAGGTCCATATTGAAAGAGAGCAGATGTGCTGCTACCTAACTCGTACTACAAGTACAACTCATCAGATAATACAAG
| || || | ||| | | ||| || || | |||||| | | | | || || ||| | || | || | | ||||| ||||||||||||| || || || | || ||||| |||||||| |||||||||||||||||||| || |||| | || || || | || ||
gtatcactctacaattattaaagtaggcttttcatgatcaatattgtatggttacatgggttaaagcatctcagtcggcgagttaccagaaaagtttcatatactttcttgacgagatcagt--ttgaccacatttattggcgctttatatattgtatttgaagatgctgaacattagttttttttccccagGTCAGCTGGTTTAGTTTCGACCCAGATTTTCACATTGAGAGAGAGCAAATGTGCTGCTACCTAACTCGCACAACAAAGATTACACACCAATTGATCAGAG
upper sequence: GLYMA08G00380.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0044g01690.t01 (Vitis vinifera), 3'ss of exon 5
atgctgagtttccaactgcttgtaagttgtaatctgtaattaaaagcatttactctaacaaaaagat-agtgtttccccgagttatcttcataattggcagGTTGGCTGGTTTAGTTTTGATCCTGAGGTCCATATTGAAAGAGAGCAGATGTGCTGCTACCTAACTCGTACTACAAGTACAACTCATCAGATAATACAAG
||| || || | || | | | | ||||| | | || | | || | ||| | | | || || || ||||| |||||||||| ||||||||||| |||||||||| || || || ||||||||||| || || |||||||||| | ||||| ||| |||| |||
-ccagtagtgatttgatgtttatctcttccatttaatggtgaaaagtgatgtatttattacatttattattgtgtttgaaatatgggttgatgataaacagGTGAGCTGGTTTAGCTTTGATCCTGATTTCCATATTGAGAGGGAACAAATGTGCTGCTATCTGACACGTACTACAAAGAGCACTCACCAGCTAATTAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatttactctaacaaaaagatagtgtttccccgagttatcttcataattggcagGTTGGCTGGTTTAGTTTTGATCCTGAGGTCCATATTGAAAGAGAGCAGATGTGCTGCTACCTAACTCGTACTACAAGTACAACTCATCAGATAATACAAG
ctctaac putative branch site (score: 2)
tcttcat putative PPT
ttatcttcataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgctgagtttccaactgcttgtaagttgtaatctgtaattaaaagcatttactctaacaaaaagatagtgtttccccgagttatcttcataattggcagGTTGGCTGGTTTAGTTTTGATCCTGAGGTCCATATTGAAAGAGAGCAGATGTGCTGCTACCTAACTCGTACTACAAGTACAACTCATCAGATAATACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
-tgctgag
- - - - - tccaact
- - - - - - - - -gcttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaaa