Sequence
atgc intronic sequence ATGC exonic sequence...agtacgaaaactagttgtaaattatgcaatttataaccagcagttgttatccatgatcattgaaatacattatgttgctaactttgtatgtttgttatagGTCTGTGCAAGTGTGTCTTCGGATTCAACTAACATGAATGAACTTATTCAATGGAATGATCTTTATGGAGAAGGTGGATCAAGGAAAAAGACTACTCTAA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g22420.1 |
intron # | 27 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 6
agtacgaaaactagttgtaaattatgcaatttataaccagcagttgttatccatgatcattgaaatacattatgttgctaactttgtatg-------tttgttatagGTCTGTGCAAGTGTGTCTTCGGATTCAACTAACATGAATGAACTTATTCAATGGAATGATCTTTATGGAGAAGGTGGATCAAGGAAAAAGACTACTCTAA
| | || | |||| ||||| | ||| |||| || || |||| | || ||||| || |||| ||| || ||||| ||||||||||| | |||||||| | |||||||| || ||| | |||||||||||||| ||||||||||| ||||||||||||||||| || ||||
-acatttgaggcgaatggga--tatggaattt-tgtacagtgtttgtaatt--tgcccatttgagc-tggtaaattgctcacacaatatggggtgactttcttgtagGTGTGTGCAAGTGTTCCCTCGGATTCCAGTAACATGAGCGAGCTTGTGCAATGGAATGATCTCTATGGAGAAGGCGGATCAAGGAAAAAGACAACGCTAA
upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 22
--agtacgaaaactagttgtaaattatgcaatttataacca-gcagttgttatccatgatcattgaaatacattatgttgctaactttgtatgtttgttatagGTCTGTGCAAGTGTGTCTTCGGATTCAACTAACATGAATGAACTTATTCAATGGAATGATCTTTATGGAGAAGGTGGATCAAGGAAAAAGACTACTCTAA
| | | | | | | |||| | || | ||||| || | | | || | | | | | | || ||| || ||||| ||||||||||| || || ||||| | ||||||||| || ||| | |||||||||||||| ||||||||||| || |||||||||||||| || ||||
tcaatgtctacatttgaggcgaattgggatatgaaattttgtgcagtgtttgttttgagttggtaaattgc-tcacaca--cagtgtggtgactttcttgtagGTGTGTGCAAGTGTTTCCTCAGATTCCAGTAACATGAACGAGCTTGTGCAATGGAATGATCTCTATGGAGAAGGCGGGTCAAGGAAAAAGACAACGCTAA
upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 22
------agtacg-aaaactagttgtaaattatgcaatttataaccagcagttgtt--atccatgatcattgaaatacattatgttgctaactttgtatgtttgttatagGTCTGTGCAAGTGTGTCTTCGGATTCAACTAACATGAATGAACTTATTCAATGGAATGATCTTTATGGAGAAGGTGGATCAAGGAAAAAGACTACTCTAA
||| |||| | ||||| | ||| | || | | ||| | | | | | | || |||| ||||| ||||| ||||| |||| |||||||||||||| || || ||||| || |||||||| || | ||||||||||| || ||||||||||| |||||||| |||| || |||| |
tacctttgtagacaaaattggttgtttttcatggtgatcat-----gtaattgctcaaagagtccttttcgtggta-attacattgcttga--tgtatttttgt-gcagGTGTGTGCAAGTGTGTCATCAGAGTCAACAAATATGAATGAGCTACTCCAATGGAATGACCTCTATGGAGAAGGAGGATCAAGAAAAATGAGATCTCTGA
upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 23
------agtacgaaaactagttgtaaattatgcaatttataaccagcagttgttatccatgatcattgaaatacattatgttgctaactttgtatgtttgttatagGTCTGTGCAAGTGTGTCTTCGGATTCAACTAACATGAATGAACTTATTCAATGGAATGATCTTTATGGAGAAGGTGGATCAAGGAAAAAGACTACTCTAA
| | | || || || | ||| | || || | | || |||| | | | ||| || ||||| || | | | || ||| | |||| ||||| |||||||| ||||| ||||| || |||| |||||| | |||||||| || ||||| ||||||||||||||||| |||| || || | |
acgtacaattccaatgatacctgggagtta---atttcatgatagtccatt-ttatggctagcaaaggtaatgtataatgtttctta-tgtatacttttat-gcagGTTTGTGCTAGTGTGTCATCGGAGTCAACAAATATGAGTGAACTACTCCAATGGAACGACCTTTACGGAGAAGGTGGATCAAGAAAAATGAGATCTTTGA
upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 26
-----agtacg-aaaactagttgtaaattatgcaatttataaccagcagttgttatccatgatcattgaaatac--attatgttgctaactttgtatgtttgttatagGTCTGTGCAAGTGTGTCTTCGGATTCAACTAACATGAATGAACTTATTCAATGGAATGATCTTTATGGAGAAGGTGGATCAAGGAAAAAGACTACTCTAA
||| |||| | ||||| | ||| | || | | ||| | | || || | | |||| || | | | | |||||| |||| |||||||| ||||| || || ||||| || |||||||| || | ||||||||||| || ||||||||||| |||||||| |||| || |||| |
acctttgtagacaaaattggttgtttttcatggtgatcat-----gtaattgctcgatagagtccttttagtggtaattacaatgtttgatgtat---tttgttgcagGTGTGTGCAAGCGTGTCATCAGAGTCAACAAATATGAATGAGCTACTCCAATGGAATGACCTCTATGGAGAAGGAGGATCAAGAAAAATGAGATCTCTGA
upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 23
agtacgaaaactagttgtaaattatgcaatttataaccagcagttgttatccatgatcattgaaa-tacattatgttgctaactttgtatgtttgt-tatagGTCTGTGCAAGTGTGTCTTCGGATTCAACTAACATGAATGAACTTATTCAATGGAATGATCTTTATGGAGAAGGTGGATCAAGGAAAAAGACTACTCTAA
| || ||| | | | | || || | | | | ||| || | || ||| || | | |||||| | | | |||| |||| ||||| || ||||| ||||| |||||||||||||| | |||||||| || ||||| ||||||||||||||||| |||| || || | |
-atgtacaatgccattg-acacctgggagttaatttcatgagagtccattttatggccagcaagggtagtgtataatgtttcatatgtatgcatttatgcagGTTTGTGTTAGTGTATCATCGGAGTCAACAAACATGAATGAACTACTCCAATGGAACGACCTTTACGGAGAAGGTGGATCAAGAAAAATGAGATCTTTGAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|33680639|gb|CF308878.1|CF308878EST: ACGATGTCCGTGCCTTACGACTAAGTGATTTCAAACATGCTCATGAACAG GTCTGTGCAAGTGTGTCTTCGGATTCAACTAACATGAATGAACTTATTCAA
genomic: ACGATGTCCGTGCCTTACGACTAAGTGATTTCAAACATGCTCATGAACAGgtatgatcca ... tttgttatagGTCTGTGCAAGTGTGTCTTCGGATTCAACTAACATGAATGAACTTATTCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttatccatgatcattgaaatacattatgttgctaactttgtatgtttgttatagGTCTGTGCAAGTGTGTCTTCGGATTCAACTAACATGAATGAACTTATTCAATGGAATGATCTTTATGGAGAAGGTGGATCAAGGAAAAAGACTACTCTAA
tgctaac putative branch site (score: 1)
attgaaatacattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtacgaaaactagttgtaaattatgcaatttataaccagcagttgttatccatgatcattgaaatacattatgttgctaactttgtatgtttgttatagGTCTGTGCAAGTGTGTCTTCGGATTCAACTAACATGAATGAACTTATTCAATGGAATGATCTTTATGGAGAAGGTGGATCAAGGAAAAAGACTACTCTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- -acgaaaa
- - - - - - - - - - -ttatgca
- - - - - - - - - - - - - - - - - - ccagcag
- - - - - - - - - - - - - - - - - - - - - - - - atccatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtatg