Sequence
atgc intronic sequence ATGC exonic sequence...aaatgaaggatacgactaacttttgagggcaaatataaagaattttctcaataaagaaattattctcagtgtaattgaaattaagttgccgcactcacagGGAAACACTTTCGTGACATTGTTGGAAGTGCCTACTATGTAGCACCAGAAGTGCTTAAGCGTAAGTCAGGCCCAGAATCTGACGTTTGGAGTATTGGCGT
Basic information
species | Oryza sativa |
transcript | LOC_Os07g22710.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g22710.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G365035_T01 (Zea mays), 3'ss of exon 5
--------aaatgaaggatacga--ctaac-ttttgagggcaaatataaagaattttctcaataaagaaattattctcagtgtaattgaaattaagttgcc-gcactcacagGGAAACACTTTCGTGACATTGTTGGAAGTGCCTACTATGTAGCACCAGAAGTGCTTAAGCGTAAGTCAGGCCCAGAATCTGACGTTTGGAGTATTGGCGT
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gtgcatgcatgcacatgtttttaacttaatgttctgtagttttccctgtttgacttttgcagtat-gtgttagttataggttacacttaactattgttgcttgcaatcacagGGAGGCAATTCCGTGACATTGTTGGAAGTGCCTACTACGTAGCACCAGAAGTACTCAAACGCAGGTCAGGGCCAGAATCCGATGTTTGGAGTATAGGTGT
upper sequence: LOC_Os07g22710.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 7
-----------------------------------------------------------aaatgaagg---atacgactaacttttgagggcaaatataaagaattttctcaataaagaaattattctcagtgtaattgaaattaagtt--gccgcactcacagGGAAACACTTTCGTGACATTGTTGGAAGTGCCTACTATGTAGCACCAGAAGTGCTTAAGCGTAAGTCAGGCCCAGAATCTGACGTTTGGAGTATTGGCGT
| ||| | | ||| | || || | ||| | | || ||| | ||||| | | || || || | |||| ||| | |||| ||| |||||||| ||||| |||||||| ||||| |||||| | || |||||||| || || |||| || || ||||||||||| ||
gtgagggaaagtcttgatttttgtggtcaatttctttctttttcttttcttccattttttgtttcaggcttgttctcctatttcttcagttgagttatcaggcatgctcttgccattt---ttatttgagatttgtttttctctatctttgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGTAAGTCTGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
upper sequence: LOC_Os07g22710.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G08180.1 (Glycine max), 3'ss of exon 6
-----aaatgaaggatacgactaacttttgagggcaaatataaagaattttctcaataaagaaattattctcag-tgtaattgaaattaagttgc-cgcactc------------acagGGAAACACTTTCGTGACATTGTTGGAAGTGCCTACTATGTAGCACCAGAAGTGCTTAAGCGTAAGTCAGGCCCAGAATCTGACGTTTGGAGTATTGGCGT
|| | | | | | || | | | | | | || || | || | || || | | || |||| | | | ||| | | ||| ||||| || |||| || |||||||| ||||| |||||||| |||||||||||| | || || |||||||| || || || || || ||||||||||| ||
gtgagcaaaaatatgtgttaatcgttattttgttccctttttatccctctttgcattcaacatgttcttgcaatctttatttgagagttatttgttctctctctttgaaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGAAAGTCAGGTCCCGAGTCAGATGTATGGAGTATTGGTGT
upper sequence: LOC_Os07g22710.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G37100.1 (Glycine max), 3'ss of exon 6
----aaatgaaggatacgactaacttttgagggcaaatataaagaattttctcaataaagaaattattctcagtgtaattgaaatta-agttgccgcactc----------acagGGAAACACTTTCGTGACATTGTTGGAAGTGCCTACTATGTAGCACCAGAAGTGCTTAAGCGTAAGTCAGGCCCAGAATCTGACGTTTGGAGTATTGGCGT
| || | || | | | | | | | | || || | || | || || | | ||| | ||| ||| | | || ||||| || |||| || |||||||| ||||| |||||||| |||||||||||| | || ||||||||||| || || || || || ||||||||||| ||
gtgagcaaaaatgtgttgatcattatctttgtttcctttttatccctcttagcattcaaaatgttcttgcaatctttatttgagttatggttttctctctttgcaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGTAAGTCAGGTCCCGAGTCGGATGTATGGAGTATTGGTGT
upper sequence: LOC_Os07g22710.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------aaatgaaggatacgactaacttttgagggcaaatataaagaattttctcaataaagaaattattctcagtgtaattgaaattaagttgccgcactcacagGGAAACACTTTCGTGACATTGTTGGAAGTGCCTACTATGTAGCACCAGAAGTGCTTAAGCGTAAGTCAGGCCCAGAATCTGACGTTTGGAGTATTGGCGT
|| ||| | ||| | || | | ||| ||| || ||| | ||||| | || || || | | |||| ||| | |||| ||| |||||||| ||||| |||||||| ||||| |||||| | || || |||||||| || |||| || || ||||||||||| ||
gtgagggaaagtcttgattttcatgctcaatttctttatttttcttttcttccattttttgttgcaggcttgttctatttctttggttgagttatcaagcatgctcttgt----aattttatttgagatttatttttctctatctgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGCAAGTCAGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
upper sequence: LOC_Os07g22710.3 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G17890.1 (Arabidopsis thaliana), 3'ss of exon 5
aaatgaaggatacgactaacttttgagggcaaatataaagaattttctcaataaagaaattattctcagtgtaattgaaattaagttgccgcactcacagGGAAACACTTTCGTGACATTGTTGGAAGTGCCTACTATGTAGCACCAGAAGTGCTTAAGCGTAAGTCAGGCCCAGAATCTGACGTTTGGAGTATTGGCGT
|| || | || ||||| |||||| | | | | | | | | ||| |||| || | ||| ||| | |||| ||| |||||||| ||||| |||||||||||||| |||||| | || |||| ||| || || ||||| || || ||||||||||| ||
--------------gttagtagcaaagtg---atttaaagt-ttttcttgacatatcact--tctttgatctaacc---attatgtaacaatgt----agGCAAAAAGTTTCATGATATTGTTGGGAGTGCATACTATGTAGCACCTGAAGTGTTAAAACGTAGGTCGGGACCTGAATCAGATGTGTGGAGTATTGGTGT
upper sequence: LOC_Os07g22710.3 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 5
aaatgaaggatacgactaacttttgagggcaaatataaagaattttctcaataaagaaattattctcagtgtaattgaaattaagttgccgcactcacagGGAAACACTTTCGTGACATTGTTGGAAGTGCCTACTATGTAGCACCAGAAGTGCTTAAGCGTAAGTCAGGCCCAGAATCTGACGTTTGGAGTATTGGCGT
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---------------------gtaaaagtttcacttgtcaagtcttgtccctgagagcagaatggtaga--taatggaggtgattttgtgaaaatggcagGAGTGAAATTTCAGGATATAGTAGGAAGCGCATACTACGTTGCACCTGAAGTGTTGAAACGTAGGTCAGGACCTGAATCAGACGTTTGGAGTATTGGTGTMapped 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|58682948|gb|CK071635.1|CK071635EST: CTCATCCCTCAAGGCTACAGATTTTGGTCTTTCAGATTTTATAAGACCAG GGAAACACTTTCGTGACATTGTTGGAAGTGCCTACTATGTAGCACCAGAAG
genomic: CTCATCCCTCAAGGCTACAGATTTTGGTCTTTCAGATTTTATAAGACCAGgtttgtgtgt ... gcactcacagGGAAACACTTTCGTGACATTGTTGGAAGTGCCTACTATGTAGCACCAGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcaataaagaaattattctcagtgtaattgaaattaagttgccgcactcacagGGAAACACTTTCGTGACATTGTTGGAAGTGCCTACTATGTAGCACCAGAAGTGCTTAAGCGTAAGTCAGGCCCAGAATCTGACGTTTGGAGTATTGGCGT
ataaagaaattattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatgaaggatacgactaacttttgagggcaaatataaagaattttctcaataaagaaattattctcagtgtaattgaaattaagttgccgcactcacagGGAAACACTTTCGTGACATTGTTGGAAGTGCCTACTATGTAGCACCAGAAGTGCTTAAGCGTAAGTCAGGCCCAGAATCTGACGTTTGGAGTATTGGCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
aaatgaag
- - - - - - - - - - - - - - - - - ataaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - aaagaaa