Sequence
atgc intronic sequence ATGC exonic sequence...atgaaaaattaaattattatagtcctcgtcgtcatcattattattgttgttattatgttcccgaaggactctatgaatggtccttttgttaactgaccagGGGGCATTGATCCTCACACCCATCTAGATATGGATGTTGGTTTTACTGCAACGGTTGATGACTTCTTCAGTGGTCAGGCAGCAGCATTGGCTGGTGGGAC
Basic information
species | Glycine max |
transcript | GLYMA02G44690.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G44690.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 6
atgaaaaattaaattattatagtcctcgtcgtcatcattattattgttgttattatgttcccgaaggactctatgaatggtccttttgttaactgac---cagGGGGCATTGATCCTCACACCCATCTAGATATGGATGTTGGTTTTACTGCAACGGTTGATGACTTCTTCAGTGGTCAGGCAGCAGCATTGGCTGGTGGGAC------------------------------------------------------------------------------------
|||||| ||| || | | ||| || ||| ||||||| | | | || | || | ||| || || || | |||| || ||||| |||||||| || || || ||||| | |||| ||| ||||||| ||||| |||||||| || ||||||||||||||||||||
--------gtaaattcttacggttttgataaacatt-ttggaatta--gttattacttgctcttcgggttt-----atcattcttctggcaaatgtcacacaggtggaattgaccctcacactcacctggagatggaattcatgggaactgtaaccattgatgatttctttagtggtcatgctgcagCATTGGCTGGTGGGACAACAATGCACATTGACTTCGTCATTCCAGTGAATGGCAATTTAACTGCAGGTTTGGAATCCTACAAACAGAAGGCAGAAAAATC
upper sequence: GLYMA02G44690.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g59340.3 (Oryza sativa), 3'ss of exon 6
atgaaaaattaaattattatagtcctcgtcgtcatcattattattgttgttattatgttcccgaaggactctatgaatggtccttttgttaactgac---cagGGGGCATTGATCCTCACACCCATCTAGATATGGATGTTGGTTTTACTGCAACGGTTGATGACTTCTTCAGTGGTCAGGCAGCAGCATTGGCTGGTGGGAC
|||||| ||| || | | ||| || ||| ||||||| | | | || | || | ||| || || || | |||| || ||||| |||||||| || || || ||||| | |||| ||| ||||||| ||||| |||||||| || ||||||||||||||||||||
--------gtaaattcttacggttttgataaacatt-ttggaatta--gttattacttgctcttcgggttt-----atcattcttctggcaaatgtcacacagGTGGAATTGACCCTCACACTCACCTGGAGATGGAATTCATGGGAACTGTAACCATTGATGATTTCTTTAGTGGTCATGCTGCAGCATTGGCTGGTGGGAC
upper sequence: GLYMA02G44690.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------atgaaaaattaaattattatagtcctcgtcgtcatcattattattgttgttattatgttcccgaaggactctatgaatggtccttttgttaac-tgaccagGGGGCATTGATCCTCACACCCATCTAGATATGGATGTTGGTTTTACTGCAACGGTTGATGACTTCTTCAGTGGTCAGGCAGCAGCATTGGCTGGTGGGAC
| |||||| | || | | || | | | | || ||| | |||| | || | | | | || | | | | | | ||| || ||||| || ||||| || || | ||||| || ||| | || ||||||| |||||||||||||||||||| ||||| |||||||| ||
gttaatcaattcatactagttgatactttccaaaattttagccttttgttttgaatccttaac-tagtttcagttctaattaagaatggttagcattttcatcttactcttgtccctgatgtaaatagGAGGAATTGACCCCCACACGCACCTCGCCATGGAATTTATGGGTACCGAGACTATTGATGATTTCTTCAGTGGTCAGGCAGCGGCATTAGCTGGTGGAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgttattatgttcccgaaggactctatgaatggtccttttgttaactgaccagGGGGCATTGATCCTCACACCCATCTAGATATGGATGTTGGTTTTACTGCAACGGTTGATGACTTCTTCAGTGGTCAGGCAGCAGCATTGGCTGGTGGGAC
tgttaac putative branch site (score: 2)
tattatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgaaaaattaaattattatagtcctcgtcgtcatcattattattgttgttattatgttcccgaaggactctatgaatggtccttttgttaactgaccagGGGGCATTGATCCTCACACCCATCTAGATATGGATGTTGGTTTTACTGCAACGGTTGATGACTTCTTCAGTGGTCAGGCAGCAGCATTGGCTGGTGGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- gaaaaat
- - - - - - - - - - - - - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgg