Sequence
atgc intronic sequence ATGC exonic sequence...taatacagagtgtttactaaatccaagtttgttttagccagattatatcatatatgaactctcttggttccaaggctgattgatatcattttgtttttagTTACTAGGAGAACCTGGAACTGGTGGATCATCCACACCATCGATGGTTGGTGCTGTTAAAAAATGGCAAAAGTCTGACCCTCAGAAATCCCTGGACACAT
Basic information
species | Glycine max |
transcript | GLYMA06G13260.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G13260.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g14830.1 (Oryza sativa), 3'ss of exon 7
taatacagagtgtttactaaatccaagtttgttttagccagattatatcatatatg--aactct----cttggttccaaggctgattgatatcattttgtttttagTTACTAGGAGAACCTGGAACTGGTGGATCATCCACACCATCGATGGTTGGTGCTGTTAAAAAATGGCAAAAGTCTGACCCTCAGAAATCCCTGGACACAT
|| || || | | ||| || || ||||| | | | | | | | | | || | | |||| | | ||| || |||| | ||||| |||||||||||||| ||||||||||| ||||| |||||||| |||| ||| | ||||| ||||| ||||||||||||||| ||| ||||
-----ttatttgattgcttgttgccttattgatt-agggagattgtgttctgttcgttgattgtaaggataagtactacttctgactatagggaattttttgttagCTTCTAGGGGAACCTGGAACTGGAGGATCATCCACTCCATCAATGGTTGGATCTGTGAAACAGTGGCAGAAGTCAGACCCTCAGAAATCCAAGGAGACAT
upper sequence: GLYMA06G13260.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G31910.1 (Arabidopsis thaliana), 3'ss of exon 9
-------------taatacagagtgtttact-----aaatccaagtttgttttagccagattatatcatatatgaactctcttggttccaaggctgattgatatcattttgtttt---tagTTACTAGGAGAACCTGGAACTGGTGGATCATCCACACCATCGATGGTTGGTGCTGTTAAAAAATGGCAAAAGTCTGACCCTCAGAAATCCCTGGACACAT
| | | | |||| ||| | | || ||| || | | | ||| ||| | || || | | | | || |||| || ||||| || ||||||||||||| ||||||||| ||||||||||| ||||| ||||| || || || ||||||| |||||| || |||| | | || | |
gtaagcaaacaatcagacctaaattcttacctagaaaaacctgttgtgaacttcaccaacttcttatttctttgacttctgtgaaatct--ggtgtactaacaagatgttgtcttatttagTTCCTTGGAGAACCTGGAAGTGGTGGATCCTCCACACCATCAATGGTAGGTGCAGTAAAGAAGTGGCAAATGTCTGATCCAGAGAAGGCACGAGAAAACT
upper sequence: GLYMA06G13260.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv02s0012g02530.t01 (Vitis vinifera), 3'ss of exon 7
--taatacagagtgtttactaaatccaagtttgttttagccagattatatcatatatgaactctctt--ggttccaaggctgattgatatcattttgtttttagTTACTAGGAGAACCTGGAACTGGTGGATCATCCACACCATCGATGGTTGGTGCTGTTAAAAAATGGCAAAAGTCTGACCCTCAGAAATCCCTGGACACAT
||| |||| ||| | | || ||| | | | || || || | ||| || | | || ||| | | | || ||||| ||||||||||| || |||| || ||||| |||||||| ||||| |||||||| || || |||||||||||||||||| |||| ||||| || ||||
tagaatggtgagtccttaacag-cctttcttcatttcatggaaaccatgagatccattatttctttttagttaccctttctggtcatggtggatgtg---gtagTTGCTAGGAGAACCAGGCGCTGGAGGTTCATCAACACCATCAATGGTAGGTGCTGTAAAGAAGTGGCAAAAGTCTGACCCTGAGAAGTCCCTAGAAACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcatatatgaactctcttggttccaaggctgattgatatcattttgtttttagTTACTAGGAGAACCTGGAACTGGTGGATCATCCACACCATCGATGGTTGGTGCTGTTAAAAAATGGCAAAAGTCTGACCCTCAGAAATCCCTGGACACAT
gattgat putative branch site (score: 4)
ttttgttttt putative PPT
attgatatcattttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taatacagagtgtttactaaatccaagtttgttttagccagattatatcatatatgaactctcttggttccaaggctgattgatatcattttgtttttagTTACTAGGAGAACCTGGAACTGGTGGATCATCCACACCATCGATGGTTGGTGCTGTTAAAAAATGGCAAAAGTCTGACCCTCAGAAATCCCTGGACACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - -gagtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggctga