Sequence
atgc intronic sequence ATGC exonic sequence...agatgttatctttgtcaaatttagatgctctatttttcttttcttgtttaaatcaaacccacatacattgactttgtttgaccttcttatcattttgcagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTTCCAAAATATCCCCCAACCAAGGAAATGGATGCTAAACGACGGGATGATGAAACAAGGA
Basic information
species | Glycine max |
transcript | GLYMA20G37360.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g22700.1 (Oryza sativa), 3'ss of exon 3
agatgttatctttgtcaaatttagatgctctatttttcttttcttgtttaaatcaaacccacatacattgactttgtttgaccttcttatcattt-tgcagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTTCCAAAATATCCCCCAACCAAGGAAATGGATGCTAAACGACGGGATGATGAAACAAGGA
||| | | | | || | | | | | || || | | | || | || || ||| ||| ||| || | ||||||||||||| || ||||||||||| ||||| || || ||||| ||| |||||| |||| ||| ||||||||||| |||||| | ||||| ||| | ||
-gataatgtgtgaagtagatctgtttattgtcatctttgttgaaattatgtagcattgttttacacttttactaaagaattgcttattacaatctatgcagTTCTTTACAACTGAACCTTATGCATGTGAACCATCAAGTCTCCCAGCATATCCTCCAAGCAAAGAAATGGATGCAAAACGAAGAGATGAAGAAGCCAGAC
upper sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G052206_T02 (Zea mays), 3'ss of exon 4
--------agatgtt-atctttgtcaaa--tttagatgctctatttttcttttcttgtttaaatcaaacccacatacattgactttgtttgaccttcttatcattttgcagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTTCCAAAATATCCCCCAACCAAGGAAATGGATGCTAAACGACGGGATGATGAAACAAGGA
|||| |||||||||| | ||| | | | || | |||| ||| | | || ||| | ||||| ||| ||| | |||||||||||| || ||||||| ||| ||||| || || ||||||||||||||||| |||| ||| ||||| |||| ||| || | || || ||| | ||
tagcacccagattcccatctttgtcacacatttggtttttgtagcatattttttttggt-------attgtgtattcatgccttctgttta--ctttctatggat--gcagTTCTTTACAACTGAACCTTTTGCATGTGAACCATCGAGTCTTCCAAAATATCCTCCAAGCAAAGAAATAGATGTGAAAAGAAGAGACGAAGAAGCCAGAC
upper sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 4
agatgttatctttgtcaaatttagatgctctatttttcttttcttgtttaaatcaaacccacatacattgactttgtttgaccttcttatcattt-tgcagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTTCCAAAATATCCCCCAACCAAGGAAATGGATGCTAAACGACGGGATGATGAAACAAGGA
| |||| | | | | | | | || || | | | || | ||| ||| || | ||| || | || |||| ||| | || || |||||||||||| | ||||| ||||| |||| |||||| |||| |||||| |||||||| || | | || || || | || |
tggccttatgcatttatgctgcttgtaatgaactattattccgtcataactaccagttactcat-catgtgctcttttttttattaaaaaaatggacttagTTTTTTTCAACCGAGCCTTATGCTTGTAACCCTTCAAGTCTGCCAACATATCCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAA
upper sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 4
agatgttatctttgtcaaatttagatgctc------tatttttcttttcttgtttaaatcaaacccacatacattga--ctttgtttgaccttcttatcattttgcagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTTCCAAAATATCCCCCAACCAAGGAAATGGATGCTAAACGACGGGATGATGAAACAAGGA
|||| | || ||| || || ||||| |||| | |||| | | |||| | | || | ||| ||| ||| ||||||||||||| || ||||||| ||| || || || || ||||||||||||||||| |||| ||| || || |||| |||||| | || || ||| | ||
-----ttatagtacccagattcccatccttgtcacacattttgtttttgtagtttttttttggttt-tgtgcattaatgccttatgtgaactttctatg--catgcagTTCTTTACAACCGAACCTTTTGCATGCGAACCGTCAAGTCTTCCAAAATATCCTCCAAGCAAAGAGATAGATGTGAAACGAAGAGACGAAGAAGCCAGAC
upper sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 7
-agatgttatct--ttgtcaa---atttagatgctctatttttcttttcttgtttaaatcaaacccacatacattgactttgtttgaccttcttatcattttgcagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTTCCAAAATATCCCCCAACCAAGGAAATGGATGCTAAACGACGGGATGATGAAACAAGGA
| || || ||| ||||| || || | | | ||| || || ||| | | | ||| | ||||| | ||||||||| || || |||||||||||||||| || ||||| ||||| ||||||| |||| |||||| |||||||| || | || ||||||||| | | |
ggagttctactaggctggcaattcatttaaatttctagttataagatacccttttgaaattttagcatatatactcattttctccttgtttcttgt------gcagTTCTTCACAACGAAACCTTATGCTTGTGAACCATCTAGCCTTCCGCAATATCCTCCAAGCAAGGAGATGGATGCCAAGAGGCGAGATGATGAAGCTCGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttaaatcaaacccacatacattgactttgtttgaccttcttatcattttgcagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTTCCAAAATATCCCCCAACCAAGGAAATGGATGCTAAACGACGGGATGATGAAACAAGGA
ccttcttatcatttt CT-rich tract
ttatcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agatgttatctttgtcaaatttagatgctctatttttcttttcttgtttaaatcaaacccacatacattgactttgtttgaccttcttatcattttgcagTTCTTTACCACAGAACCTTATGCTTGTGATCCTTCTAGTCTTCCAAAATATCCCCCAACCAAGGAAATGGATGCTAAACGACGGGATGATGAAACAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - -gatgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - tcaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gactttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttctt