Sequence
atgc intronic sequence ATGC exonic sequence...tattttaagtattgggtaatgtgttcctggtacctgaactcaatattcagtttttgttgattatattatatgactgaacgtgtcatctgtttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACGTATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
Basic information
species | Glycine max |
transcript | GLYMA03G02610.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 6
-tattttaagtattgggtaatgtgttcctggtacctgaactcaatattcagtttttgttgattatattatatgactgaacgtgtcatctgtttattac-tagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACGTATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
| || | || | | || | || | || | || | |||||| ||| || | || || | | ||| | | || | | ||||||| | | ||||| ||||| |||||||||||||| |||||||| ||||| | ||| ||||| |||||||| || ||||| |||||||||| | |
gtgcttattgcatggttttatatattagttttagcataatcataaattcagccttttctgttctcatgcta--atttgttgtggctacgaattgcttcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACCTGTGTTTCTCGTTTTGAAAATCTACATCTCGTAG
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 6
-tattttaagtattgggtaatgtgttcctggtacctgaactcaatattcagtttttgttgattatattatatgactgaacgtgtcatctgtttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACGTATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
| | ||| | | | || ||| ||| || | | ||| | ||| | | | | || | || | ||||||| | | ||||| ||||| |||||||||||||| |||||||| ||||| | ||| ||||| |||||||| || ||||| ||||||||||| |||
gtgctgctagttgcagtcttccatattttagtttgagaa-tcatgataaaatcttttatcattcttatgttctcttcttatggtggtggattgcctcacagGCAATTCTATTAATTGCAGATGAAGATGGAAATTACTTGCAAGAAGCATGGGAGCATATATTGACATGTGTTTCTCGTTTTGAAAATCTACATCTTGTTG
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 6
tattttaagtattgggtaatgtgttcctggta--cctgaactcaatattcagtttttgttgattatattatatgactgaacg--tgtcatctgtttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACGTATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
|| || | | | | || | |||| | | | | | | | | | || |||| | || | | |||||| | | ||||||||||| | || || || || ||||| || ||||||| |||||||| | ||| ||||||||||||| |||||||||||||| ||||| | |
---ttgggttagctgacattcaaacctgattaatcttgaaaataccaat-ggatgataagaaatgtcttctatgtataaattgtttttttctgttcactgatagGCAATAGTAAAACTGGCGGAGGAAGAAGGAAACTATCTACAAGATGCTTGGGAGCATATACTGACTTGTGTTTCACGGTTTGAGCATCTTCATCTCTTGG
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 6
tattttaagtattgggtaatgtgttcctggtacctgaac---tcaatattcagtttttg--ttgattatattat-atgactgaacgtgtcatctgtttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACGTATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
|| | || | || ||| || | | | | | ||| |||| ||| | | || ||| | | | | | || ||| ||||||||||| |||||| ||||| ||||| || |||||||| || || ||||||| ||| ||||| ||||| || |||||||||||| | ||||| | |
-----tatggtgtgagcgataaattcttgaattttaagcaaatgaccatttgcttttaaatctgaagttgtgattgtgatttggcattctactttgtttgtac-agGCAATAGTTACTATTGCAGATGAAGATGGGAACTACTTACAGGAGGCCTGGGAACATATTTTGACATGTGTGTCTCGGTTTGAGCATTTGCATCTCTTGG
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ24773 (Selaginella moellendorffii), 3'ss of exon 6
tattttaagtattgggtaatgtgttcctggtacctgaactcaatattcagtttttgttgattatattatatgactgaacgtgtcatctgtttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACGTATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
| ||||| || | | || | ||| | ||| || | | | | |||| | | ||||||||||| |||||||| || |||| ||||| ||||||| || |||| |||||||| || ||||||||||| |||||| |||
----------------------------------------------gtattttttctttctcctcttttcatactcataatgtaat-tccatgctgc-agGCGGTGATATCCATTGCTGATGAAGATGGAAACTATCTACAGGAAGCCTGGGAACACGTCCTGACGTGTGTTTCTCGCTTTGAGCATCTCCATCTTATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcagtttttgttgattatattatatgactgaacgtgtcatctgtttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACGTATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
tgttgat putative branch site (score: 4)
tctgttt putative PPT
tttttgttgattatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattttaagtattgggtaatgtgttcctggtacctgaactcaatattcagtttttgttgattatattatatgactgaacgtgtcatctgtttattactagGCAATAGTTGTTATTGCTGATGAGGATGGAAATTACTTACAAGAAGCTTGGGAACGTATCTTGACTTGTGTTTCCCGGTTTGAGCATCTACATCTTCTTG
- - - - - - - - - -tgtgttc
- - - - - - - - - - - - - - - -acctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catctgt