Sequence
atgc intronic sequence ATGC exonic sequence...tttttattatctgagtgaattgtggttaattatcgtgttgtaagtaattttgtcttcatatatttatatgtttaatatcctgggaaatgtgttgttgcagATTAACATTATTGACACGCCTGGTCACGTTGATTTTACCATCGAGGTTGAGAGGGCTTTGCGTGTCCTTGATGGTGCCATTCTTGTTCTTTGTAGTGTTG
Basic information
species | Glycine max |
transcript | GLYMA11G16460.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G45030.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------------------------tttttattatctgagtgaattgtggttaattatcgtgttgta-agtaattttgtcttcatatatttatatgtttaatatcctgggaaatgtgttgttgcagATTAACATTATTGACACGCCTGGTCACGTTGATTTTACCATCGAGGTTGAGAGGGCTTTGCGTGTCCTTGATGGTGCCATTCTTGTTCTTTGTAGTGTTG
|| | || | ||||| || || | |||| |||||| | | | ||| | | | ||| | || | |||||| ||| |||| || ||||| || |||||||||||||| || ||||| || || ||||||||||| ||||| || || ||||| ||||| || || || ||||| |
gtgaggagatagaaaaaaagatcttccttgtggattctgtgattctaatttcttctcagattcgtcaaaattggccttggttgtttaattgtgtagtaatcctat-----tgcattgagctttgaaatttgttgttatgattgttgt--cagGTTAATATAATTGATACTCCTGGTCACGTTGACTTCACCATTGAAGTGGAGAGGGCTTTACGTGTACTAGACGGTGCGATTCTAGTCCTATGCAGTGTGG
upper sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 3'ss of exon 1
tttttattatctgagtgaattgtggtta-attatcgtg-ttgtaagtaattttgtcttcatatatttatatgtttaatatcctgggaaatgtgttgttgcagATTAACATTATTGACACGCCTGGTCACGTTGATTTTACCATCGAGGTTGAGAGGGCTTTGCGTGTCCTTGATGGTGCCATTCTTGTTCTTTGTAGTGTTG
|| | | | | | ||| || ||| | || ||| | | | | | | | | ||| | | || ||| || |||||| ||||||| |||||||| |||||||| || || || ||||| || ||||||||||||||||||||||||||||||||||||||||| |||||||||||||
-ttgcaccctttttgctagatgtttatatattcttttggttgcccattcaaaagaaaaaaaaaaaaaagaagaaaaatcatccagaaattgtttt-ttgcagGTTAACATAATTGACACTCCTGGTCATGTCGACTTCACCATTGAAGTTGAGAGGGCTTTGCGTGTCCTTGATGGTGCCATTCTTGTCCTTTGTAGTGTTG
upper sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S20_94V6.1 (Physcomitrella patens), 3'ss of exon 1
tttttattatctgagtgaattgtggttaattatcgtgttgtaagtaattttgt--cttcatatatttatatgtttaatatcctgggaaatgtgttgttgcagATTAACATTATTGACACGCCTGGTCACGTTGATTTTACCATCGAGGTTGAGAGGGCTTTGCGTGTCCTTGATGGTGCCATTCTTGTTCTTTGTAGTGTTG
| | ||| || |||| | | | || | | ||| | | | | | | || | | | | || | | || || ||||| || |||||||||||||| |||||||||||||||||||| |||||||| |||||| | || || |||||||| || | ||||| |||||||||||||
ctcgcacgatccatgttaatt-tctcacgtgcccatgccttttttcattgaatagcatagtccactgat-cgactggtgttctctgtatgctggtggaacagATCAATATTATTGACACGCCAGGTCACGTTGATTTTACCATTGAGGTTGAAAGGGCTCTTCGCGTGCTTGATGGAGCAGTACTTGTGCTTTGTAGTGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattttgtcttcatatatttatatgtttaatatcctgggaaatgtgttgttgcagATTAACATTATTGACACGCCTGGTCACGTTGATTTTACCATCGAGGTTGAGAGGGCTTTGCGTGTCCTTGATGGTGCCATTCTTGTTCTTTGTAGTGTTG
gtttaat putative branch site (score: 4)
tgtcttcatatattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttattatctgagtgaattgtggttaattatcgtgttgtaagtaattttgtcttcatatatttatatgtttaatatcctgggaaatgtgttgttgcagATTAACATTATTGACACGCCTGGTCACGTTGATTTTACCATCGAGGTTGAGAGGGCTTTGCGTGTCCTTGATGGTGCCATTCTTGTTCTTTGTAGTGTTG
- - - - - -tgagtga
- - - - - - - - - - tgtggtt
- - - - - - - - - - - - - - - - - -tgttgta