Sequence
atgc intronic sequence ATGC exonic sequenceTGCGATGGACAAACTACCTGAGACCAGACATCAAGAGAGGAAAATTCAGCTTACAAGAAGAGCAGACCATCATCCAACTTCATGCTCTTCTTGGAAACAGgtaacaatgaagcagttcactcaagatttttccctcttcaagttacctttacagtagtagtgatccttctgctgcaacatcattgaaaaatcatgacttc...
Basic information
species | Oryza sativa |
transcript | LOC_Os08g33660.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g33660.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G079123_T01 (Zea mays), 5'ss of exon 1
TGCGATGGACAAACTACCTGAGACCAGACATCAAGAGAGGAAAATTCAGCTTACAAGAAGAGCAGACCATCATCCAACTTCATGCTCTTCTTGGAAACAGgtaa----caatgaagc-agttcactcaagatttttccctcttcaagttacctttacagtagtagtgatccttctgctgcaacatcattgaaaaatcatgacttc--
|| | |||||||||||||||||||| ||||||||||| || || |||||||| ||||||||||||||||||||||| |||||||||||| | || ||||||| | || |||| ||| |||| ||||| || | |||| | | || | |||| || | | ||| || | | | | |||
TGAGGTGGACAAACTACCTGAGACCGGACATCAAGAGGGGCAAGTTCAGCTTGCAAGAAGAGCAGACCATCATCCAGCTTCATGCTCTTTTAGGCAACAGgtgagtaccagtgaaattagtcaactccagattgttacagt---aagtcatat---catctgcagtgctcagagcac-aagagatcctttagcatacgtatcttatc
upper sequence: LOC_Os08g33660.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G111117_T01 (Zea mays), 5'ss of exon 2
TGCGATGGACAAACTACCTGAGACCAGACATCAAGAGAGGAAAATTCAGCTTACAAGAAGAGCAGACCATCATCCAACTTCATGCTCTTCTTGGAAACAGgtaacaatgaagcagttcactcaagatttttccctcttcaagttacctttacagtagtagtgatccttctgctgcaacatcattgaaaaatcatgacttc-
|| | ||||||||||||||||| || ||||||||||| || || |||||||| |||||||| |||||||||||||| ||||| |||||| | || ||||||| | | || | | | |||| | | |||| | | || | | || ||||| | | | | | || |
TGAGGTGGACAAACTACCTGAGGCCGGACATCAAGAGGGGCAAGTTCAGCTTGCAAGAAGAACAGACCATCATCCAGCTTCACGCTCTTTTAGGCAACAGgtgagtaccaatgaaattagtcaactccagatcgttacaaagtgatcctttggcttat-gtatcttatctgccctctttctgctaagagaagactgctgcc
upper sequence: LOC_Os08g33660.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv17s0000g06410.t01 (Vitis vinifera), 5'ss of exon 2
TGCGATGGACAAACTACCTGAGACCAGACATCAAGAGAGGAAAATTCAGCTTACAAGAAGAGCAGACCATCATCCAACTTCATGCTCTTCTTGGAAACAGgtaacaatgaagcagttcactcaagatttttccctcttcaagttacctttacagtagtagtgatccttctg-----ctgcaacatcattgaa----aaatcatgacttc------------------------------------------------------------------
|| ||||||| |||||||| ||||| || ||||||||||| ||||||||||||| |||||||||||||| || ||||||||||||||||| || ||||||| | | | || || || | | || | ||| | | |||| ||| | | || | | | || ||| || | ||| ||
TGAGATGGACGAACTACCTCAGACCTGATATCAAGAGAGGCAAATTCAGCTTACGGGAAGAGCAGACCATTATTCAACTTCATGCTCTTCTAGGCAACAGgtta-actaaactagatc--ttatgaatcttcaaatgccctgcacatgatacaaaagttgggcattttttaagtctttttgaaatgattaaattttggaatatggttttgtaggacatgcttcacagggttgtaaattgtgggtggaattgtaatttgggtattgttttatgcagMapped 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|66923102|gb|CX109950.1|CX109950EST: AGAGCAGACCATCATCCAACTTCATGCTCTTCTTGGAAACAG GTGGTCTGCCATTGCAACACATCTACCAAAGCGCACTGACAATGAGATCAA
genomic: AGAGCAGACCATCATCCAACTTCATGCTCTTCTTGGAAACAGgtaacaatga ... tcctgttcagGTGGTCTGCCATTGCAACACATCTACCAAAGCGCACTGACAATGAGATCAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGCGATGGACAAACTACCTGAGACCAGACATCAAGAGAGGAAAATTCAGCTTACAAGAAGAGCAGACCATCATCCAACTTCATGCTCTTCTTGGAAACAGgtaacaatgaagcagttcactcaagatttttccctcttcaagttacctttacagtagtagtgatccttctgctgcaacatcattgaaaaatcatgacttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcttc