Sequence
atgc intronic sequence ATGC exonic sequence...gtattgtactattcagaatttctgatccatccctgcttgtactgaactcttagctagttattcttgatcagctaaattcaatgagtgacatttgtaacagGATATGATCGAGAATGTACTAGAGATAAAAGATACACACGTCAGGGAGGTAATGACGCCTCTGGTGGATGTAGTTGCAATTGATGCTACCGCAACACTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g39640.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g39640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 6
-------gtattgtactattcagaatttctgatccatccctgcttgt--actgaactcttagctagttattcttgatcagctaaattca-atgagtgacatttgtaacagGATATGATCGAGAATGTACTAGAGATAAAAGATACACACGTCAGGGAGGTAATGACGCCTCTGGTGGATGTAGTTGCAATTGATGCTACCGCAACACTGA
|||| | ||| || | |||||| | |||| | || | | ||| ||| | | || || | || | | ||| |||||||||||| || ||||| ||||||||||||| ||||| ||||| ||||| ||||| ||||| || ||||| |||||||||||||| | ||| |||
cttatcttcattgattgttatagatattttaatccatttttatttgtctgttaaaatttaagca------tctcaaatatatatatatatatatataatatt----acagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAGGTTATGACACCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
upper sequence: LOC_Os03g39640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 6
gtattgtactattcagaatttctgatccatccctgcttgtactgaactcttagctagttattcttga----tcagctaaattca-atgagtgacatttgtaacagGATATGATCGAGAATGTACTAGAGATAAAAGATACACACGTCAGGGAGGTAATGACGCCTCTGGTGGATGTAGTTGCAATTGATGCTACCGCAACACTGA
||| | | | | ||| || || | || | | || | || | | | | | | ||| | | || | | ||||||||||| || ||||| ||||||||||||| ||||| ||||| || || ||||||||||| || ||||| |||||||||||||| | ||| |||
---ttgcaaaagccttatcttc--attgattgttatagatattttaatccatttttatttctgtcaaaatttaaacatctctcacacatatataatatattgcagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAAGTTATGACGCCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
upper sequence: LOC_Os03g39640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 6
gtattgtactattcagaatttctgatccatccctgcttgtactgaactcttagctagttattcttgatcagctaaattcaatgagtgacatttgtaacagGATATGATCGAGAATGTACTAGAGATAAAAGATACACACGTCAGGGAGGTAATGACGCCTCTGGTGGATGTAGTTGCAATTGATGCTACCGCAACACTGA
| || ||| | || || | || ||| ||| | | | | |||| | |||| ||| | | | ||||||||||| || ||||| |||||||||| ||||| || || | ||||| ||||| ||||| || |||||||||||||| |||| | || | |||
-----------gtatgagtttgttatatatggat--tttcgatgag-tctataccatagacttgtgat------agttcac---atgatacatattgcagGATATGATTGAAAATGTGTTAGAGATAAAGGATACGCATGTTCGAGAGGTGATGACTCCTCTTGTTGATGTAGTTGCAATAGATGGCAGCGGCAGCCTGG
upper sequence: LOC_Os03g39640.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 6
gtattgtactattcagaatttctgat-ccatccctgcttgtactgaactcttagctagttattcttgatcagctaaattcaatgagtgacatttgtaacagGATATGATCGAGAATGTACTAGAGATAAAAGATACACACGTCAGGGAGGTAATGACGCCTCTGGTGGATGTAGTTGCAATTGATGCTACCGCAACACTGA
||||| || | | | | | | || | | || | || || | | || | | ||| || | || || | || | | |||||||||||||| ||||| | ||||||||||||||||| || || || || ||||| ||||| |||||||| |||||||||||||| | ||||||||
ttattgacttaatgggcagaagtaaagctatacttagtttt-tggatctgtgtgtgtgtgtgtgtggataagatgctatcgctgtaataaatctcttgcagGATATGATCGAAAATGTGTTGGAGATAAAAGATACACATGTTAGAGAAGTGATGACACCTCTTGTGGATGTTGTTGCAATTGATGCCAGTGCAACACTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actcttagctagttattcttgatcagctaaattcaatgagtgacatttgtaacagGATATGATCGAGAATGTACTAGAGATAAAAGATACACACGTCAGGGAGGTAATGACGCCTCTGGTGGATGTAGTTGCAATTGATGCTACCGCAACACTGA
agctaaa putative branch site (score: 3)
taaattcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgtactattcagaatttctgatccatccctgcttgtactgaactcttagctagttattcttgatcagctaaattcaatgagtgacatttgtaacagGATATGATCGAGAATGTACTAGAGATAAAAGATACACACGTCAGGGAGGTAATGACGCCTCTGGTGGATGTAGTTGCAATTGATGCTACCGCAACACTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA