Sequence
atgc intronic sequence ATGC exonic sequencegtgcgtggatgaatttcttgtttgcagacctactaccttagttcaaaagaagatttgagtaactttgtttgactaataaatgtgcagAGGAAAATGGGATATCCTACAGTCCAGATCAGGTGCTGGTGAGCAATGGAGCTAAGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g65090.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G400604_T01 (Zea mays), 3'ss of exon 3
----------------gtgcgtggatgaatttct-tgtttgcagacctactaccttagttcaaaagaagatttgagtaactttgt-ttgactaataaatgtgcagAGGAAAATGGGATATCCTACAGTCCAGATCAGGTGCTGGTGAGCAATGGAGCTAAGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGA
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gtgtgtggatgtatgaagttatgaacggacgtctgttttcgcagagctac--ctttcgatcgatgaaa---ctgaatgacttcgtgtttaattatgactgtacagAGGAGAACGGGGTATCCTACCTCCCAGATGAGGTGCTGGTGAGCAATGGAGCTAAGCAATGCATCACACAAGCTGTGCTTGCAGTTTGCTCACCTGGTGA
upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G400604_T03 (Zea mays), 3'ss of exon 3
------gtgcgtggatgaatttct-tgtttgcagacctactaccttagttcaaaagaagatttgagtaactttgt-ttgactaataaatgtgcagAGGAAAATGGGATATCCTACAGTCCAGATCAGGTGCTGGTGAGCAATGGAGCTAAGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGA
|| | | | ||| | || ||||| |||| | || | || | || ||| | |||| || || | | || | ||| ||||||| || ||| |||||||| |||||| |||||||||||||||||||||||||||||||||| || ||||| || ||||| |||||||||||||||||
gtatgaagttatgaacggacgtctgttttcgcagagctac--ctttcgatcgatgaaa---ctgaatgacttcgtgtttaattatgactgtacagAGGAGAACGGGGTATCCTACCTCCCAGATGAGGTGCTGGTGAGCAATGGAGCTAAGCAATGCATCACACAAGCTGTGCTTGCAGTTTGCTCACCTGGTGA
upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ15807 (Selaginella moellendorffii), 3'ss of exon 2
gtgcgtggatgaatttcttgtttgcagacctactaccttagttcaaaagaagatttgagtaactttgtttgacta-ataaatgtgcagAGGAAAATGGGATATCCTACAGTCCAGATCAGGTGCTGGTGAGCAATGGAGCTAAGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGA
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----------------------------------------gtgagtgatgttttccgaaagcttttgtaagacttcgtatttctccagAGGAAAATGGGCTCACGTACAAAACGGACGAGATCCTTGTGAGCAATGGAGCGAAACAATGTATCACGCAAGCTGTTCTTTCCGTTTGCTCGCCTGGTGAMapped 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|88396984|gb|CI578133.1|CI578133EST: TAATGCTGGGACTTTGGAGCTGAGAAAGGCTATCTGCAATAAACTCCAAG AGGAAAATGGGATATCCTACAGTCCAGATCAGGTGCTGGTGAGCAATGGAG
genomic: TAATGCTGGGACTTTGGAGCTGAGAAAGGCTATCTGCAATAAACTCCAAGgtgcgtggat ... aaatgtgcagAGGAAAATGGGATATCCTACAGTCCAGATCAGGTGCTGGTGAGCAATGGAG
EST:
gi|29645872|gb|CB650879.1|CB650879EST: TAATGCTGGGACTTTGGAGCTGAGAAAGGCTATCTGCAATAAACTCCAAG AGGAAAATGGGATATCCTACAGTCCAGATCAGGTGCTGGTGAGCAATGGAG
genomic: TAATGCTGGGACTTTGGAGCTGAGAAAGGCTATCTGCAATAAACTCCAAGgtgcgtggat ... aaatgtgcagAGGAAAATGGGATATCCTACAGTCCAGATCAGGTGCTGGTGAGCAATGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaccttagttcaaaagaagatttgagtaactttgtttgactaataaatgtgcagAGGAAAATGGGATATCCTACAGTCCAGATCAGGTGCTGGTGAGCAATGGAGCTAAGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGA
gactaat putative branch site (score: 2)
tttgactaataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgtggatgaatttcttgtttgcagacctactaccttagttcaaaagaagatttgagtaactttgtttgactaataaatgtgcagAGGAAAATGGGATATCCTACAGTCCAGATCAGGTGCTGGTGAGCAATGGAGCTAAGCAATGCATTACGCAAGCCGTACTTGCCGTTTGCTCACCTGGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA