Sequence
atgc intronic sequence ATGC exonic sequence...tttaaagaaaacttgaagcacaaatatatgattttcattttttttgtgctatgctatcactgaaaccataatgattttaaattttgtaatgaatgaccagGGTACACCAATGATGCTAATGGGGGATGAATATGGCCATACTCGCAATGGAAATAACAATAGTTATGGGCATGATACTGCCATTAATAATTTTTT
Basic information
species | Glycine max |
transcript | GLYMA06G10540.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os09g29404.1 (Oryza sativa), 3'ss of exon 18
tttaaagaaaacttgaagcacaaatatatgattttcattttttttgtgctatgctatcactgaaaccataatgattttaaattttgtaatgaatgaccagGGTACACCAATGATGCTAATGGGGGATGAATATGGCCATACTCGCAATGGAAATAACAATAGTTATGGGCATGATACTGCCATTAATAATTTTTT-----
| |||| | | | || || ||| || | | || ||| ||| | |||||| | | ||| || | ||||| || ||||||||| | ||||| ||||||||||| ||||| || |||| || |||||||| ||||| ||||||||| ||||||||||||
------gtaaacattgtgaagtaacctacagtttattttatgtgtgcatcatgtataaacttatcacataatcaccat---tttcatat------atcagGGCACCCCAATGATGTTGATGGGCGATGAATATGGTCATACACGTTATGGGAACAACAATAGCTATGGACATGATACTTGCATTAATAATTTCCAATGGG
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G150796_T01 (Zea mays), 3'ss of exon 19
tttaaagaaaacttgaagcacaaatatatgattttcattttttttgtgctatgctatcactgaaaccataatgattttaaattttgtaatgaatgaccagGGTACACCAATGATGCTAATGGGGGATGAATATGGCCATACTCGCAATGGAAATAACAATAGTTATGGGCATGATACTGCCATTAATAATTTTTT-----
||||| || | | || | || | | | ||||| |||| || | | || | || | | ||||||| ||||||||||| ||||| ||||||||||| || || || ||||||| |||||||| ||||| ||||||||| ||| |||||||||
---------------------gtttatattatcgaccatagttaccttttacg-tgtaactgag--tataac--ttatgagttacattatatacaat-agGGTACTCCAATGATGCTGATGGGAGATGAATATGGTCACACACGTTATGGAAACAACAATAGCTATGGACATGATACTCACATAAATAATTTTCAGTGGG
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G076508_T01 (Zea mays), 3'ss of exon 6
tttaaagaaaacttgaagcacaaatatatgattttcattttttttgtgctatgctatcactgaaaccataatgattttaaattttgtaatgaatgaccagGGTACACCAATGATGCTAATGGGGGATGAATATGGCCATACTCGCAATGGAAATAACAATAGTTATGGGCATGATACTGCCATTAATAATTTTTT-----
| ||| || | | || | || | | | ||||| | |||| |||| | || | | |||| || ||||||||||| ||||| ||||||||||| || || || ||||||| |||||||| ||||| ||||||||| ||| |||||||||
---------------------gtttgtattatcgaccatagttaccttttacg-tgtaactgagtataacttgat---gaattacatcatatacaat-agGGCACTCCAATGATGCTGATGGGAGATGAATATGGTCACACGCGTTATGGAAACAACAATAGCTATGGACATGATACTCACATAAATAATTTTCAGTGGG
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 16
lower sequence: AT4G09020.1 (Arabidopsis thaliana), 3'ss of exon 19
tttaaagaaaacttgaagcacaaatatat-gattttcattttttttgtgctatgctatcactgaaaccataatgattttaaatt--ttgtaatgaatgaccagGGTACACCAATGATGCTAATGGGGGATGAATATGGCCATACTCGCAATGGAAATAACAATAGTTATGGGCATGATACTGCCATTAATAATTTTTT-----
| | || | | | || | ||| || || || | | | | || | ||| | || || ||||| ||||| |||||||||||||||||||| || |||||||| ||||| || |||| || |||||||| || || |||||||| || |||| |||||
-----------------gtgcgtatttgccaacatacactcgtttaa----atactgtctaaaattctaaatgcatatgaaaccgatggtgatcaatgatcagGGAACACCAATGATGCTAATGGGAGACGAATATGGACATACACGGTATGGTAACAACAATAGCTACGGACATGATACCTCCCTTAACAATTTCCAGTGGA
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv18s0001g06520.t01 (Vitis vinifera), 3'ss of exon 19
-tttaaagaaaac-ttgaagcacaaatatatgattttcattttttttgtgctatgctatcactgaaaccataatgattttaaattttgtaatgaatgaccagGGTACACCAATGATGCTAATGGGGGATGAATATGGCCATACTCGCAATGGAAATAACAATAGTTATGGGCATGATACTGCCATTAATAATTTTTT-----
| | | |||| | | |||| | | | | | |||| || || | ||| | | ||| ||| ||| | || | ||||| |||||||||||||||||||| ||||||||||| || |||||| |||||||||| || |||||||| || |||||||| |||||| ||||| |
atacatatcaaacgctctaacacacttcaaataagaataatcattttatggtaatggactactttgagtttgatgcactta--tttgattgctcattatcagGGAACACCAATGATGCTAATGGGTGATGAATATGGGCACACTCGCTATGGAAATAATAACAGTTATGGACACGATACTGCTATTAATCATTTTCTGTGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgctatgctatcactgaaaccataatgattttaaattttgtaatgaatgaccagGGTACACCAATGATGCTAATGGGGGATGAATATGGCCATACTCGCAATGGAAATAACAATAGTTATGGGCATGATACTGCCATTAATAATTTTTT
ataatgattttaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttaaagaaaacttgaagcacaaatatatgattttcattttttttgtgctatgctatcactgaaaccataatgattttaaattttgtaatgaatgaccagGGTACACCAATGATGCTAATGGGGGATGAATATGGCCATACTCGCAATGGAAATAACAATAGTTATGGGCATGATACTGCCATTAATAATTTTTT
- - aagaaaa
- - - - - - - - -gcacaaa
- - - - - - - - - - - - - - - - - - - - - - - - ctatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactgaa