Sequence
atgc intronic sequence ATGC exonic sequence...cgagtattttttggatgccatgtttcatttttgtacatctcattatctgatttgccctgctatgatgcgtgtacttaatgttagtccctgaaattgccagGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g55580.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G104246_T01 (Zea mays), 3'ss of exon 3
cgagtattttttggatgccatgtttcatttttgtacatctcattatctgatttgcc---ctgctatgatgcgtgtacttaatgttagtccctgaaattgccagGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
| | | | || | |||| |||| ||| | | | | | || |||| |||| ||| ||||| |||||| ||||||||| |||||| | || ||||||| || ||||| ||||||||||||||||||||||| |||||||||||||| || |||||||||||||||||||||||||||||||
ctatcaaatactgaa-attatgt--cattattgcatttaatttggaccaagttattgtgctgccatgacatgtggcattaattctagtccatgaaattgctagGAGGTGTCTAGTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGCCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
upper sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G059678_T01 (Zea mays), 3'ss of exon 3
cgagtattttttggatgccatgtttcatttttgtacatctcattatc--tgat-ttgccctgctatgatgcgtgtacttaatgttagtccctgaaatt--gccagGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
|| || | || | | ||||| ||| | || | | || | ||| |||| ||| ||| ||||| |||||| ||||||| ||||||||| | || ||||||| || ||||| ||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||||
-----atcaattacaggcattatatcattattgcatttcatttcggccatgttattgtgctgccttgacacgtcacattaattctagtccatgaaattttgccagGAGGTGCCTAGTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
upper sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G04180.1 (Glycine max), 3'ss of exon 3
cgagtattttttggatgccatgtttcatttttgtacatctcattatctg--atttgccctgctatgatgcgtgtacttaatgttagt---ccctgaaattgcc--agGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
|||| || | | | || || | |||| | | || | |||| | || | | | | | | || | |||| |||||| ||||| || || || | || |||||||||||||||||||| || || || || || || ||||||||||| ||||||||||||||||| |
------ttttctgaactcagtaattt-ttctagtactggtaaagatgttgcattttttttcttactttttaattgttgactatctgtgaacttcaaaataaatgtagGAGGATGCTGGGGAAATTTTGATATTGGGAAAGCATAATAAAGGGTGCCATTGTAAAAAATCTGGGTGCCTCAAGAAGTATTGTGAGTGCTTCCAAGCCA
upper sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G08670.1 (Glycine max), 3'ss of exon 3
-----------------------------------cgagtattttttgg-atgccatgtttca------tttttgtacatctcattatctgatttgccctgctatgatgcgtgtacttaatgttagtccctgaaa---ttgccagGAGGCGGCTG-GTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA------
| | ||||||| ||| ||| | ||||||| || | | ||| | || | |||| |||| |||| | | | || ||| | | | | |||| || | || | || ||||| |||||||| || ||||||||||| ||||| || || |||||||| ||||||||||||||||| |
gtttgtagttcaatttcaactccctcaaacatgtgttattggtttttggcatgaggcttttaagccaagtttttgtg-atgatacttactgttctgggtttagctgatat-tgtagttaacttgtgcatttaaatatcttgtttgaacacagGAATGTGAAATTAAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGCTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
upper sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G32420.1 (Glycine max), 3'ss of exon 6
-cgagtattttttggatgccatgtttcatttttgtacatctcattatctgatttgccctgctatgatgcgtgtacttaatgttagtccctgaaattgc---cagGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
| | ||| | | | ||| |||| || | | |||| || | | ||| | | | || | | | | | ||||| | |||||| |||||| || || | || | || || ||||| || ||||| || || || || || || || ||||||||||||||||| ||||||||||| |
atgtgctgaacttgaacatcttttttgtattttatat-ttaaaaaatct--ttagtttttcta-gttttgagtcttgactatctaactttgaaaataaatgtagGAGGAGGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAATCTGGGTGCCTCAAGAAGTACTGTGAATGCTTCCAAGCCA
upper sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G08780.1 (Glycine max), 3'ss of exon 6
-----------------------------------cgagtattttttgg-atgccatgtttca-------tttttgtacatctcattatctgatttgccctgctatgatgcgtgtacttaatgttagtccctgaaa-----ttgccagGAGGCGGCTG-GTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA------
| | ||||||| ||| ||| | ||||||| || | | ||| | || | | |||| | | | | | || | | || ||| | | | | |||| ||| | || | || ||||| |||||||| || ||||||||||| |||||||| || |||||||| ||||||||||||||||| |
gtttgtaattcaatttcaactccctcaaacaggtgttattgctttttggcatgatgcttttaagtcaagttttttgtg-atgatacttactgttctgggtttatctgatattttagttaacttgtggtgcatttaaatatcttgtttgaacacagGAATGTGAAATTCAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGTTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
upper sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G29000.1 (Arabidopsis thaliana), 3'ss of exon 3
cgagtattttttggatgccatgtttcatttttgtacatctcattatctgatttgccctgctatgatgcgtgtacttaatgttagtccctgaaattgccagGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
| || | | || | | | | | || | | | ||| |||| | || ||| |||||| ||||| || || | ||||| ||||| ||||| ||||||||||| || ||||| || || |||||||| || |||||||| ||||| |
-----------------gtacgtggtcctgaggaacttgttctagatcgtgggagagttctttaagcttctaagttattgttgat--ttgcctttgt-agGAGGATATCGGTGAAGTTGTGTTGTTAGGGAAACATAACAAAGGATGCCACTGCAAAAAATCAGGATGCCTTAAGAAGTATTGCGAGTGCTTTCAAGCAA
upper sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G25790.1 (Arabidopsis thaliana), 3'ss of exon 3
cgagtattttttggatgccatgtttcatttttgtacatctcattatctgatttgccct-gctatgatgcgtgtacttaatgttagtccctgaaattgccagGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
||||| |||| ||| ||| | | | | | ||| ||| |||| || ||| | | | | | ||| |||| ||||| | ||||| |||||||||| ||| ||||| ||||||||||||||||||||||| | ||| || |
----------------------------gtttgtg-atcttgttacttgaaaaaaaaaagatgtaactttagggcttgatggtagttttataacttgtagGAGAATGTGCAGCAAGTGTTGCTTA-TTGGAAAGCACAGCAAAGGATGCCACTGCAGGAAATCAGGATGTCTCAAGAAGTACTGTGAGTGTTACCAGGCGA
upper sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G20110.2 (Arabidopsis thaliana), 3'ss of exon 3
cgagtattttttggatgccatgtttcatttttgtacatctcattatctgatttgccctgctatgatgcgtgtacttaatgttagtccctgaaattgccagGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
| | | ||| ||| ||| ||| || | | | | | | | ||| | | || | |||| |||||| || |||||| || | | | || || || ||||| || ||||||||||| || || ||||| |||||||| ||||||||||| ||||| |
-------------------gtatgtggtttgtgttatgctctttaaactgttggtcttaaggttgttggataagttataaattttgactcgatttgc-agGAGGAGGTTGGTGACGTTGTGATGTTAGCGAGACACAACAAAGGCTGTCACTGCAAGAAATCCGGATGTCTTAAGAAGTATTGTGAGTGCTTTCAAGCAA
upper sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0008g03670.t01 (Vitis vinifera), 3'ss of exon 4
------cgagtattttttggatgccatgtttc--atttttgtacatctcattatctgatttgccctgctatgatgcgtgtacttaatgttagtccctgaaattgccagGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
| | | |||| | || ||||| | || | || ||||||| | | || | | || ||| || | | | |||| | |||||| | | ||||| || || ||||| |||||||| |||||||||||||| |||||||| ||||||||||||||||||||||| ||||| |
aatgtgttatttccctaaagatgtgaaattatcaattttcatgaatattgataactgatttacttttctttctgggctgaact--------gttcaaaacgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAAMapped 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|29621005|gb|CB626016.1|CB626016EST: CATTCAGGCCTAAGATTGGGAGTAGCCCGCATGCTAACCGGAATAATATG GAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCAC
genomic: CATTCAGGCCTAAGATTGGGAGTAGCCCGCATGCTAACCGGAATAATATGgtatgttttg ... aaattgccagGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgatttgccctgctatgatgcgtgtacttaatgttagtccctgaaattgccagGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
acttaat putative branch site (score: 4)
ttaatgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgagtattttttggatgccatgtttcatttttgtacatctcattatctgatttgccctgctatgatgcgtgtacttaatgttagtccctgaaattgccagGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT