Sequence
atgc intronic sequence ATGC exonic sequence...attagattttggaggatgcttgttttgaacaatgtctgtatcactcactcaagaagtatcatgaacataaaatcaatttttaatttcttttttcttgtagGTGTTTCCTTGAAAACACAGGAGCTATATGCTCTTGTTTTCGCCACTCGCTACTTGGACATATTTACAGACTTTATATCCCTATACAATACAGTCATGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g30800.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g30800.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv05s0029g00180.t01 (Vitis vinifera), 3'ss of exon 1
attagattttggagga-tgcttgttttgaacaatgtctgtatcactcactcaagaagtatcatgaacataaaat-caatttttaatttcttttttct-tgtagGTGTTTCCTTGAAAACACAGGAGCTATATGCTCTTGTTTTCGCCACTCGCTACTTGGACATATTTACAGACTTTATATCCCTATACAATACAGTCATGAA
| | ||| | || || | || | | || | || || | || ||| || ||| | || || | || ||| |||| | || || || || || |||||||||||||| || |||||||| ||||| |||||||| || | ||| || || || ||||| || |||||
--tggctttcacctcagtgtttaatctggtcgct-cctacgttttggctgtaacaaactgttttgacttaatccatgatatttggctcctccattttatgcagGAATTTCTCTAAAGACTCAAGAACTTTATGCTCTTGTTTTTGCAACTCGCTATTTGGATATATTTACCGATTATATCTCACTTTATAATACTGTAATGAAMapped 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|88325105|gb|CI646523.1|CI646523EST: GAGCGTCCTCGTCCTCCTGCTCAAGATCCACACCATCAAGTCTTGCGCTG GTGTTTCCTTGAAAACACAGGAGCTATATGCTCTTGTTTTCGCCACTCGCT
genomic: GAGCGTCCTCGTCCTCCTGCTCAAGATCCACACCATCAAGTCTTGCGCTGgtgagtgact ... tttcttgtagGTGTTTCCTTGAAAACACAGGAGCTATATGCTCTTGTTTTCGCCACTCGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactcaagaagtatcatgaacataaaatcaatttttaatttcttttttcttgtagGTGTTTCCTTGAAAACACAGGAGCTATATGCTCTTGTTTTCGCCACTCGCTACTTGGACATATTTACAGACTTTATATCCCTATACAATACAGTCATGAA
tttttaatttcttttt CT-rich tract
tatcatgaacataaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attagattttggaggatgcttgttttgaacaatgtctgtatcactcactcaagaagtatcatgaacataaaatcaatttttaatttcttttttcttgtagGTGTTTCCTTGAAAACACAGGAGCTATATGCTCTTGTTTTCGCCACTCGCTACTTGGACATATTTACAGACTTTATATCCCTATACAATACAGTCATGAA
- - - - - - - -atgcttg
- - - - - - - - - - - - - gaacaat
- - - - - - - - - - - - - - - - - -ctgtatc
- - - - - - - - - - - - - - - - - - - - - - - - - aagaagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatcaa