Sequence
atgc intronic sequence ATGC exonic sequence...aaaccttgtttctttatgtttttcccatctctggattgcttcaaagtattgttgagtatgattactttttagtgaaaattttcctaaaaattaccttcagGGAAGACTGTGATTACCAGTGACCACGCACTCAAACTGGAGTCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA
Basic information
species | Glycine max |
transcript | GLYMA17G03560.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 4
aaaccttgtttctttatgtttttcccatctctggattgcttcaaagtattgttgagtatgattac--tttttagtgaaaattttcctaaaaattaccttcagGGAAGACTGTGATTACCAGTGACCACGCACTCAAACTGGAGTCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA
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aagattagcacaattgggtttg--cagacccaaatgtgttgcctaccatttcttgttatacctattgttcttacagaagcctgctgggcaacttttgtgcagGGAAAACTGTTTTTACCAGTGATCATGCACTAAAACTTGAGTCTGTCCCGGACTGGATAGCAATCGTTGGAAGTGGATACATTGGGCTTGAATTCAGTGA
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 3
aaaccttgtttctttatgtttt-tcccatctctggattgcttcaa--agtattgttgagt-atgattactttttagtgaaaattttcctaaaaattaccttcagGGAAGACTGTGATTACCAGTGACCACGCACTCAAACTGGAGTCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA
|||| | | |||||| | | | || | ||| | ||| | | || | | | | ||| || | | || | |||| || ||||| |||| ||||| || ||||| ||||| ||||| || ||||| ||||| || ||||| |||||||| || ||||| ||||||||||||||
---ccttatca-tatatgttgcatactacagcttaaatgcatttgttgccattcctatttcattctagcatccctttaaaagcttgcaccatggttttatgcagGTAAAACTGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTCCCTGAATGGATTGCTATTGTTGGAAGTGGTTACATTGGACTTGAATTCAGTGA
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 4
aaaccttgtttctttatgtttttcccatctctggattgcttcaaagtattgttgagtatgattactttttagtgaaaattttcctaaaaattaccttcagGGAAGACTGTGATTACCAGTGACCACGCACTCAAACTGGAGTCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA
| | | || || | | ||| | || || | |||||| | || ||| ||| | | || |||| ||||||||||| ||||||||||| || | ||| | |||||||| ||||| ||||| ||||||||||||||||| |||||||||||||| ||||||||
---------gtacgtttcttgttttggacgtagagttgttaagggagcatgcagact-tgattattcctt---gaatgtttacattttggc--gctgcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 4
aaaccttgtttctttatgtttttcccatctctgga---ttgcttcaaagtattgttgagtatgattactttt----tagtgaa------aattttcctaaaaattac--cttcagGGAAGACTGTGATTACCAGTGACCACGCACTCAAACTGGAGTCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA
||||| | ||| | | || |||| ||||| | | | | ||| ||||| ||| | ||| ||||| | | || || |||| |||||||| || || ||||| || ||| | ||| ||||||| |||||||| ||||| || || ||||||||||| ||||| |||||||| ||||||||
-gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctcaaaa-accaaagcttctcatttcttttagtatagcaagtaccctaatattcctcatattttgtgctgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtattgttgagtatgattactttttagtgaaaattttcctaaaaattaccttcagGGAAGACTGTGATTACCAGTGACCACGCACTCAAACTGGAGTCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA
tcctaaa putative branch site (score: 2)
ttaccttc putative PPT
tttttagtgaaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaccttgtttctttatgtttttcccatctctggattgcttcaaagtattgttgagtatgattactttttagtgaaaattttcctaaaaattaccttcagGGAAGACTGTGATTACCAGTGACCACGCACTCAAACTGGAGTCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - -cccatct
- - - - - - - - - - - - - - - - - - tgcttca
- - - - - - - - - - - - - - - - - - - - - - - - -tgttgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctaaaaa