Sequence
atgc intronic sequence ATGC exonic sequence...tgtgctacctagtttccaaagcttgtttatcaattaagatctttgtctttatcttgccttgttttggattattatatgatgtttgtttatctgtttttagTGTCTATATGGTGGTGCTCCAAAAGGCCCCCAGCTAAGAGATTTGGATAGAGGGGTCGATGTCGTTGTTGCTACACCAGGAAGGTTGAATGACATCCTAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g36860.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g36860.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G078826_T02 (Zea mays), 3'ss of exon 3
--------tgtgct-acctagtttccaaagcttgtttatcaattaagatctttg-tctttatcttgccttgttttggattattatatgatgtttgtttatctgtttttagTGTCTATATGGTGGTGCTCCAAAAGGCCCCCAGCTAAGAGATTTGGATAGAGGGGTCGATGTCGTTGTTGCTACACCAGGAAGGTTGAATGACATCCTAG
||| || ||||| || |||||| | | ||||| || | | ||| || | |||||| || || || || |||| ||||||||| |||||||||||||||| ||||| || ||| | |||||||| ||||||||||| ||||| |||||||| ||||| |||||||| ||||||||| | |
tatgatattgtccttgttctgtttctaatatttgtttcagtgtcatgatctctgatttctatttttcattgtttgacctt---------tggttcttgatct-tttttagTGCTTATATGGTGGTGCTCCTAAAGGTCCTCAGTTGAGAGATTTAGATAGAGGGGTTGATGTTGTTGTTGCAACACCTGGAAGGTTAAATGACATCTTGG
upper sequence: LOC_Os01g36860.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G077125_T01 (Zea mays), 3'ss of exon 3
tgtgctacctagtttccaaagcttgtttatcaattaagatctttgtctttatct-tgccttgttttggattattatatgatgtttgttt----atctgtttttagTGTCTATATGGTGGTGCTCCAAAAGGCCCCCAGCTAAGAGATTTGGATAGAGGGGTCGATGTCGTTGTTGCTACACCAGGAAGGTTGAATGACATCCTAG
|| || | | | || | || || || |||| | |||| || || | | | ||| | | | |||| || ||||| || ||||| ||||| ||||||||||| ||||| || ||| | |||||||| ||||||||||| ||||| |||||||| ||||| |||||||| |||||||| | |
-gtacttgttgatctgtgtgactgtctaat--gtttgtctcactgtcatgatctctggtttatat--attcattgtttaacctttggttcttgatctgcttgtagTGCCTATACGGTGGTGCTCCTAAAGGTCCTCAGTTGAGAGATTTAGATAGAGGGGTTGATGTTGTTGTTGCAACACCTGGAAGGTTAAATGACATTTTGGMapped 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|29680158|gb|CB676433.1|CB676433EST: TTTTGGAAGAAGCTGTGAAATTTGGCAGATCATCAAGAATTTCTTCCACG TGTCTATATGGTGGTGCTCCAAAAGGCCCCCAGCTAAGAGATTTGGATAGA
genomic: TTTTGGAAGAAGCTGTGAAATTTGGCAGATCATCAAGAATTTCTTCCACGgtcagttcat ... ctgtttttagTGTCTATATGGTGGTGCTCCAAAAGGCCCCCAGCTAAGAGATTTGGATAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttatcttgccttgttttggattattatatgatgtttgtttatctgtttttagTGTCTATATGGTGGTGCTCCAAAAGGCCCCCAGCTAAGAGATTTGGATAGAGGGGTCGATGTCGTTGTTGCTACACCAGGAAGGTTGAATGACATCCTAG
tctgttttt CT-rich tract
attattatatgatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgctacctagtttccaaagcttgtttatcaattaagatctttgtctttatcttgccttgttttggattattatatgatgtttgtttatctgtttttagTGTCTATATGGTGGTGCTCCAAAAGGCCCCCAGCTAAGAGATTTGGATAGAGGGGTCGATGTCGTTGTTGCTACACCAGGAAGGTTGAATGACATCCTAG
- tgctacc
- - - - - - - - - - gcttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgatgt