Sequence
atgc intronic sequence ATGC exonic sequenceAGCAGACATATCTGTGAGGCCTCCTATGGATATTGTTATTCTTATTGTGGGCACAAGAGGTGATGTTCAGCCATTCATTGCTATAGGCAAACGCTTACAGgttagatcaaaagctaccattgtttgttaatttcacattattttatctctcatcaggtgaactattttgcttctcaagcttaatgtttctaaatacatggtttctgtatgactaggattatccattacctgttttttttag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g04254.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g04254.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G007721_T01 (Zea mays), 5'ss of exon 1
AGCAGACATATCTGTGAGGCCTCCTATGGATATTGTTATTCTTATTGTGGGCACAAGAGGTGATGTTCAGCCATTCATTGCTATAGGCAAACGCTTACAGgttagatcaaaagctaccattgtttgttaatttcacattattttatctctcatcaggtgaactattttgcttctcaagcttaatgtttctaaatacatggtttctgtatgactaggattatccattacctgttttttttag
| | || ||| |||||||||||| | || ||||| ||||||||||| ||| |||| ||||| |||||||| ||||||| || ||| | ||||||||||| | || | || | ||| | || || | |||||| | | || ||||||| | | | ||| || | | | || | ||
AACGGAGATACTATACAGGCCTCCTATGCAAATAGTTATACTTATTGTGGGTACACGAGGAGATGTGCAGCCATTTGTTGCTATCGGGAAATGTTTACAGgttagtcta---gcctaagtgtattatcaatccagttctcttgtaaat----tcaggttaggt-ttgtgcttcttgtagcagaaatgccagcatatttgtcgtttctgatccttgtcgtag--------------------
upper sequence: LOC_Os04g04254.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S110_116V6.1 (Physcomitrella patens), 5'ss of exon 5
AGCAGACATATCTGTGAGGCCTCCTATGGATATTGTTATTCTTATTGTGGGCACAAGAGGTGATGTTCAGCCATTCATTGCTATAGGCAAACGCTTACAGgttagatcaaaagctaccattgtttg--ttaatttcacattattttatctctcatcaggtgaactattttgcttctcaagcttaatgtttctaaatacatggtttctgtatg--actaggatt-atccattacctgtt----ttttttag-------------------------
|| | | |||||| || | || || || || ||||| |||||| | || |||||||||||||| ||||||| ||||||| ||||||||| || || |||| | ||||| ||| |||| | | | ||| | | | |||| | | ||| | | | ||| | | || ||| |||| | |||| ||| || | ||
GAATGATCAAAGTCCAGTTCCTCCTTTGAAAATAGTCATGCTCATTGTTGGCACACGTGGGGATGTTCAGCCATTTGTTGCTATCGGCAAACAGTTACAGgtt--attgaatttggtcatttccagagttaatatcattttataagaaatttttaatggtttattttgttgcaatgaattttaaattctattggcaatgaggtgtgcttgtggcacttggatggagtttttacaagttaagtttctctaataaaaaatatcccaatacgctgcag
upper sequence: LOC_Os04g04254.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S159_62V6.1 (Physcomitrella patens), 5'ss of exon 4
AGCAGACATATCTGTGAGGCCTCCTATGGATATTGTTATTCTTATTGTGGGCACAAGAGGTGATGTTCAGCCATTCATTGCTATAGGCAAACGCTTACAGgtt----agatcaaaagctacca-----ttgtttgttaatt--tcacattattttatctc--tcatcaggtgaactattttgcttc--tcaagctta-----atgtttctaaatacatggtttct-gtatgactaggatt-atccattacctgttttttttag------------------------------------
||| | | | ||||| | | || || || || || || || || | |||||||||||||| ||||||||||| |||||| ||||||||| | || | | | || |||||| || | | | | ||| || | || || | | ||||| || | || || ||| || || | ||| || | | |||| || | || | || || ||
GAATGACCAAAATCCAATTCCTCCACTTAAAATAGTCATGCTCATCGTTGGTACTCGTGGTGATGTTCAGCCGTTCATTGCTATCGGCAAAAAGTTACAGgttttataaattggtcgttttctggattttatttgttcataggttagctattcctatttcaatgttcttatgcagt-ttttgttttagttgaggctattaacatgcaataaagtaggttgttacttgcagcactacaatggaaatatcatgagtagttgttgtgggacaacacaagtgaacctgattatgtttttgcagMapped 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|29623072|gb|CB628083.1|CB628083EST: GCACAAGAGGTGATGTTCAGCCATTCATTGCTATAGGCAAACGCTTACAG GATTATGGACACCGTGTGAGATTGGCAACCCATGCAAACTTTAAGGAGTTC
genomic: GCACAAGAGGTGATGTTCAGCCATTCATTGCTATAGGCAAACGCTTACAGgttagatcaa ... ttttttttagGATTATGGACACCGTGTGAGATTGGCAACCCATGCAAACTTTAAGGAGTTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGCAGACATATCTGTGAGGCCTCCTATGGATATTGTTATTCTTATTGTGGGCACAAGAGGTGATGTTCAGCCATTCATTGCTATAGGCAAACGCTTACAGgttagatcaaaagctaccattgtttgttaatttcacattattttatctctcatcaggtgaactattttgcttctcaagcttaatgtttctaaatacatggtttctgtatgactaggattatccattacctgttttttttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG