Sequence
atgc intronic sequence ATGC exonic sequenceTTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAGgtgagtttttttctttctgaagaaagaattgtgagtttatctatctgaagaaagaattgaacaaattcaaaatcgttgtgcttctttcaattgaatttag
Basic information
species | Oryza sativa |
transcript | LOC_Os09g29830.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g29830.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G818643_T01 (Zea mays), 5'ss of exon 3
TTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAGgtgagttt--ttttctttctgaagaaagaattgtg------agtttatctatctgaagaaagaattgaacaaattcaaaatcgttgtgcttctttcaattgaatttag
||||| ||||||||||| || ||||||||||| || || |||||||| ||||||||||||||||| || || | || | | |||||||||| | | | || | | || | | | ||| |||| | || | || | |||| ||
TTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTGCTGCAGGACCTCGTTCCTGGCTGCAGCAAAgtaggtctatcttccacacagaagaaagaaaaggggaacagaacttgcttgtgtgtttttatgttggttttcattacaaatgaacat-ctctgtccattggaatccag
upper sequence: LOC_Os09g29830.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G137541_T01 (Zea mays), 5'ss of exon 3
TTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAGgtgagtttttttctttctgaagaaagaattgtgagtttatctatctgaag---aaagaattgaacaaattcaaaatcgttgtgcttctttcaatt---gaatttag
||||| ||||||||||| || ||||||||||| ||||| |||||||| |||||||| |||||||| || || | | | || ||| || || | | | | |||| | ||| | || | ||| | ||| ||
TTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTTCTGCAGGACCTTGTTCCTGGTTGCAGCAAAgtaggtctatcttgccaaaaaaaaaaggaatagaacttgcttgtgagtgctttatttcattgctgattatcagtacaaatgaacaccttcgacccttgaaatccag
upper sequence: LOC_Os09g29830.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA02G13860.1 (Glycine max), 5'ss of exon 5
TTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAGgtgagtttt---tttctttctgaagaaagaattgtga-gtttatctatctgaagaaaga-attgaacaaattcaaaatcgttg--tgcttctttcaattgaatttag
|||| ||||| ||||| |||||||||||||| ||||||| ||||| || ||||| |||||||||||| || | ||| || | || | | || | | ||| || || || || || || ||| | | ||||| || | |||||
GTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGgtggcttctaagtttgaaactagaaaatttactatgtcatattgttatttgtgtttaggtatcacttccttttaacattgtttattattactttctat-gcttttag
upper sequence: LOC_Os09g29830.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv01s0010g00740.t01 (Vitis vinifera), 5'ss of exon 4
TTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAGgtgagtttttttctttctgaagaaagaattgtgagtttatctatctgaagaaagaattgaacaaattcaaaatcgtt---gtgcttctttcaattgaatttag-------------
| |||||||| ||||||||||| |||||||| ||||||| ||||| || ||||| ||||||||||| |||| || ||| || || | | | || || || || || | ||||| | | | | ||| || ||| || | | ||
GTAAGAAGGGAAAAGATCAGTGAAAGGATGAAGTTTCTTCAAGACCTGGTACCTGGTTGCAGCAAGgttggtttgtt------ggaattaataacttggggaccata-attagattgaattatctatggaattcgatgttgcttccgtggctcattccatgggaattgcttgatttttgtagMapped 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|218493872|gb|FG957202.1|FG957202EST: TCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAG GTCACCGGAAAAGCGGTGATGCTTGACGAGATCATCAACTATGTTCAGTCC
genomic: TCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAGgtgagttttt ... ttgaatttagGTCACCGGAAAAGCGGTGATGCTTGACGAGATCATCAACTATGTTCAGTCC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAGgtgagtttttttctttctgaagaaagaattgtgagtttatctatctgaagaaagaattgaacaaattcaaaatcgttgtgcttctttcaattgaatttag
- - - - - - - - - - GAGAGG
- - - - - - - - - - - AGAGGA
- - - - - - - - - - - GAGGAT
- - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG