Sequence
atgc intronic sequence ATGC exonic sequencegtccgaaaattgttatttgttattgatttatattttgatctctaaatttttaatattcatttaacctgtatgcaaactacttgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAGG
Basic information
species | Glycine max |
transcript | GLYMA08G28320.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G28320.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g37870.1 (Oryza sativa), 3'ss of exon 6
gtccgaaaattgttatttgttattgatttatattttgatctctaaatttttaatattcatttaacctgtatg--caaactacttgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAGG
|| || | |||| | || || || | | || ||| || || ||| | | | | | |||| ||| |||||||| || | ||||| ||||||||||| ||||||||||| || ||||| || ||||| || || || |||||||| |||||||||| || ||||||
--gtaaaggcgcatagcttctatttgtata-atatt--tttttatgtttccaagtttagtttcagttttgagatcgaacttgctgtgtagGTTGGCCCAAGGTTCTGTTTGAACCCAATCAAAATATTTGGCGGTAGTTTCGGTGGCCCTACATTGTACGAGAATCCATTCTATGTGTCTCCCAATCAG-
upper sequence: GLYMA08G28320.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G168176_T02 (Zea mays), 3'ss of exon 6
gtccgaaaattgttatttgttattgatttatattttgatctctaaatttttaatattcatttaacctgtatgcaaactact-tgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAGG
|| |||| || ||| ||| | | || | ||| ||| | | | || || ||| | | || | | |||||||| || | ||||| ||||| ||||| |||||||||||||| |||||||| || || || |
gtaattgcattgagcttctatatggatactttatgtgcttcctagttttgtctaaataat--aatttgtgcttggattgctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATG-----------------------------------
upper sequence: GLYMA08G28320.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G160458_T01 (Zea mays), 3'ss of exon 6
gtccgaaaattgttatttgttattgatttatattttgatctctaaatttttaatattcatttaacctgtatgcaaactacttgtt-tagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAGG
|| | || || |||| ||| | | | | | | ||| || | | || || ||| | | || || |||||||| || | ||||| ||||| ||||| |||||||||||||| |||||||| || || || | |||||||| || ||| | || || ||||||
gtaactgcactgagcttctttatggatactcaggt-gcttcccagttttgtataaataat--aaattgtgc-tggattgctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG-
upper sequence: GLYMA08G28320.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G168176_T01 (Zea mays), 3'ss of exon 6
gtccgaaaattgttatttgttattgatttatattttgatctctaaatttttaatattcatttaacctgtatgcaaactact-tgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAGG
|| |||| || ||| ||| | | || | ||| ||| | | | || || ||| | | || | | |||||||| || | ||||| ||||| ||||| |||||||||||||| |||||||| || || || | |||||||| || ||| | || || ||||||
gtaattgcattgagcttctatatggatactttatgtgcttcctagttttgtctaaataat--aatttgtgcttggattgctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG-
upper sequence: GLYMA08G28320.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0005g04550.t01 (Vitis vinifera), 3'ss of exon 6
gtccgaaaattgttatttgttattgatttatattttgatctctaaatttttaatattcatttaacctg-tatgcaaactacttgtt--tagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAGG
|| |||| || | || ||||| | |||| || | |||| | | || | | | | |||| ||||| ||||||||||| |||| || ||||| || || || |||||||||||||| |||||||||||||| |||||||||||||| | || | ||||| ||| ||
gtttgaaa--tgattcacctttctgattatagaacttatctagttgttgtaaataat--tctagcttaatcttggaactggttgttgatagGTTGGTCCAAGATTTTGTTTGAATCCCATCAAGATATTTGGTGGCAGCTTTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAG- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgatctctaaatttttaatattcatttaacctgtatgcaaactacttgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAGG
atttaac putative branch site (score: 3)
cttgttt putative PPT
taaatttttaatattc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtccgaaaattgttatttgttattgatttatattttgatctctaaatttttaatattcatttaacctgtatgcaaactacttgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG