Sequence
atgc intronic sequence ATGC exonic sequence...ttttcaatccctaaatactgctgactttctagactgggtttggttccctgcagctgcttctagaaaaacttaccggcctctacctgttgttgctatgcagGGGTTCCGAAAGGTCACTCCAGATCGGTGGGAGTTTGCAAATGAAGCCTTCTTAGCTGGTCAGAAGCATTTGCTGAAAAACATCAAGAGGAGGCGTGTTT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g39020.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g39020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G005815_T01 (Zea mays), 3'ss of exon 1
ttttcaatccctaaatactgctgactttctagactgggtttggttccctgcagctgcttctagaaaaacttaccggcctcta-----cctgttgttgctatgcagGGGTTCCGAAAGGTCACTCCAGATCGGTGGGAGTTTGCAAATGAAGCCTTCTTAGCTGGTCAGAAGCATTTGCTGAAAAACATCAAGAGGAGGCGTGTTT
|| ||| | || | ||| | | | | | || | | ||| | | | ||| ||||| | | ||||||| ||| | ||||| | ||||||||| |||||||||||||| ||| | |||||||| || ||||||||| ||||||||| ||||| ||||||||| | |
-ttgcaaac---gaaca-tgcccttactaggaattaaaccccctcaatccatatggattggggtagaaccgaacaagccctaatggttctgttccttttgtgcagGGATTCAGGAAGGTGAATCCAGATCGTTGGGAGTTTGCAAACGAATCATTCTTAGCAGGCCAGAAGCATCTGCTGAAAAGCATCAGGAGGAGGCGCGCGTMapped 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|33801246|gb|CF326496.1|CF326496EST: TCTTCAAGCACGCCAACTTCTCCTCCTTCGTTCGCCAGCTCAACACCTAC GGGTTCCGAAAGGTCACTCCAGATCGGTGGGAGTTTGCAAATGAAGCCTTC
genomic: TCTTCAAGCACGCCAACTTCTCCTCCTTCGTTCGCCAGCTCAACACCTACgtacgtatcc ... tgctatgcagGGGTTCCGAAAGGTCACTCCAGATCGGTGGGAGTTTGCAAATGAAGCCTTC
EST:
gi|218501036|gb|FG961274.1|FG961274EST: CTTCAAGCACGCCAACTTCTCCTCCTTCGATTCGCCAGCTCAACACCTAC GGGTTCCGAAAGGTCACTCCAGATCGGTGGGAGTTTGCAAATGAAGCCTTC
genomic: CTTCAAGCACGCCAACTTCTCCTCCTTCG-TTCGCCAGCTCAACACCTACgtacgtatcc ... tgctatgcagGGGTTCCGAAAGGTCACTCCAGATCGGTGGGAGTTTGCAAATGAAGCCTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctgcagctgcttctagaaaaacttaccggcctctacctgttgttgctatgcagGGGTTCCGAAAGGTCACTCCAGATCGGTGGGAGTTTGCAAATGAAGCCTTCTTAGCTGGTCAGAAGCATTTGCTGAAAAACATCAAGAGGAGGCGTGTTT
aacttac putative branch site (score: 2)
aaaaactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttcaatccctaaatactgctgactttctagactgggtttggttccctgcagctgcttctagaaaaacttaccggcctctacctgttgttgctatgcagGGGTTCCGAAAGGTCACTCCAGATCGGTGGGAGTTTGCAAATGAAGCCTTCTTAGCTGGTCAGAAGCATTTGCTGAAAAACATCAAGAGGAGGCGTGTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - tgctgac
- - - - - - - - - - - - - - - - - - - - - - - -ctgcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaaa