Sequence
atgc intronic sequence ATGC exonic sequence...gcaactttactgctggaaatgttcattggtgtgaatttgatatgcaagtatattttgaactttaaagtacctgattgtatgttcttgtgttttgaaacagGAGATGCTTTGCATAGTCTGAGGACAAACTTACAGGATCCCAACAATGTTTTGCAAAGTTGGGATCCTACACTTGTTAATCCATGTACATGGTTTCATGT
Basic information
species | Glycine max |
transcript | GLYMA20G31320.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G31320.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G115420_T01 (Zea mays), 3'ss of exon 1
gcaactttactgctggaaatgttcattggtgtgaatt-tgatatgcaagtatattttgaactttaaagtacctgattgt-atgttcttgtgttttgaa-acagGAGATGCTTTGCATAGTCTGAGGACAAACTTACAGGATCCCAACAATGTTTTGCAAAGTTGGGATCCTACACTTGTTAATCCATGTACATGGTTTCATGT
| ||| | | | ||| | | | || | || || || || || | || ||| || | | || | || ||||| ||||| ||||| || | || ||| | | ||| | ||| | |||||||| ||||| ||||||||||| || ||||||||||||||||||||||| |||||
--tattttgc-atacaagctcatcaccgataaaagttcttatctgtttgttcatcttaactgggaatatacttgctgctgataatgttaccttttgtccacagGTGATGCCCTGTACAGCCTGCGTCAGAGCTTGAAAGATGCTAACAATGTCTTGCAGAGTTGGGATCCCACTCTTGTTAATCCATGTACATGGTTCCATGT
upper sequence: GLYMA20G31320.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G150024_T03 (Zea mays), 3'ss of exon 1
gcaactttactgctggaaatgttcattggtgtgaatt-tgatatgcaagtatattttgaactttaaagtacctgattgt-atgttcttgtgttttgaa-acagGAGATGCTTTGCATAGTCTGAGGACAAACTTACAGGATCCCAACAATGTTTTGCAAAGTTGGGATCCTACACTTGTTAATCCATGTACATGGTTTCATGT
| ||| | | | ||| || | || | ||||| || || || | || ||| || | | || | | ||||| ||||| |||||| | | || ||| || | ||| ||| | |||||||| ||||| ||||||||| | || |||||||||||||||||||||||||| ||
--gattttgc-atacaagctcatcacctgtagaatttcttatatgtttgttcatcttaactggaaatatacttgctgctgatcatgctaccttttgtccacagGCGATGCTCTATACAGCCTGCGGCAGAGCTTGATAGATACGAACAATGTCTTGCAGAGTTGGGATTCCACTCTTGTTAATCCATGTACATGGTTTCACGT
upper sequence: GLYMA20G31320.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G870959_T01 (Zea mays), 3'ss of exon 1
gcaactttactgctggaaatgttcattggtgtgaa---tttgatatgcaagtatattttgaactttaaagtacctgattgtatgttcttgtgttttga-aacagGAGATGCTTTGCATAGTCTGAGGACAAACTTACAGGATCCCAACAATGTTTTGCAAAGTTGGGATCCTACACTTGTTAATCCATGTACATGGTTTCATGT
| | ||||| || | | || || | ||| || || | | || || | | | | || || | ||| | | | | |||| |||||| | | || || | || | | | ||| |||||| || |||| ||||||||||| || || |||||||||||||||||||| |||||
--atcgttactaacggca-tattaatgaaggggaaagcttatgcatcctattaaatgtcttgtgtgtagattattgcttat-tgtgatgatacctcaatggcagGTGATGCTCTATACAGCCTACGACAAAGCCTGAAAGATAACAACAACGTGCTGCAGAGTTGGGATCCAACTCTGGTTAATCCATGTACATGGTTCCATGT
upper sequence: GLYMA20G31320.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G384439_T02 (Zea mays), 3'ss of exon 1
---gcaactttactgctggaaatgttcattggtgtgaat-ttgatatgcaagt-atattttgaacttta-aagtacctgattgtatgttcttgtgttttgaaacagGAGATGCTTTGCATAGTCTGAGGACAAACTTACAGGATCCCAACAATGTTTTGCAAAGTTGGGATCCTACACTTGTTAATCCATGTACATGGTTTCATGT
| ||| | | | || |||| | || | ||| ||| | |||| ||| | ||||| | ||| | |||| | || ||||| ||||| |||||||| ||||||| |||||| | ||||| || |||||| | |||||||||||||| || || || || || || || |||||||||||
tatctagggatacagtttttttt-ttgattgacgcactcctttgtttgcgagtgacatttctgactaaagaagtatgt-attttccattctgctatt----gacagGTGATGCCTTGCATAGCTTGAGGACTAACTTAAATGATCCTAATAATGTTCTACAAAGTTGGGATCCCACTCTGGTCAACCCCTGCACTTGGTTTCATGT
upper sequence: GLYMA20G31320.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0164g00070.t01 (Vitis vinifera), 3'ss of exon 1
--gcaactttactgctggaaatgttcattggtgtgaatttgatatgcaagtatattttgaactttaa--agtacctgattgtatgttcttgtgttttgaaacagGAGATGCTTTGCATAGTCTGAGGACAAACTTACAGGATCCCAACAATGTTTTGCAAAGTTGGGATCCTACACTTGTTAATCCATGTACATGGTTTCATGT
|| | | | ||| ||| | | | | || | || || | | |||| | ||| || |||||||| | || ||| | || ||||||| ||||||||||||| |||||||| ||||| |||| || |||||||| | || ||||||||||| || ||||| || || || ||||||||||||||
gtcaaatctcagttctgatgcggttgaatcttct--atataat-tgtatatttattgaaatttttgggtagcgactgattgt-tcttgttgcatatttaaacagGTGATGCTTTGCATACACTGAGGACCAACTTGGAGGACCCAAACAATGTCCTACAGAGTTGGGATCCGACCCTTGTCAACCCCTGCACATGGTTTCATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagtatattttgaactttaaagtacctgattgtatgttcttgtgttttgaaacagGAGATGCTTTGCATAGTCTGAGGACAAACTTACAGGATCCCAACAATGTTTTGCAAAGTTGGGATCCTACACTTGTTAATCCATGTACATGGTTTCATGT
acctgat putative branch site (score: 4)
tattttgaactttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaactttactgctggaaatgttcattggtgtgaatttgatatgcaagtatattttgaactttaaagtacctgattgtatgttcttgtgttttgaaacagGAGATGCTTTGCATAGTCTGAGGACAAACTTACAGGATCCCAACAATGTTTTGCAAAGTTGGGATCCTACACTTGTTAATCCATGTACATGGTTTCATGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - -ctgctgg
- - - - - - - - - - - - - tggtgtg
- - - - - - - - - - - - - - - - - - - - - tgcaagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgatt