Sequence
atgc intronic sequence ATGC exonic sequencegtaatgctttgaacataactccctaaattgtttccttgtgcttgtcattagttgatataaaacatttgtttcttccccagTATGATCCACCTCAAGATCCCAATGTGTTCATACATAGAGCTGGCCGTACTGCACGTTATGATCAAGAAGGAGATGCTATTGTATTCCTCTTACCGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g07080.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g07080.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G303752_T03 (Zea mays), 3'ss of exon 6
gtaatgctttgaacataactccctaaattgtttccttgtgctt-gtcattagttgatataaaacatt--tgtttcttc-cccagTATGATCCACCTCAAGATCCCAATGTGTTCATACATAGAGCTGGCCGTACTGCACGTTATGATCAAGAAGGAGATGCTATTGTATTCCTCTTACCGAAG
|| || | || | | ||||||||||| || || | | ||| || ||||| || || ||||| ||| ||||||||||||||||||||||||||| || ||||||||||||||||||||||| ||||| |||||||||||||| ||||||||||| || |||||||| |||
gttatattctgctcttccctccctaaatttgaatctcatgttcaggcatcagctgatagtaaggatgcatgtttgttcatccagTATGATCCACCTCAAGATCCCAACGTTTTCATACATAGAGCTGGCCGTACAGCACGCTATGATCAAGAAGGGGATGCTATTGTTTTTCTCTTACCAAAG
upper sequence: LOC_Os01g07080.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA18G02760.1 (Glycine max), 3'ss of exon 6
--------------gtaatgc-tttgaacat--aactccctaaattgtttccttgtgcttgtcattagttgatataaaacatttg------tttcttccccagTATGATCCACCTCAAGATCCCAATGTGTTCATACATAGAGCTGGCCGTACTGCACGTTATGATCAAGAAGGAGATGCTATTGTATTCCTCTTACCGAAG
|| ||| ||| || | | || | | || | || | | | || || || | ||| |||||| ||||||||||| ||||||||||| ||||| ||||||||||||| || || ||||| || | | || |||| ||||| |||| ||| | ||||| |||
gtattgtctattgactattgcatttcaattttcatcttctttggttctgtctctctcttggttgctaaaccatgcattgtggttgaaatgttttcttgtgcagTATGATCCTCCTCAAGATCCAAATGTTTTCATACATAGAGTAGGTCGAACTGCTCGGCTGGGTAAACAAGGTCATGCTGTTGTCTTCTTATTACCAAAG
upper sequence: LOC_Os01g07080.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA11G35640.1 (Glycine max), 3'ss of exon 6
--------------------------------------------------gtaatgctttgaacataactccctaaattgtttccttg--tgcttg------tcat-tagttgatataaaacatttgtttcttccccagTATGATCCACCTCAAGATCCCAATGTGTTCATACATAGAGCTGGCCGTACTGCACGTTATGATCAAGAAGGAGATGCTATTGTATTCCTCTTACCGAAG
| | | | | | || || | | ||||| |||| ||| ||| ||||| ||| |||||| ||||||||||| ||||||||||| || || ||||||||||||| || || ||||| || | | || |||| ||||| |||| ||| | ||||| |||
gtagctctgtgcttctgtgaccttgtatatgatactgtctattgactattgcatttcatcttctttggttctctctctctctcccttggctgctaaaatagaccatacagtgtggttaaaatgttt-tttcttgtgcagTATGATCCTCCTCAAGATCCAAACGTTTTCATACATAGAGTAGGTCGAACTGCTCGGCTGGGTAAACAAGGTCATGCTGTTGTCTTCTTATTACCAAAG
upper sequence: LOC_Os01g07080.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv13s0067g01900.t01 (Vitis vinifera), 3'ss of exon 6
-------------------gtaatgctttgaacataactccctaaattgtttccttgtgcttgtcattagttgat-ataaaacatttgtttcttccccagTATGATCCACCTCAAGATCCCAATGTGTTCATACATAGAGCTGGCCGTACTGCACGTTATGATCAAGAAGGAGATGCTATTGTATTCCTCTTACCGAAG
|| | |||| | || | || | |||| | || ||| |||| || | || ||||| ||||||||||| ||||||||||| ||||| |||||||| |||| ||| || ||||| || | | ||||| |||| |||| || || ||||| |||
tacactggcaggattgaacatatctaacacatcatacattccccatttatctcctgtttctgaaagctaggtgatgattttctgtctgcttcttatgcagTATGATCCCCCTCAAGATCCAAATGTCTTCATACACAGAGTTGGTCGGACTGCTCGGATGGGCAGACAAGGAAGTGCTGTTGTTTTTCTATTACCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattgtttccttgtgcttgtcattagttgatataaaacatttgtttcttccccagTATGATCCACCTCAAGATCCCAATGTGTTCATACATAGAGCTGGCCGTACTGCACGTTATGATCAAGAAGGAGATGCTATTGTATTCCTCTTACCGAAG
catttgtttcttcccc CT-rich tract
attagttgatataaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgctttgaacataactccctaaattgtttccttgtgcttgtcattagttgatataaaacatttgtttcttccccagTATGATCCACCTCAAGATCCCAATGTGTTCATACATAGAGCTGGCCGTACTGCACGTTATGATCAAGAAGGAGATGCTATTGTATTCCTCTTACCGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG