Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaatttggttgaataaaaaaaattgcatatgaagctttcttttccaaaatttctacaaaacatggtaactgtttactcctataaattttagAGCTCGGTATTCTAGTTGGGAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG
Basic information
species | Glycine max |
transcript | GLYMA18G02440.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02440.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagaaatttggttgaataaaaaaaattgcatatgaagctttcttttccaaaatttctacaaaacatggtaactgtttactcctataaattttagAGCTCGGTATTCTAGTTGGGAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG
|||| || | | | |||| || | | | || || || ||||| | | || || ||| || | ||| || || ||||| || || |||||||| || ||||| || ||||| ||||| |||||||||||||||||||| |||||||||||||
gtaaacaacat--taaagccaaaagcatcgatttgataagcatcagtt-----ggttaaccaaaatgttttg-ctcctttctcttaatga----agAACTTGGCATTCTCGTCGGAAAAGGAGGACTTCATGGGAACGTTTTCAGGATAAAGCCACCAATGTGTTTCACTAAAGATGATGCAG
upper sequence: GLYMA18G02440.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 7
gtaagaaatttggttgaataaaaaaaattgcatatgaagctttcttttccaaaatttctacaaaacatggtaactgtttactc-ctataaattttagAGCTCGGTATTCTAGTTGGGAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG
||| | | || || ||| | || || | ||| || || || | |||| | | | || | ||||| |||||||||| | || || ||||| || ||||||||||| || || || |||||||| ||||||||||||||||||||||| |
------------gtttgcaactccaccatgattaagaaaaaattaattgtaa----tttaccaa-cacactacttatttattaatttttaactgtagAGATCGGTATTCTTATCGGAAAGGGAGGACTACATGGAAATGTCTTCAGAATAAAGCCACCTATGTGTTTCACCAAAGATGATGCTG
upper sequence: GLYMA18G02440.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S32_198V6.1 (Physcomitrella patens), 3'ss of exon 7
--------------------------------------------gtaagaaatttggttgaa----taaaaaaaattgcatatgaagctttcttttccaaaatttctacaaaacatggtaactgtttactcctataaattttagAGCTCGGTATTCTAGTTGGGAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG
|| || ||| || | | | | ||| || ||| | || | |||| | || | | | | || ||| ||||| || |||||||||| || ||||| ||||||||||| ||||| |||||||| || ||||||||| | | || |||||||
gtgatgctgcacttcacctagggctggcctagttctgtgtatcactagcaagttttgtactgctccttgacatggtggcaagtggggctgtgc-------aactcctaccattcacttacgcataggctttttggatgttgcagACCTCGGAGTTTTAGTTGGGAAGGGCGGGCTTCATGGAAATGTCTTTAGAATCAAGCCTCCTATGTGTTTCTCAATGGAAGATGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttttccaaaatttctacaaaacatggtaactgtttactcctataaattttagAGCTCGGTATTCTAGTTGGGAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG
tggtaac putative branch site (score: 2)
ctcctat putative PPT
aaaatttctacaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaatttggttgaataaaaaaaattgcatatgaagctttcttttccaaaatttctacaaaacatggtaactgtttactcctataaattttagAGCTCGGTATTCTAGTTGGGAAAGGAGGGCTGCATGGAAATGTTTTTAGGATCAAGCCACCAATGTGTTTCACCAAAGATGATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG