Sequence
atgc intronic sequence ATGC exonic sequence...ctcttgatggcaatgtactgataaggtatacggtctactagtttaatactccaccccatctctctattgacttgtatatcttcactttctttttctgcagGCTAAAACTGATAGGGAAGTGGGTGGGAACAAAGGTGTATCAAACAAGCAGATCCGACTTAAGATTTTTTCACCAAATGTTCTTGATATCACACTGGTAG
Basic information
species | Glycine max |
transcript | GLYMA20G06670.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G06670.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 1
ctcttgatggcaatgtactgataaggtatacg---gtctactagt--ttaatactccaccccatctctctattgacttgtatatcttcactttctttttc--tgcagGCTAAAACTGATAGGGAAGTGGGTGGGAACAAAGGTGTATCAAACAAGCAGATCCGACTTAAGATTTTTTCACCAAATGTTCTTGATATCACACTGGTAG
| || || | || ||| | | || | ||| | || | | |||| | || || ||| | ||| | | || ||||||| |||| || || || | |||||| ||||||||||| ||| | |||||||| ||||| ||||| | |||||||||||||| | || || |||| |
-----agttatgctggtttgtttagttatgccaatgcctgcaagtgttgaacaaactgtaccatagggc-atagagcactat-taatcattcccccaatcaatgcagGCCGAAACAGACAGAGAGGCGGGTGGTAACAAAGGTGTGTCAGATAAGCAGATACGACTGAAGATCTACTCACCAAATGTTCTAAACATTACGTTGGTTG
upper sequence: GLYMA20G06670.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G180335_T01 (Zea mays), 3'ss of exon 1
--ctcttgatggcaatgtactgataaggtatacggtctactagtttaatactccaccccatctctctattgacttgtatatcttcactttctttttctgcagGCTAAAACTGATAGGGAAGTGGGTGGGAACAAAGGTGTATCAAACAAGCAGATCCGACTTAAGATTTTTTCACCAAATGTTCTTGATATCACACTGGTAG
| || | ||| | | || | | || | ||| | ||| | ||| | | ||| | | | ||||||| |||| || | || | ||||| |||||||||||||| | | |||||| ||| | ||||||||||| |||||||||||| | || || |||| |
tgtttggtattttgtttcacttcttttctttagttagtgtgggcttgagttgccatt--agtgctccacagaccattgttaaaagactctgcatctatgcagGCAGAAACAGACCGAGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAGATACGATTGAAGATTTTTTCTCCAAATGTTCTTAACATTACTTTGGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atactccaccccatctctctattgacttgtatatcttcactttctttttctgcagGCTAAAACTGATAGGGAAGTGGGTGGGAACAAAGGTGTATCAAACAAGCAGATCCGACTTAAGATTTTTTCACCAAATGTTCTTGATATCACACTGGTAG
tattgac putative branch site (score: 2)
tatatcttcactttct putative PPT
tttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcttgatggcaatgtactgataaggtatacggtctactagtttaatactccaccccatctctctattgacttgtatatcttcactttctttttctgcagGCTAAAACTGATAGGGAAGTGGGTGGGAACAAAGGTGTATCAAACAAGCAGATCCGACTTAAGATTTTTTCACCAAATGTTCTTGATATCACACTGGTAG
- - tgatggc
- - - - - -aatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcttcac