Sequence
atgc intronic sequence ATGC exonic sequencegtatcattgtttggcacactttttttttcatacttgtgattatttatattgatattaatataaaacacagGTAAAACTTATTGATTTTTCGCCTGGTGAGAAGTATTTGGTAACATATATTAGCCATGAACCAAGCAATCCCCGAGATGCCAAT
Basic information
species | Glycine max |
transcript | GLYMA04G06080.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G06080.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 3'ss of exon 5
--gtatcattgtttggcacacttt-ttttttcatacttgtgattatttatattgatattaatataaaacacagGTAAAACTTATTGATTTTTCGCCTGGTGAGAAGTATTTGGTAACATATATTAGCCATGAACCAAGCAATCCCCGAGATGCCAAT
| ||| | | |||| || | ||| | ||| || ||||| | || | | |||||| ||||| ||||| || || ||||||||||| |||||||| ||||||| |||||| || || ||||| || |||| | ||
gtacgtgatt-tacgctgcactgagttatgtcagatatgtaatattttatctacctaacactgcttgtaacagGTGAAACTGATTGACTTCTCCCCTGGTGAGAAATATTTGGTCACATATAGTAGCCACGAGCCCAGCAACCCTAGAGACACTCAT
upper sequence: GLYMA04G06080.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G27640.2 (Arabidopsis thaliana), 3'ss of exon 6
---------------gtatcattgtttggcacactttttttttcatacttg---tgattatttatattgatattaatataaaacacagGTAAAACTTATTGATTTTTCGCCTGGTGAGAAGTATTTGGTAACATATATTAGCCATGAACCAAGCAATCCCCGAGATGCCAAT
|| | | || ||||| | ||| ||| ||| | | || || || |||||||||| ||||||| ||||| |||||||| ||| | ||||| || |||||| ||||||||||| || |||||||| | |
gtttgaatttcctttcaattgctacatattacttccgtttttcctctgttggcctgaaaattgcatcttttgttgat-tatgttttagGTAAAACTAGTTGATTTCTCGCCAGGTGAGAAATATCTTGTAACTTACCATAGCCAAGAACCAAGCAACCCGCGAGATGCAAGT
upper sequence: GLYMA04G06080.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G25780.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------gtatcattgtttggcacactttttttttcatacttg---tgattatttatat-tgatattaatataaaacacagGTAAAACTTATTGATTTTTCGCCTGGTGAGAAGTATTTGGTAACATATATTAGCCATGAACCAAGCAATCCCCGAGATGCCAAT
|| | | | || ||||| | ||| ||| ||| | | | | || || | |||| ||||| ||||||| |||||||||||||| ||| | ||||| || |||||| |||||||||||||| ||||||| | |
gtttgaaattcctttcaattgctacatagtacttccgtttttcctgtgttggtctgaaaattgacttcttttgttgat-tccgttttagGTCAAACTAGTTGATTTCTCGCCTGGTGAGAAATATCTTGTAACTTACCATAGCCAAGAACCAAGCAATCCGAGAGATGCAAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acactttttttttcatacttgtgattatttatattgatattaatataaaacacagGTAAAACTTATTGATTTTTCGCCTGGTGAGAAGTATTTGGTAACATATATTAGCCATGAACCAAGCAATCCCCGAGATGCCAAT
tattaat putative branch site (score: 2)
ttttttttcatacttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcattgtttggcacactttttttttcatacttgtgattatttatattgatattaatataaaacacagGTAAAACTTATTGATTTTTCGCCTGGTGAGAAGTATTTGGTAACATATATTAGCCATGAACCAAGCAATCCCCGAGATGCCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG