Sequence
atgc intronic sequence ATGC exonic sequenceTGGAACAAATATGAATGTTGAGAGCTCAAGGTCTCATTTAATTCTTTCAATCATTATTGAAAGTACCAACCTCCAGACTCAATCTTATGCAAGAGGAAAGgtatggtgggttgtaactggaaacctcatgctagccttgctgtgtcgcataaccaatttgtttcacaattttttttataaaaaaactatatttgagtatt...
Basic information
species | Oryza sativa |
transcript | LOC_Os04g57140.1 |
intron # | 20 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g57140.2 (Oryza sativa), 5'ss of exon 21
lower sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 20
TGGAACAAATATGAATGTTGAGAGCTCAAGGTCTCATTTAATTCTTTCAATCATTATTGAAAGTACCAACCTCCAGACTCAATCTTATGCAAGAGGAAAGgtatggtgggttgtaactggaaacctcatgctagccttgctgtgtcgcataaccaatttgtttcacaattttttttataaaaaaactatatttgagtatt-----
|||||| |||||||||| |||||| ||||||||||||||||||||||||||||||||||||||||| || ||||| |||||||| ||||||||||| |||||||| || || | ||| ||| | | | | | | | ||| | || ||| || || | | || ||| || ||||| || | ||
TGGAACGAATATGAATGATGAGAGTTCAAGGTCTCATTTAATTCTTTCAATCATTATTGAAAGTACAAATCTCCAAACTCAATCATATGCAAGAGGCAAGgtatgtcaggatgaagctgtgaacttaaccccaatttggtcgagtctagtgac-aatacttt---catctataacaatgaaataaaaatatt-gaatgttctgtc
upper sequence: LOC_Os04g57140.2 (Oryza sativa), 5'ss of exon 21
lower sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 20
TGGAACAAATATGAATGTTGAGAGCTCAAGGTCTCATTTAATTCTTTCAATCATTATTGAAAGTACCAACCTCCAGACTCAATCTTATGCAAGAGGAAAGgtatgg-tgggttgtaactggaaacctcatgctagccttgctgtgtcgcataaccaatttgtttcacaatttttttta-taaaaaaactatatttgagtatt
||||| |||||||||| |||||| |||||||||||||||||||||||| |||||||||||||||| || || || || ||||| ||||||||||| ||||||||| | || | ||| ||| | | | | | | || ||| | |||| || || || | | | |||||| | | | | | |
CGGAACTAATATGAATGATGAGAGTTCAAGGTCTCATTTAATTCTTTCAGTCATTATTGAAAGTACAAATCTTCAAACCCAATCATATGCAAGAGGCAAGgtatggacagaatgaagctgcgaacataactccaatttggttgagtc-tactggcaatactttcgactataataatgaataaaaatattgaacgttc-tgtc
upper sequence: LOC_Os04g57140.2 (Oryza sativa), 5'ss of exon 21
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 21
TGGAACAAATATGAATGTTGAGAGCTCAAGGTCTCATTTAATTCTTTCAATCATTATTGAAAGTACCAACCTCCAGACTCAATCTTATGCAAGAGGAAAGgtatggtgggttgtaactggaaacctcatgctagccttgctgtgtcgcataaccaatttgtttcacaattttttttataaaaaaactatatttgagtatt--------
||| || | ||||||| || || ||||| |||||||| ||||||||||| || |||||||||||||| || || || ||||| ||| ||||||||||||| | || | ||| | | | || | | | | | | | | | | ||||| || || | | || || | | |
TGGCACTCAAATGAATGAAGAAAGTTCAAGATCTCATTTGATTCTTTCAATTATCATTGAAAGTACCAATCTTCAAACCCAATCAGTTGCCAGAGGAAAGgtattatct-ttatcacttggagc---atattctcttgggttaatttctt---tgacctcccctgagattttgccta-aatacacttagtttccattggtttgaaattMapped 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|218496230|gb|FG959153.1|FG959153EST: TCATTATAGAAAGTACCAACCTCCAGACTCAATCTTATGCACGAGGAAAG CTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAGTCCGGCTCA
genomic: TCATTATTGAAAGTACCAACCTCCAGACTCAATCTTATGCAAGAGGAAAGgtatggtggg ... gtgtgaacagCTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAGTCCGGCTCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGGAACAAATATGAATGTTGAGAGCTCAAGGTCTCATTTAATTCTTTCAATCATTATTGAAAGTACCAACCTCCAGACTCAATCTTATGCAAGAGGAAAGgtatggtgggttgtaactggaaacctcatgctagccttgctgtgtcgcataaccaatttgtttcacaattttttttataaaaaaactatatttgagtatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa