Sequence
atgc intronic sequence ATGC exonic sequence...aagcttttgaacctgatttacttggattcttttgtggcttcattgatgacatcattgtttaaagtcaatgttgatctattagctaagttccaatgtgcagGTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGTTGGGCCAAGGATGAACGCACATTAAAG
Basic information
species | Glycine max |
transcript | GLYMA10G12560.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G12560.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G878139_T02 (Zea mays), 3'ss of exon 3
aagcttttgaacctgatttac---ttggattcttttgtggcttcattgat-gacatcattgttta-aagtcaatgttg-atctattagctaagttccaatgtgcagGTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGTTGGGCCAAGGATGAACGCACATTAAAG
| || |||| ||| || | | || || |||| | | || | | | | | | || || | | | | | | ||||||||||||| ||||||||||||||| | || || || || ||||||| || ||||||||||||||| ||| |||||
------tagagcctgtgttaactattaccctttcttctgacttctgtagtagatgttctggcacatgatttggcattctataaactgtttttgcttacttttgcagGTCATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAGAGGAGCTGGGCCAAGGATGAAAAGACACTAAAG
upper sequence: GLYMA10G12560.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 5
aagcttttgaacc--tgatttacttggattcttttgtggcttcattgatgacatcattgtttaaagtcaatgttgatctattagctaagttcca---atgtgcagGTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGTTGGGCCAAGGATGAACGCACATTAAAG
|| ||| | ||| || | || | || | | ||| |||| | | || | || | || || || | | |||||||| || |||||||||||||| || || ||||| || ||||| |||| |||||||||||||||| |||| |||||
---tttgagaaaaaatcattgttttaggttaatacacttctccgccttttttatc--tgttacatattcatagtactcataaacagaattttcacacacatacagGTCATAGGCTGGTCAATGTGGTTCTCGGAGTATCTCTTTCTGGAAAGAAATTGGGCCAAGGATGAAAGCACTCTAAAG
upper sequence: GLYMA10G12560.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 5
aagcttttgaacctgatttacttggattctt--ttgtggct--tcattga------tgacatcattgtttaaagtcaatgttgat-ctattagctaagttccaatgtgcagGTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGTTGGGCCAAGGATGAACGCACATTAAAG
| | | | | | | ||| || ||| | ||||||| ||||| | | | || | || | || ||| | | || | | ||||| || ||||||||||||||||||||||| ||| | || ||||| |||| ||||||||||||||| ||| | |||||
-------tagatgtcgtctgcatacatttttctttgcaattgctcattgaacactttgacacctctatatatatacaggataaatgttatgtgtccaatt----tattcagGTGATAGGTTGGTCAATGTGGTTTTCTGAGTATTTATTTCTGGAAAGAAACTGGGCCAAGGATGAAAGCATAATAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgacatcattgtttaaagtcaatgttgatctattagctaagttccaatgtgcagGTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGTTGGGCCAAGGATGAACGCACATTAAAG
tgttgat putative branch site (score: 4)
attgtttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagcttttgaacctgatttacttggattcttttgtggcttcattgatgacatcattgtttaaagtcaatgttgatctattagctaagttccaatgtgcagGTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGTTGGGCCAAGGATGAACGCACATTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG