Sequence
atgc intronic sequence ATGC exonic sequence...ttatcacatgacttgaaaaagcaaaatgagtcaaaaactagatggctcataaaaaccgacagttactgactgtctactctgaattttggtaattatgcagATCTACATTCTTTTGTACAAGGAAGTTGCTCTTGCATTGAAAATCAACAGCTTGTACAGTAAACAAAAGCTACTTAACATTCATGAGAATGTAAAAGTTC
Basic information
species | Oryza sativa |
transcript | LOC_Os05g29050.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 7
ttatcacatgacttgaaaaagcaaaatgagtcaaaaactagatggctc-ataaaaaccgacagttactgactgtctactctgaattttgg---taattatgcagATCTACATTCTTTTGTACAAGGAAGTTGCTCTTGCATTGAAAATCAACAGCTTGTACAGTAAACAAAAGCTACTTAACATTCATGAGAATGTAAAAGTTC
| | | || | ||| | || | | | | || |||| || | | || || || | ||||||| | || ||||||| |||||||| ||||||||||||||||||||||| |||||||| |||||||| ||||||||||| | |||||||||||||||||| ||||| |||||||
-gaaaaaaagaacacagaaaatagcatcaaatggattcagactttctttataattacttattatc-ttggatgact--ttgaaattttgaattcatttttgcagATTTACATTCTCTTGTACAAGGAAGTTGCTCTTGCTTTGAAAATTAACAGCTTATACAGTAAACAGAGGCTACTTAACATTCATGAAAATGTTAAAGTTC
upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 8
ttatcacatgacttgaaaaagcaaaatgagt-caaaaactagatggctcataaaaaccgacagttactgactgtctactctgaattttggtaattatgcagATCTACATTCTTTTGTACAAGGAAGTTGCTCTTGCATTGAAAATCAACAGCTTGTACAGTAAACAAAAGCTACTTAACATTCATGAGAATGTAAAAGTTC
| | ||| | | | | ||| | | | | | || | || | | | |||| | | | | | | |||||||| ||||||||| | ||||| || || |||||||| |||||||||||||| | || || || ||||||| |||| ||||||||||||||| | ||
tagttaca-aaggtactcagctatgatgtatgccactgggataatgcatgttccaattgctttatttccattgtcaagatttacatggatttttaatgcagATTTACATTCTTCTCTACAAAGAGGTGGCTCTTGCTTTGAAAATCAACAGTGTTTATAGCAAGAAAAAGCTTCTTAGCATTCATGAGAATGTGAGGGTAT
upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 8
ttatcacatgacttgaaaaagcaaaatgagtcaaaaactagatggct-cataaaaaccgacagttac-tgactgtctactctgaattttggtaatt------atgcagATCTACATTCTTTTGTACAAGGAAGTTGCTCTTGCATTGAAAATCAACAGCTTGTACAGTAAACAAAAGCTACTTAACATTCATGAGAATGTAAAAGTTC
||| | | || ||| ||| || || | ||| | | | |||| ||||| | || | |||| | | | |||||||| ||||||||| | ||||| || || |||||||| |||||||| ||||| | || || || ||||||| |||| ||||||||||||||| | ||
------tgccactgggacaat--gcatgttccaattgctttatttccatgtaagtgtcaagatttacatgactttttaatgcagatttacatgaattttttaatgcagATTTACATTCTTCTCTACAAAGAGGTGGCTCTTGCTTTGAAAATAAACAGTGTTTATAGCAAGAAAAAGCTTCTTAGCATTCATGAGAATGTGAGGGTAT
upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA20G38200.1 (Glycine max), 3'ss of exon 9
------ttatcacatgacttgaaaaagcaaaatgagtc-------------aaaaactagatggctcataaaa---accgacagttact-gactgtctactctgaattttggtaattatgcagATCTACATTCTTTTGTACAAGGAAGTTGCTCTTGCATTGAAAATCAACAGCTTGTACAGTAAACAAAAGCTACTTAACATTCATGAGAATGTAAAAGTTC
||| || | | | || || | || || | | || | ||| | | ||| | | || | | || || | || |||||||| | ||| | |||||||| ||| |||| || || |||||||||||||||||||||| || || | || |||||||||||||| | ||
gtacacttactactctcatcaatacagtcaagtttgtttttgttcatcttagaagatttaattctttctaagattgatttacaataaagagaataatgcttatgccattaaatgatccaacagATCTATGTGCTTCTCTACAAGGAGGTTTCTCTAGCTTTAAAAATCAACAGCTTGTACAGTATGAGAAGACTGTTCAAAATTCATGAGAATGTGAGGGTAT
upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 8
-ttatcacatgacttgaaaaagcaaaatgagtcaaaaactagatggctcataaaaaccgacagttactgactgtctactctgaattttggtaattatgcagATCTACATTCTTTTGTACAAGGAAGTTGCTCTTGCATTGAAAATCAACAGCTTGTACAGTAAACAAAAGCTACTTAACATTCATGAGAATGTAAAAGTTC
|||| | || | | || | | | | | || | || || | | || | || ||||||| ||||||||| | ||||| || ||||||||||| |||||||||||||| | ||||||||| ||||| |||| ||||||||||||||| | ||| |
gaaatcattattcctgcatttttttttctttctgttgattatgggacctactttgatccactagaaggga-tgctggtgttaatttatcttatgactgcagATTTACATTCTTCTCTACAAAGAGGTTGCTCTTGCTTTGAAAATCAACAGTGTCTACAGTAAAAGGAAGCTTCTTAGCATTCATGAGAATGTGAGAGTAC
upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ21271 (Selaginella moellendorffii), 3'ss of exon 8
ttatcacatgacttgaaaaagcaaaatgagtcaaaaactagatggctcataaaaaccgacagttactgactgtctactctgaattttggtaattatgcagATCTACATTCTTTTGTACAAGGAAGTTGCTCTTGCATTGAAAATCAACAGCTTGTACAGTAAACAAAAGCTACTTAACATTCATGAGAATGTAAAAGTTC
| | || | | | | | | | || | | || | | | | | |||| || ||||| |||||||||||||||| | || ||||||||||||||| |||||| ||| |||||||||| || || || || | ||||||
------------------------------------gtttgttgtcctt---atgctggtattcat---ctttttgatc---gtcctttttctcttctagATTTATGTTCTTCTGTACAAGGAAGTTGCGTTGGCTTTGAAAATCAACAGCCTGTACACGAAAAGAAAGCTACTTGGAATACACGAAAACATTAAAGTTT
upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ12042 (Selaginella moellendorffii), 3'ss of exon 8
ttatcacatgacttgaaaaagcaaaatgagtcaaaaactagatggctcataaaaaccgacagttactgactgtctactctgaattttggtaattatgcagATCTACATTCTTTTGTACAAGGAAGTTGCTCTTGCATTGAAAATCAACAGCTTGTACAGTAAACAAAAGCTACTTAACATTCATGAGAATGTAAAAGTTC
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------------------------------------gtttgttgtcctt---atgctggtattcac---ctttttgatc---gtcctttttctcttctagATTTATGTTCTTCTGTACAAGGAAGTTGCCTTGGCTTTGAAAATCAACAGCCTGTACACGAAAAGAAAGCTACTTGGAATACACGAAAACATTAAAGTTTMapped 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|58692366|gb|CK081053.1|CK081053EST: CATCTAGGCTTGATGCTCTACTGGAAGCTAGAGCTAAGCAGGGTGTACAG ATCTACATTCTTTTGTACAAGGAAGTTGCTCTTGCATTGAAAATCAACAGC
genomic: CATCTAGGCTTGATGCTCTACTGGAAGCTAGAGCTAAGCAGGGTGTACAGgtatcataat ... aattatgcagATCTACATTCTTTTGTACAAGGAAGTTGCTCTTGCATTGAAAATCAACAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcataaaaaccgacagttactgactgtctactctgaattttggtaattatgcagATCTACATTCTTTTGTACAAGGAAGTTGCTCTTGCATTGAAAATCAACAGCTTGTACAGTAAACAAAAGCTACTTAACATTCATGAGAATGTAAAAGTTC
tactgac putative branch site (score: 1)
aattttggtaattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatcacatgacttgaaaaagcaaaatgagtcaaaaactagatggctcataaaaaccgacagttactgactgtctactctgaattttggtaattatgcagATCTACATTCTTTTGTACAAGGAAGTTGCTCTTGCATTGAAAATCAACAGCTTGTACAGTAAACAAAAGCTACTTAACATTCATGAGAATGTAAAAGTTC
- - - - tgacttg
- - - - - - - - -aaagcaa
- - - - - - - - - - - - - - - -caaaaac
- - - - - - - - - - - - - - - - - - - - - - - - ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgactg