Sequence
atgc intronic sequence ATGC exonic sequence...tttcaattatgagcattcattagaaccatatttttctactacatataattatcactttgaaattttcaatgtggattgagactgaacatattttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os06g03760.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------tttcaattatgagcattcattagaaccatatttttctactac-ata-taattatcactt-tgaaattttcaatgtggattgagactgaacatattttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA
| | | | || | || || ||| | | | ||| ||||||| || | | ||||||| ||||| | ||||| | | |||||||||||||||||||| || |||||||| |||| || || ||||| ||||||||||| ||||||||||| | ||||||||| |||||| | ||||||||||
gtgggcatacattctcatgtacaacattttgatcataacggaaaaacggatgcttgtgtctcttgtgatca-atctttttgttgctatagtaattattgattgttcggatatcaatgtttcttgaggttaaacatgtatcctgcagGAAGCAACTGAACTGGGAAAGAAGGCCAGGGAGTTAAAAAAAGCTGCTGAAGCCCTACACCAAGAAGAAAGAAGTGGGAACAAGGGCCGGAAATGGCGCA
upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 5
--------------------------tttcaattatgagca--------ttcattagaaccatatttttctactac-ata-taattatcactt-tgaaattttcaatgtggattgagactgaacatattttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA
||| || || | ||||| | || |||||| | | ||| ||||| | || | | ||||||| | | || || | |||||||||||||||||| | || |||||||| |||| |||| || || |||||||| |||||||||||||| | ||||||||| |||||| | |||||||| |
gtgggcatacattctcatgtacaccattttgatcataaaggatgcttgcctcatttgtgatcaatctttctattgctatagtaattgttgattgtttggatatcaatgtttccttgaggttaaaatctgccctgcagGAAGCAACTGAATTGGGGAAGAAGGCCAGGGAGCTGAAAAAGGCGGCTGAAGCTCTTCACCAAGAAGAAAGAAGTGGGAACAAGGGCCGGAAATGGCGAA
upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 5
tttcaattatgagcattcattagaaccatatttttctactacatataattatcactttgaaattttcaatgtggattgagactgaacatattttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA
||| || || || || | | | | | || || || | || || | |||| | | ||| || || |||||||||||||||||| ||||| || || ||| ||||||||||||||||| | ||||| || ||||| | |||||| |||||| || |||| || |
---gtgctatatgcttttat-agcaggagacatactaaatattgattgaatatgctgtattatatttattgtgtggtt-ggctggttatggtt---gcagGAAGCAACTGAACTGGGTAAAAAAGCAAAAGAACTGAAGAAAGCAGCTGAATCACTTCATCAGGAAGAAAGAAGTGGTTCGAAGGGTAGGAAATTTCGTA
upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------tttcaattatgagcattcattagaaccatatttttctactacatataattatcactttga--aattttcaatgtggattga--gactgaacat---att-ttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA
|| || | | | || | | ||||||| ||| | || ||||| | | || || ||| | | ||| ||| ||| || | ||||||||||||||||||||||| ||||| | || | |||||||||||||| || |||||||| ||||| |||||| ||||| || || ||| | |
gttcatttgtgctggttattgttgtctacttgtcttcatgcaaagcttttctaaagaatacatgta-cacttcgggtagttggcagtgttagtggcctgacaagtcatctaattgtttttcagGAAGCAACTGAACTAGGTAAAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAAGGGAAGGAAGTGGAGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taattatcactttgaaattttcaatgtggattgagactgaacatattttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA
tattttct CT-rich tract
tttgaaattttcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcaattatgagcattcattagaaccatatttttctactacatataattatcactttgaaattttcaatgtggattgagactgaacatattttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - gcattca
- - - - - - - - - - - -aaccata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacata