Sequence
atgc intronic sequence ATGC exonic sequence...ttattggttactatgtagggtcaaacttcagatattctttgaggctaatatgtcttgcaaatctgaagctactattcttttatatgatgcttttatgcagTAACATTTAGTCGGATAGATCCTGGAGGCAAACTAGTTATGGGTTTCAGAAAAGCATCAAATTCTACAGATACACAG
Basic information
species | Glycine max |
transcript | GLYMA11G31270.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G31270.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 6
ttattggttactatgtagggtcaaacttcagatattctttgaggctaatatgtcttgcaaatctgaagctactattcttttata-tgatgctt-----ttatgcagTAACATTTAGTCGGATAGATCCTGGAGGCAAACTAGTTATGGGTTTCAGAAAAGCATCAAATTCTACAGATACACAG
| || ||| | || || | | | || | | |||| | | | |||| | | | || || |||| ||| | | |||| || |||||||||||||| |||||||| ||||| |||||||| ||| | || || |||| || | |
------ggtaatatatttaaacatgctaagtagaattgttccatattaaatgtgatctcactgggaaggttttcatacttaatggtgattcttgttttcttttcagTGACTTTTAGTCGGATAGAACCTGGAGGGAAACTTGTTATGGGCTTCCGGAAGGCCACAAACACTGTCAGTTTGCCA
upper sequence: GLYMA11G31270.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 6
-ttattggttactatgtagggtcaaacttcagatattctttgaggctaatatgtcttgcaaatctgaagctactattcttttatatgatgcttttatgcagTAACATTTAGTCGGATAGATCCTGGAGGCAAACTAGTTATGGGTTTCAGAAAAGCATCAAATTCTACAGATACACAG
|| || || | | | | ||| || | | || || | | || | |||| | || | |||| |||||| || |||||||| |||||||||||||| ||||| |||||||| || | || || ||||| || | |
tccatgctatagtaaattacgctgagtagtat-tatgtcatgtgtcccatgctctctggatgttgtttactggaacctttttttgtggttattttctgcagTGACCTTTAGTCGTATAGATCCTGGAGGGAAACTTGTTATGGGCTTTCGGAAGGCCACAAATACTGTCAGTCTGCCA
upper sequence: GLYMA11G31270.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G172621_T01 (Zea mays), 3'ss of exon 6
------ttattggttactatgtagggtcaaacttcagatattctttgaggctaatatgtcttgcaaatctgaagctactattcttttatatgatgcttttatgcagTAACATTTAGTCGGATAGATCCTGGAGGCAAACTAGTTATGGGTTTCAGAAAAGCATCAAATTCTACAGATACACAG
| | ||| || | || | ||| ||||| || |||| || | ||| || || |||| | || | |||| |||||| || |||||||| |||||||||||||| ||||| |||||||| || | || || ||||| || | |
atgctatagtaaattatgctgcatagtactatgtcatgtattccatgctctctgaatgt--tgtttactggaatcttct----ttttgtgtggttattttctgcagTGACCTTTAGTCGTATAGATCCTGGAGGGAAACTTGTTATGGGCTTTCGGAAGGCCACAAATACTGTCAGTCTGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatatgtcttgcaaatctgaagctactattcttttatatgatgcttttatgcagTAACATTTAGTCGGATAGATCCTGGAGGCAAACTAGTTATGGGTTTCAGAAAAGCATCAAATTCTACAGATACACAG
ggctaat putative branch site (score: 3)
tgctttt putative PPT
tactattcttttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttattggttactatgtagggtcaaacttcagatattctttgaggctaatatgtcttgcaaatctgaagctactattcttttatatgatgcttttatgcagTAACATTTAGTCGGATAGATCCTGGAGGCAAACTAGTTATGGGTTTCAGAAAAGCATCAAATTCTACAGATACACAG
- - - - - -tatgtag
- - - - - - - - - - tcaaact
- - - - - - - - - - - - - - - - - - - ttgaggc
- - - - - - - - - - - - - - - - - - - - - - - - - - -cttgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgatgc