Sequence
atgc intronic sequence ATGC exonic sequencegtttgatatcttgtcatgcatatttttcctttcttttaccttagcctatgttcctaaccataaaaaacctttagGGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATGGAGAGGGTTTTGGGTCCACTCCCAGAACACATGATAAGGAAAGCCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g40840.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G366935_T09 (Zea mays), 3'ss of exon 8
gtttgatatcttgtca---tgcatatttttcctttcttttacc---ttagc--ctatgttcctaaccataaaaaacctttagGGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATGGAGAGGGTTTTGGGTCCACTCCCAGAACACATGATAAGGAAAGCCAG
||| ||| ||| ||| | | | |||| || || |||| | | ||| || ||||| | | |||||||||||||||||||||| ||||||||||| || || ||| |||||||||||||||| |||||||| || || ||||| || |||||| ||||| | ||
gttagatctctgctcagttttctcacttttttttcctagtaccagtctggtaattatttttctaacatcacactttttttagGGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG
upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G094039_T06 (Zea mays), 3'ss of exon 7
gtttgatatcttgtcatgcatatttttcctttcttttacctta-gcctatgttcctaaccataaaaaacctttagGGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATGGAGAGGGTTTTGGGTCCACTCCCAGAACACATGATAAGGAAAGCCAG
||| ||| |||| || | | |||| || || | | |||||||| | | |||||||||||||||||||||| ||||| ||||| || || ||| ||||||||||||||||||||||||| || || ||||| | |||||| ||||||| ||
gttagatctcttcacacactttatttttctagtaccagtctggtaattgttttcctaacatcaca--ttttttagGGGGAAGCATTGTTTCAGACACACGAGAATCTGGAACACCTAGCAATGATGGAGAGGGTTTTGGGACCTCTACCAGAGGATATGATACGGAAAGCAAG
upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA06G08480.1 (Glycine max), 3'ss of exon 9
------gtttgatatcttgtcatgcatatttttcctttcttttacct--------tagcctatgt-tcctaaccataaaaaacctt--tagGGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATGGAGAGGGTTTTGGGTCCACTCCCAGAACACATGATAAGGAAAGCCAG
|| |||||| || |||| | | ||| | | ||| || || | |||| | ||| || |||| |||||||||||||| || ||||| ||| | |||||| | ||||||||||| || |||||||| || | ||||| || ||||| | | | |
gtttgtcttccatatctatcaatatgtattaggcatggcttgaatatggaacaactagtcttagtgttctaaatgtggaaacttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA
upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 9
------------gtttgatatcttgtcatgcatatttttcctttcttttaccttagcctatgttcctaa-ccataaaaaacctt--tagGGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATGGAGAGGGTTTTGGGTCCACTCCCAGAACACATGATAAGGAAAGCCAG
| | | | | | || || | | | | | | |||||| | | | || || |||| |||||||| ||||| |||||||||||| | ||||| || || |||||||||||||| ||||| || || ||||| || ||||| ||| || ||
gtcagtccccacttattctgatgtattaagccctgttgtgatatggaacattgtgatcagaactcctaaactgtgtataattttgacagGGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAG
upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S425_6V6.2 (Physcomitrella patens), 3'ss of exon 9
------------------------------------------------------------------------------------------------------gt-ttgatatcttgtcatgcatatttttcctttc--------ttttaccttagcctatgttcctaaccataaaaaacctt------------tagGGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATGGAGAGGGTTTTGGGTCCACTCCCAGAACACATGATAAGGAAAGCCAG
|| || | | ||| || || ||||| || ||| | ||| ||||| ||| ||| ||| |||| || |||||||||||||| || ||||| || ||||| || || ||||||||| | ||||||||||| |||| | |||||||||| || ||
gtatgtggcttcatccctgccttgatcttacctgtaattccatttacaatatatatatatatatatatatatgtcctgtttatttcaacttttattattagtgtactgttgccatgttattcagattttgatactcgtggatattttgagattatggtatgtatctattagtaattgtgcttgtttgcgggtggcagGGTGATGCATTGTTTCAAACTCACGAGAATCTAGAGCATTTGGCTATGATGGAGCGAGTTTTGGGTCCCATCCCTGTGCACATGATAAAGAGGGCAGAMapped 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|58596016|gb|CK006544.1|CK006544EST: TCCCTTGTGACCTTTGGAGTGTCGGATGCATCCTTGTTGAGCTATGCTCG GGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATG
genomic: TCCCTTGTGACCTTTGGAGTGTCGGATGCATCATTGTTGAGCTATGCTCGgtttgatatc ... aaacctttagGGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATG
EST:
gi|86493399|gb|CI136032.1|CI136032EST: TCCCTTGTGACCTTTGGAGTGTCGGATGCATCATTGTTGAGCTATGCTCG GGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATG
genomic: TCCCTTGTGACCTTTGGAGTGTCGGATGCATCATTGTTGAGCTATGCTCGgtttgatatc ... aaacctttagGGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatttttcctttcttttaccttagcctatgttcctaaccataaaaaacctttagGGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATGGAGAGGGTTTTGGGTCCACTCCCAGAACACATGATAAGGAAAGCCAG
tcctaac putative branch site (score: 1)
ccttt putative PPT
ataaaaaaccttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgatatcttgtcatgcatatttttcctttcttttaccttagcctatgttcctaaccataaaaaacctttagGGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATGGAGAGGGTTTTGGGTCCACTCCCAGAACACATGATAAGGAAAGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA