Sequence
atgc intronic sequence ATGC exonic sequence...gtagaatctctgtattatggagagtgctttcttttctttgttaaatacatgattaattttttatttcttcttcagtggcactgaactaagcattttgtagGTCCTCTTCCAAAATGATTCACCTGCAACATTACTTGCTCGGGTGATTGGGATCATTGGTCCAATTGATCAAAATATGCTTGCAAAAGGACGGGACACAT
Basic information
species | Glycine max |
transcript | GLYMA08G06160.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g51020.1 (Oryza sativa), 3'ss of exon 5
--gtagaatctctgtattatggagagtgctttcttttctttgttaaatacatgattaattttttatttcttcttcagtggcactgaactaagcattttgtagGTCCTCTTCCAAAATGATTCACCTGCAACATTACTTGCTCGGGTGATTGGGATCATTGGTCCAATTGATCAAAATATGCTTGCAAAAGGACGGGACACAT
| | | || | | | | | | ||| || | || ||| | || ||| | ||| ||| |||| | | | || ||| || || |||| || |||||||||||||| |||||||| |||||||| || ||||| || ||||||||| | || || ||| |||||||||| | ||||| || ||||
tgatcttagcaggcaatgtttgcaatttatctatttactgttatacatagagaatgaatatgttagttcatcttgattcaccatggtctatgctcttc--agGTTCTTTTCCAAAATGATTCTCCTGCAACTTTACTTGCACGTGTGATGGGCATCATTGGTTCGATAGAACAAGCTATGCTTGCACAGGGACGTGAAACAT
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 5
-gtagaatctctgtattatggagagtgctttcttttctttgttaaatacatgattaattttttatttcttcttcagtggcactgaactaagcattttgtagGTCCTCTTCCAAAATGATTCACCTGCAACATTACTTGCTCGGGTGATTGGGATCATTGGTCCAATTGATCAAAATATGCTTGCAAAAGGACGGGACACAT
| || | | | | || | ||| | || | | ||| || | | | | || | || ||| ||||||| |||||||||||||| |||||||||||||||||||| ||||| || |||||||| | || || ||| |||||||||| | ||||| ||||| |
ttttttattattatttcaaggtatatattttttacctattttctgtcatatgcttg-tatggtgcatggaagctgatgagtgcgtcctctatgcttttcagGTCCTTTTCCAAAATGATTCTCCTGCAACATTACTTGCTCGCGTGATGGGCATCATTGGCTCCATAGAACAAGCTATGCTTGCACAGGGACGCGACACCT
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G181002_T01 (Zea mays), 3'ss of exon 5
----gtagaatctctgtattatggagagtgct-ttcttttctttgttaaatacatgattaattttttatttcttcttcagtggcactgaactaagcattttgtagGTCCTCTTCCAAAATGATTCACCTGCAACATTACTTGCTCGGGTGATTGGGATCATTGGTCCAATTGATCAAAATATGCTTGCAAAAGGACGGGACACAT
|| | | |||| || |||| || |||| |||||| | | || | | || | | || ||| || ||| |||| || |||||||| ||||| |||||||||||||||||||| ||||| || |||||||| | || || ||| |||||||||| | ||||||||||| |
gaaggtggtgattagaagctatgcagcttgctattttttttgttgttatacgcttgtatggtggacggaagctgatgtgtgcgtcct---ctatgcttttc--agGTTCTTTTCCAAAACGATTCGCCTGCAACATTACTTGCTCGTGTGATGGGCATCATTGGCGCCATAGAACAAGCTATGCTTGCACAGGGACGGGACACCT
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 11
-gtagaatctctgtattatggagagtgctttcttttctttgttaaatacatgattaattttttatttcttcttcagtggcactgaactaagcattttgtagGTCCTCTTCCAAAATGATTCACCTGCAACATTACTTGCTCGGGTGATTGGGATCATTGGTCCAATTGATCAAAATATGCTTGCAAAAGGACGGGACACAT
| | || ||| || | | || || ||| | || || | || | | | | || | | || || |||||||||||||||||||||||||| || || |||||||| ||||||||||| || || ||| ||||||| ||| |||||||| |||||||| || ||||
agcaagatatct-tacctggtttaatgtggtcattttccttaaaactatcaattatgattcctggtgcaaagcgctttacataaagtttgctatgttttagGTCCTCTTCCAAAATGATTCACCAGCGACGTTACTTGCACGGGTGATTGGAATAATAGGTTCAATTGACCAAGGCATGCTTGCTAAAGGACGTGATACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacatgattaattttttatttcttcttcagtggcactgaactaagcattttgtagGTCCTCTTCCAAAATGATTCACCTGCAACATTACTTGCTCGGGTGATTGGGATCATTGGTCCAATTGATCAAAATATGCTTGCAAAAGGACGGGACACAT
gattaat putative branch site (score: 3)
attaattttttatttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagaatctctgtattatggagagtgctttcttttctttgttaaatacatgattaattttttatttcttcttcagtggcactgaactaagcattttgtagGTCCTCTTCCAAAATGATTCACCTGCAACATTACTTGCTCGGGTGATTGGGATCATTGGTCCAATTGATCAAAATATGCTTGCAAAAGGACGGGACACAT
- - - -ctctgta
- - - - - - - - -tggagag
- - - - - - - - - - - - tgctttc
- - - - - - - - - - - - - - - - - - - - - - -tacatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactgaa