Sequence
atgc intronic sequence ATGC exonic sequence...aaaattcttctctaagatggtgtgatattggacctttacgtaatagatcttatttttgtcatgcttctaggaagcatctaatgttttgtcattgctgcagATTCAAGTAGGTAATTCTCCAGAATATATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTA
Basic information
species | Oryza sativa |
transcript | LOC_Os07g07560.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 2
----aaaattcttctctaagatggtgtgatattggacctttacgtaatagatcttatttttgtcatgcttctaggaagcatctaatgttttgtcattgctgcagATTCAAGTAGGTAATTCTCCAGAATATATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTA
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agaggcccttttgctatacaaagattttatgttgaactttgacataat--ttcttatttccagaagtttttttgg--tcacctaatcttatttcatttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTG
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 2
--aaaattcttctctaag--atggtgtgatattggacctttacgtaatagatcttatttttgtcatgcttctaggaagcatctaatgttttgtcattgctgcagATTCAAGTAGGTAATTCTCCAGAATATATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTA
| | ||| ||| | |||| | || ||| | | | |||| ||||||| | | || || |||||||| || | ||||| |||||| |||||||||||||||||||||| || |||||||||||||| ||||||||||||||||||||||| || ||||||||| ||||||| |||||||| ||
agagaccctttcgctatgcagtggttttatgttgaatttgggcataat--ttcttattcccaagaggttt--gggggtcatctaatcttatttcatttctgcagGTTCAAGTAGGTAATTCTCCAGAGTACATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTGTATGTTGGTCGAAGGGTTTCTGGTGGTGCTG
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 2
aaaattcttctctaagatggtgt-gatattggacctttacgta-atagatcttatttttgtcatgctt--ctaggaagcatctaatgttttgtcattgctgcagATTCAAGTAGGTAATTCTCCAGAATATATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTA
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---attccagactgcattgtagttgttgtttttagttaatatagatagat-ttggcagtaccttacttaccttatctgtggtgtatattttctcattgatgcagGTACAAGTAGGTAACTCTCCTATATATAAGATAGAGAGGAAATTGGGTAAGGGTGGTTTTGGTCAAGTTTATGTTGGCCGGAGGTTAAGTGGTGGCTCTG
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 2
aaaattcttctctaagatggtgtgatattggacctttacgtaatagatcttatttttgtcatgcttctaggaag-catctaatgt---tttgtcattgctgcagATTCAAGTAGGTAATTCTCCAGAATATATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTA
|| | | | | || | || | ||| |||| | | | ||||||| | ||| || || || | | | || || | | || | ||||| || |||||||| | |||| || || |||||| | ||||||||||| |||||||||||||||||||| |||||||| |||||| | |
--aaatgtggtttgcgaggccatgccaatggg--tttaagccttgcactagctttttgttctcctttgagagagatattcactatgatttcgttttctgtatagGTACAAGTTGGAAATTCTCCTGTTTATAAGACGGAGAGGAAACTTGGTAAAGGTGGCTTTGGTCAAGTTTATGTTGGCAGAAGGGTGAGTGGTGGCAGTG
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 2
aaaattcttctctaagatggtgtgatattggacctttacgtaatagatcttatttttgtcatgcttctaggaagcatctaatgttttgtcattgctgcagATTCAAGTAGGTAATTCTCCAGAATATATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTA
||| || | || || || || || | | || | || |||| | | | | | || | | | | | | || | ||||| || |||||||| | ||||| ||||| |||||| | |||||||| || ||||||||||||| ||||||||||||||| |||||| |
-----------gtaaaatt-tatgctaatg-acattcaatcacaagttttttttttcatttgagagagatgctgatattgatttcattttacttgtatagGTACAAGTTGGAAATTCTCCTGTATATAAGACTGAGAGGAAACTCGGTAAAGGAGGCTTTGGTCAAGTTTTTGTTGGTAGAAGGGTGAGTGGTGGCAGCG
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 2
---aaaattcttctctaagatggtgtgatattggacctttacgtaatagatcttatttttgtcatgcttctaggaagcatctaatgttttgtcattgctgc-agATTCAAGTAGGTAATTCTCCAGAATATATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTA
| || | | || | | ||| |||| || | | |||| | | ||| | | | | | | || ||| ||| | | || | ||||| ||||||||||| ||| | | || ||||| |||||||| ||||||||||||||||| |||||||| ||||||||| |||||| |||
tctgaggggctaatggagcatttgttaaaatttttccttcac----tcgttcttcaacacggattctttcaaagcatctagttgttttctgtttttggttctagGTACAAGTGGGTAATTCTCCTATATACAAGATAGAAAGGAAGTTAGGTAAGGGTGGTTTTGGTCAAGTGTATGTTGGCAGAAGGGTAAGTGGTGGCACTGMapped 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|66915500|gb|CX102348.1|CX102348EST: AAAAGCTTGTTGCGGCTGACGATGAATCATCACTACCTGTCCCTGAGAGG ATTCAAGTAGGTAATTCTCCAGAATATATAACTGACAGGAAATTACGTAAA
genomic: AGAAGCTTGTTGCGGCTGACGATGAATCATCACTACCTGTCCCTGAGAGGgtatgagtaa ... attgctgcagATTCAAGTAGGTAATTCTCCAGAATATATAACTGACAGGAAATTAGGTAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatcttatttttgtcatgcttctaggaagcatctaatgttttgtcattgctgcagATTCAAGTAGGTAATTCTCCAGAATATATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTA
atctaat putative branch site (score: 3)
tatttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaattcttctctaagatggtgtgatattggacctttacgtaatagatcttatttttgtcatgcttctaggaagcatctaatgttttgtcattgctgcagATTCAAGTAGGTAATTCTCCAGAATATATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - -gatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg