Sequence
atgc intronic sequence ATGC exonic sequence...tcatttgatcttttgtcttaatattgatacagttaagaatccttgtttgattaaaattattaattcttgtgattctaactactgaaatatttttctgtagTGTTTGTTTGCCACCGAGACATTTAGCATTGGTTTGAACATGCCTGCAAAAACTGTTGTTTTCACAAATGTCCGGAAGTTTGACGGGGACAAGTTTAGGT
Basic information
species | Glycine max |
transcript | GLYMA08G47700.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G47700.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g18140.1 (Oryza sativa), 3'ss of exon 6
tcatttgatcttttgtcttaatattgatacagttaagaatccttgtttgattaaaat-tat-taattcttgtga-ttctaact------actgaaatatttttctgtagTGTTTGTTTGCCACCGAGACATTTAGCATTGGTTTGAACATGCCTGCAAAAACTGTTGTTTTCACAAATGTCCGGAAGTTTGACGGGGACAAGTTTAGGT
| | || | | | || ||| || |||| | | |||| || || | || |||| | || || || | ||||| || | ||||||| ||||||||||| || ||||| || ||||||||||||||||||||||| |||||||| || || ||||| || || |||||||| || || || |
--------tttattatatggagcttagcacacttgtatg-ccttatctatttaagatatacctttttgttgtaacttttagcttctgagattgaaaccttgtgttgtagTGCTTGTTTGCCACAGAAACATTCAGTATTGGTTTGAACATGCCTGCAAAGACTGTTGTGTTTACCAATGTGCGAAAATTTGACGGTGATCGATTCAGAT
upper sequence: GLYMA08G47700.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G040995_T02 (Zea mays), 3'ss of exon 6
---tcatttgatcttttgtcttaatattgatacagtt--aagaat-ccttgtttgattaaaattattaattcttgtgattctaactactgaaatatttttctgtagTGTTTGTTTGCCACCGAGACATTTAGCATTGGTTTGAACATGCCTGCAAAAACTGTTGTTTTCACAAATGTCCGGAAGTTTGACGGGGACAAGTTTAGGT
|| | |||| | | || | | | |||| | ||| || | | || ||| |||||| || | | | ||| || | | ||||||||||||||||| || ||||| || ||||||||||||||||||||||| |||||||| || || ||||| || || |||||||| ||| || || |
cttccactgagcattttagatatgttttctttctatctcaagactatgctgtgtgctgtacctttttatttcttg-----ctgaa-attaaaacatggtgttatagTGTTTGTTTGCCACAGAAACATTCAGTATTGGTTTGAACATGCCTGCAAAGACTGTTGTGTTTACCAATGTGCGAAAATTTGACGGAGACCGATTCAGAT
upper sequence: GLYMA08G47700.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G59760.1 (Arabidopsis thaliana), 3'ss of exon 6
---------tcatttgatcttttgtcttaatattgatacagttaagaatccttgtttgattaaaattattaa---ttcttgtgattctaactactg-------------aaatatttttctgtagTGTTTGTTTGCCACCGAGACATTTAGCATTGGTTTGAACATGCCTGCAAAAACTGTTGTTTTCACAAATGTCCGGAAGTTTGACGGGGACAAGTTTAGGT
| || || | || |||||| | | | | || || ||| || | | ||| | | || || || || || |||||| |||||||||||||| || ||||||||||| ||||| ||||||||||| ||||| || ||||| || || ||||| || |||||||| || |||||||| |||
gtaggtgaaggcgtagaactacaattttcatattgtcaattcttgctaccttttgttatgtaattttgtgatgttttcctttagtttgaagtattgccactgaagtttgaagtattttctcttagTGTTTGTTTGCAACAGAGACATTTAGTATTGGATTGAACATGCCGGCAAAGACGGTTGTATTTACCAATGTACGTAAGTTTGATGGAGACAAGTTCCGGT
upper sequence: GLYMA08G47700.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0009g01750.t01 (Vitis vinifera), 3'ss of exon 6
-tcatttgatcttttgtcttaatattgatacagttaagaatccttgtt---tgattaaaattattaattcttgtgattctaactactgaaatatttttctgtagTGTTTGTTTGCCACCGAGACATTTAGCATTGGTTTGAACATGCCTGCAAAAACTGTTGTTTTCACAAATGTCCGGAAGTTTGACGGGGACAAGTTTAGGT
||| || || | | || | || | ||||||||| | | |||||| || ||| | | | ||| || |||||| |||| || ||||||||||||||||| ||||| || |||||||||||||||||||| ||||| ||||| || || |||||||| || || ||||| ||||| || ||||| |
aaaattagaatattctagtcaccgtttgtccaatggtgaatccttgctaattaattaaattttttaggtgt----gctttaaatattgaaatgttttcctttagTGTTTGTTTGCCACAGAGACTTTCAGCATTGGTTTGAACATGCCAGCAAAGACTGTAGTGTTTACAAATGTTCGTAAATTTGATGGGGATAAATTTAGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgattaaaattattaattcttgtgattctaactactgaaatatttttctgtagTGTTTGTTTGCCACCGAGACATTTAGCATTGGTTTGAACATGCCTGCAAAAACTGTTGTTTTCACAAATGTCCGGAAGTTTGACGGGGACAAGTTTAGGT
ttctaac putative branch site (score: 1)
tatttttct putative PPT
ttaaaattattaattc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatttgatcttttgtcttaatattgatacagttaagaatccttgtttgattaaaattattaattcttgtgattctaactactgaaatatttttctgtagTGTTTGTTTGCCACCGAGACATTTAGCATTGGTTTGAACATGCCTGCAAAAACTGTTGTTTTCACAAATGTCCGGAAGTTTGACGGGGACAAGTTTAGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actactg