Sequence
atgc intronic sequence ATGC exonic sequence...gaacattttgaggctagctttgttatactgttgcatctgcgtgtgcttactcccactgtttgattcaaattcgtgtttatgtgcaatcttctgatatcagGCTGCAAAGAGGCATCTGGCAGGAAGAATAGATCATGTAGATTGTACTTTAGATGAATGCCAGGAAATTACAGAATCCACAAGAAAAGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g01070.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g01070.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G432653_T01 (Zea mays), 3'ss of exon 1
gaacattttgaggc-tagctttgttatactgttgcatctgcgtgtgcttactcccactgtttgattcaaattcgtgtttatgtgcaatcttctgatatcagGCTGCAAAGAGGCATCTGGCAGGAAGAATAGATCATGTAGATTGTACTTTAGATGAATGCCAGGAAATTACAGAATCCACAAGAAAAGAG
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-aatgcaatacaatataattctatgacaatacctcctctaacagttctggttcttattgtcacatctggtaatctgtttatgtgaaatattttcatatcagGTTGCAAAGAAACATCTTGCTGGAAGGATTGATCGTGTAGATTGTAGTTTAGATGAATGCCAAGTAATTACAGAAGCCACAAGGGAAGAG
upper sequence: LOC_Os01g01070.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G078711_T01 (Zea mays), 3'ss of exon 6
gaacattttgaggctagctttgttatactgttgcatctgcgtgtgcttactcccactgtttgattcaaattcgtgtttatgtgcaatcttctgatatcagGCTGCAAAGAGGCATCTGGCAGGAAGAATAGATCATGTAGATTGTACTTTAGATGAATGCCAGGAAATTACAGAATCCACAAGAAAAGAG
| | || | || | | ||| |||||| ||| | |||| |||||| || | | |||| || ||| || | |||||||| ||||| ||| ||||| |||||||| || |||| ||||||||||| |||||||||||| || |||||||||||| ||||||| || ||
tccagtcattagattgatttatcttgattgtggcatctaaatgttttgactcttactgttgcatctgataatctacttatatgaaatattttcatatcagGTTGCAAGGAGACATCTTGCAGGAAGGATTGATCGTGTAGATTGTAGTTTAGATGAATGTCATGAAATTACAGAAGCCACAAGGGAACAG
upper sequence: LOC_Os01g01070.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G147587_T01 (Zea mays), 3'ss of exon 6
gaacattttgaggctagctt-tgttatactgttgcatctgcgtgtgcttactcccactgtttgattcaaattcgtgtttatgtgcaatcttctgatatcagGCTGCAAAGAGGCATCTGGCAGGAAGAATAGATCATGTAGATTGTACTTTAGATGAATGCCAGGAAATTACAGAATCCACAAGAAAAGAG
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-ttcaatgcaatacaatctaattctatgacagtacctctaacagttctgattcttattgtcgcatctggtaatctgtttatgtgaaatattttcatatcagGTTGCAAAGAAACATCTTGCTGGAAGGATTGATCGTGTAGATTGTAGTTTAGATGAATGCCAAGAAATTACAGAAGCCACAAAGGAAGAGMapped 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|33658119|gb|CF280733.1|CF280733EST: CTGCGATGTTGGTTGGCAAACAGTTGGAACATGTTTCAGAGAATGTTAAT GCTGCAAAGAGGCATCTG
genomic: CTGCGATGT-GGTTGGCAAACAGTTGGAACATGTTTCAGAGAATGTTAATgtaagtttct ... ctgatatcagGCTGCAAAGAGGCATCTG
EST:
gi|58687220|gb|CK075907.1|CK075907EST: CCTGCGATGTGGTTGGCAAACAGTTGGAACATGTTTCAGAGAATGTTAAT GCTGCAAAGAGGCATCTGGCAGGAAGAATAGATCATGTAGATTGTACTTTA
genomic: CCTGCGATGTGGTTGGCAAACAGTTGGAACATGTTTCAGAGAATGTTAATgtaagtttct ... ctgatatcagGCTGCAAAGAGGCATCTGGCAGGAAGAATAGATCATGTAGATTGTACTTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttactcccactgtttgattcaaattcgtgtttatgtgcaatcttctgatatcagGCTGCAAAGAGGCATCTGGCAGGAAGAATAGATCATGTAGATTGTACTTTAGATGAATGCCAGGAAATTACAGAATCCACAAGAAAAGAG
tcttct CT-rich tract
attcaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaacattttgaggctagctttgttatactgttgcatctgcgtgtgcttactcccactgtttgattcaaattcgtgtttatgtgcaatcttctgatatcagGCTGCAAAGAGGCATCTGGCAGGAAGAATAGATCATGTAGATTGTACTTTAGATGAATGCCAGGAAATTACAGAATCCACAAGAAAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - tgaggct
- - - - - - - - - - - - - -ctgttgc
- - - - - - - - - - - - - - - - - - ctgcgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtgc