Sequence
atgc intronic sequence ATGC exonic sequence...gagtcttgatttatcaattatcttttttgtcagtttctgtgtatgttgcaggattttgcagctcccctttagtctaatggtttattttcaatttgtgcagGATCCAAAAGAGAAGGCAAAAGCTGAAACAAGAGATTGGCTTAACAATGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g44900.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AC197122.3_FGT003 (Zea mays), 3'ss of exon 4
-gagtcttgatttatca-attatcttttttgtcagtttctgtgtatgttgcaggattttgcagctcccctttagt--ctaatggtttattttcaatttgtgcagGATCCAAAAGAGAAGGCAAAAGCTGAAACAAGAGATTGGCTTAACAATGTG
| || | | | | | ||||| | ||| |||| ||||| | | || || ||||| | || ||| | ||||| || || | | || ||||||||||| ||||| ||||| ||||||||||||||||| |||||||| ||||||
caactcagggtgtgtagtactatctatcttg--agttgctgtggacct--cattatcttgcaacacctgtttcttgactaataattatttcttatttggtgcagGATCCCAAAGAAAAGGCCAAAGCTGAAACAAGAGACTGGCTTAATAATGTG
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G340749_T01 (Zea mays), 3'ss of exon 1
gagtcttgatttatcaattatcttttttgtcagtttctgtgta-tgttgcaggattttgca-gctcccctttagtctaatggtttattttcaatttgtgcagGATCCAAAAGAGAAGGCAAAAGCTGAAACAAGAGATTGGCTTAACAATGTG
| | | | | | | | | | | || || ||||| | | | || | | | ||||| || || | | || ||||||||||| ||||| ||||| ||||||||||||||||| |||||||| ||||||
--gacaccaataactcagggtgtgtagtactatttatcttgagctgttgtggacctcattatgcctgtttctggactaataattatttcttatttggtgcagGATCCCAAAGAAAAGGCCAAAGCTGAAACAAGAGACTGGCTTAATAATGTG
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G04690.1 (Glycine max), 3'ss of exon 3
-------------------------gagtcttgatttatcaa----ttatcttttttgtcagtttctgtgta-tgttgcaggattttgc--agctcccctttagtctaatgg-tttattttc--aatttgtg-cagGATCCAAAAGAGAAGGCAAAAGCTGAAACAAGAGATTGGCTTAACAATGTG
| || ||| | ||| | |||| || || | | | |||| ||| || | || ||| |||| | | ||| || || | ||| | ||||||||||||||||||| ||| | || ||||| |||||| | |||||||||
gtgagtctttgaccagggaaatattacctttttgtttgttgtagttttaccactttttggagcttttttttggtgttctttgatcgtgtttatgtcaattttggtctgaggaatttgttatctgactttctaatagGATCCAAAAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTAAACAATGTG
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ20408 (Selaginella moellendorffii), 3'ss of exon 3
gagtcttgatttatcaattatcttttttgtcagtttctgtgtatgttgcaggattttgcagctcccctttagtctaatggtttattttcaatttgtgcagGATCCAAAAGAGAAGGCAAAAGCTGAAACAAGAGATTGGCTTAACAATGTG
|| || ||| ||||| | |||| |||| | | |||| |||||||||||||||| |||||||| |||||| |||| ||| | |||||| ||
--------------------------------------gtaagtgctgc--cattttaga---tttctttggtctgacacgcaac-----gattgtctagGATCCAAAAGAGAAAGCAAAAGCCGAAACACGAGAATGGTTAAACAATATGMapped 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|29630458|gb|CB635467.1|CB635467EST: CTAAAACGAAGGCCTTTTCCAAGGAAGGGTTAGGTCAACAACCGAAAACT GATCCAAAAGAGAAGGCAAAAGCTGAAACAAGAGATTGGCTTAACAATGTG
genomic: CTAAAACGAAGGCCTTTTCCAAGGAAGGGTTAGGTCAACAACCGAAAACTgtaagaactt ... atttgtgcagGATCCAAAAGAGAAGGCAAAAGCTGAAACAAGAGATTGGCTTAACAATGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcaggattttgcagctcccctttagtctaatggtttattttcaatttgtgcagGATCCAAAAGAGAAGGCAAAAGCTGAAACAAGAGATTGGCTTAACAATGTG
gtctaat putative branch site (score: 3)
tttattttcaatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gagtcttgatttatcaattatcttttttgtcagtttctgtgtatgttgcaggattttgcagctcccctttagtctaatggtttattttcaatttgtgcagGATCCAAAAGAGAAGGCAAAAGCTGAAACAAGAGATTGGCTTAACAATGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA