Sequence
atgc intronic sequence ATGC exonic sequence...cttagatttgtggacgaaggaagtacttcatctgttattgccatatggaagcagagcacaaggaatgatgcatctattatttggttttgcccccctgcagGAGTGTCAGTAAGGTGCATGATGAATGGTTTGCTGATGAAGAACATGTTCGTAAGGTTGTTGGTTTTCCGGAAAAGCTCATCGAAATGCCAAATGACAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g41470.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 2
--------cttagatttgtggacgaaggaagtacttcatctgttattgccatatggaagcagagcacaaggaatgatgcatctattatttggttttgcccccctgcagGAGTGTCAGTAAGGTGCATGATGAATGGTTTGCTGATGAAGAACATGTTCGTAAGGTTGTTGGTTTTCCGGAAAAGCTCATCGAAATGCCAAATGACAGA
|||||| | | || || | | | || ||| | | | | || || ||| | ||| | |||| ||||||||| |||||||||||||| |||||||||||||||||||| | |||||| ||||| |||||||| || || |||| || ||||||||||||||||||
tacttgattgcttctttgtgtatcgattcagcacatggtgcttatctgtcatttt---tcgtgttgttaattttagtgt-tcgattctaacgtt----caccctacagGAGTGTTAGTAAGGTGCATGACGAATGGTTTGCTGATGAAGAGCGTGTTCGGAAGGTGGTTGGTTTACCAGAGAAGCATATTGAAATGCCAAATGACAGA
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G157933_T01 (Zea mays), 3'ss of exon 1
cttagatttgtggacgaaggaagtacttcatctgttattgccatatggaagcagagcacaaggaatgatgcatctattatttggttttg----cccccctgcagGAGTGTCAGTAAGGTGCATGATGAATGGTTTGCTGATGAAGAACATGTTCGTAAGGTTGTTGGTTTTCCGGAAAAGCTCATCGAAATGCCAAATGACAGA
||| ||| | | |||| || | | || | | || | | | | || | || | | |||| ||||||||| |||||||||||||| |||||||||||||||||||| |||||||| ||||| |||||||| || || |||| || ||||||||||||||||||
cttga--ttgcttctttgtgtatcgattcagggcacatggtgcttatctgtcatttttcgtgt--tgttaatttcagtgttcgattctaatgttcaccctacagGAGTGTTAGTAAGGTGCATGACGAATGGTTTGCTGATGAAGAGCATGTTCGGAAGGTGGTTGGTTTACCAGAGAAGCATATTGAAATGCCAAATGACAGA
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G431691_T01 (Zea mays), 3'ss of exon 1
---cttagatttgtggacgaaggaagtacttcatctgttattgccatatggaagcagagcacaaggaatgatgcatctattatttggttttg----cccccctgcagGAGTGTCAGTAAGGTGCATGATGAATGGTTTGCTGATGAAGAACATGTTCGTAAGGTTGTTGGTTTTCCGGAAAAGCTCATCGAAATGCCAAATGACAGA
| | || | | | || || || || | | | | | | || | | | | || | || | | |||| ||||||||| ||||||||||||||||||||||||||||| ||||| | |||||| ||||| |||||||| || || |||| || ||||||||||||||||||
cttgattgcttctttgtgtatcgatttagggcacatggtgcttatctgtc-------atttttcgtgttgttaatttcagtgttcgattctaatgttcaccctacagGAGTGTTAGTAAGGTGCATGATGAATGGTTTGCTGACGAAGAGCGTGTTCGGAAGGTGGTTGGTTTACCAGAGAAGCATATTGAAATGCCAAATGACAGA
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 2
------cttagatttgtggacgaaggaagtacttcatctgttattgccatatggaagcagagcacaaggaatgatgcatctattatttggttttgcccccctgcagGAGTGTCAGTAAGGTGCATGATGAATGGTTTGCTGATGAAGAACATGTTCGTAAGGTTGTTGGTTTTCCGGAAAAGCTCATCGAAATGCCAAATGACAGA
| | | || ||| || || || || | | | | || | | | | | || || | | || | | ||||||||| |||||||||||||| |||||||||||||||||||| | ||| || |||||||| ||||| || || |||| | ||||||||||||||||||
gtacttcattgtttcttggtgcgttgatttaaggcacatggtgccgatctgt-----cattttttgtgttaatttcagtgtcttgttctaatgt-ccactgtacagGAGTGTTAGTAAGGTGCATGACGAATGGTTTGCTGATGAAGAGCGTGTCCGGAAGGTTGTGGGTTTACCAGAGAAGCATAATGAAATGCCAAATGACAGA
upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 2
cttagatttgtggacgaaggaagtacttcatctgttattgccatatggaagcagagcacaagg----aatgatgcatctattatttggttttgcccccctgcagGAGTGTCAGTAAGGTGCATGATGAATGGTTTGCTGATGAAGAACATGTTCGTAAGGTTGTTGGTTTTCCGGAAAAGCTCATCG---AAATGCCAAATGACAGA
| | | | | | || ||| | | | | | | | ||| | | || | || |||| ||||||||||||||| |||||||||||||||||||| |||||||| | || || |||| |||||| || || || | ||| || | || ||||
----gtactcttcattgatcatgttcttttccagcaggctttaagttatgatgtattatggtgtcttgatgttctaaataaattatgtttttttgaatgcacagGAGTGTCAGTAAAGTGCATGATGAATGGTTTGCAGATGAAGAGAAGGTCCGAAAGGCTGTTGGCTTGTTAGAGAAACCAGTCGTTCAATTCCCTAATGCT---Mapped 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|29623493|gb|CB628504.1|CB628504EST: CTTTCAATTTCAAAGTCAGAAGCATGTGTTCTTCTTCGTAATTATAACTG GAGTGTCAGTAAGGTGCATGATGAATGGTTTGCTGATGAAGAACATGTTCG
genomic: CTTTCAATTTCAAAGTCAGAAGCATGTGTTCTTCTTCGTAATTATAACTGgtaatggcca ... ccccctgcagGAGTGTCAGTAAGGTGCATGATGAATGGTTTGCTGATGAAGAACATGTTCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggaagcagagcacaaggaatgatgcatctattatttggttttgcccccctgcagGAGTGTCAGTAAGGTGCATGATGAATGGTTTGCTGATGAAGAACATGTTCGTAAGGTTGTTGGTTTTCCGGAAAAGCTCATCGAAATGCCAAATGACAGA
ttttgcccccctgc CT-rich tract
tattatttggtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttagatttgtggacgaaggaagtacttcatctgttattgccatatggaagcagagcacaaggaatgatgcatctattatttggttttgcccccctgcagGAGTGTCAGTAAGGTGCATGATGAATGGTTTGCTGATGAAGAACATGTTCGTAAGGTTGTTGGTTTTCCGGAAAAGCTCATCGAAATGCCAAATGACAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA