Sequence
atgc intronic sequence ATGC exonic sequenceGAAATTATATTCTCTTTGCTACCTGCGTGCAAGGAGCCTGATCCTGACACTGGTATTCCTTTCAAAGTGGATGCTATCATTGCTAACCCTCCAGCATATGgtcagtatatcttaccagctttggattgatttcttgcgctttgctttactttctctctaccttacaagtgtaactccaagtttgtttattatatgctcaa...
Basic information
species | Oryza sativa |
transcript | LOC_Os04g04254.1 |
intron # | 5 |
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 5
lower sequence: GRMZM2G007721_T01 (Zea mays), 5'ss of exon 3
GAAATTATATTCTCTTTGCTACCTGCGTGCAAGGAGCCTGATCCTGACACTGGTATTCCTTTCAAAGTGGATGCTATCATTGCTAACCCTCCAGCATATGgtcagtatatcttaccagctttggattga---tttcttgcgctttgctttactttctctctaccttacaagtgtaactccaagtttgtttattata--tgctcaa
|||||||| || |||||||| ||||| |||||||| ||||||||||||||||| |||||||| || || ||||| || ||||| ||||| || || ||||||||||||| ||| |||| | | || | | |||||||| |||||| | | || || |||| ||| | | | | || |
GAAATTATTTTTTCTTTGCTGCCTGCATGCAAGGAACCTGATCCTGACACTGGCATTCCTTTTAATGTTGATGCAATTATTGCGAACCCACCCGCGTATGgtcagtataccttgttcattttgaaaaaaaggttcttcacagtttgctttg-tttctcacc-cgttgtaattgtagctctagagacaatccccaaagttgtt---
upper sequence: LOC_Os04g04254.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S281_20V6.1 (Physcomitrella patens), 5'ss of exon 7
GAAATTATATTCTCTTTGCTACCTGCGTGCAAGGAGCCTGATCCTGACACTGGTATTCCTTTCAAAGTGGATGCTATCATTGCTAACCCTCCAGCATATGgtcagtatatcttaccagctttggattgatttcttgcgctttgctttactttctctctaccttacaagtgtaactccaagtttgtttattatatgctcaa---
||| | | ||| | ||||| || |||| | || ||| || ||||||| ||||| | | | ||||| |||||||||||||||||||||||| | | | ||| | || | ||||| | || | | | | | | | | |||| | ||| |
TCGATTGTGTATTCTCTACTACCAGCTTGCACTCAACCAGATTTACACTCTGGTATCCCTTTTCAGGCACAGGCTATAATTGCTAACCCTCCAGCATATGgtatgcaagttttagaacctccaatct--tttctaattttccaaatttttcgagtgatggccttcttggaca-cagcaagcaaggaagggatacaacaataat
upper sequence: LOC_Os04g04254.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S245_59V6.1 (Physcomitrella patens), 5'ss of exon 8
GAAATTATATTCTCTTTGCTACCTGCGTGCAAGGAGCCTGATCCTGACACTGGTATTCCTTTCAAAGTGGATGCTATCATTGCTAACCCTCCAGCATATGgtcagtatatcttaccagct-ttggattgatttct-tgcgctttgctttactttctctctaccttacaagtgtaactccaagtttgtttattatatgctcaa
|||| | ||||| || || || |||| | ||||| | |||| || ||||| ||| | ||||||||||| |||||||||||||||||| | ||| | | | ||| ||| | | | ||| || | | | |||||| | || ||| || | || ||||
TCAATTGTGCATTCTTTACTCCCAGCTTGCACTCAACCTGACTTAGCTTCTGGCATCCCTTTTCAAGCACAAGCTATCATTGCCAACCCTCCAGCATATGgtacacacatcacagaacttcttgtattagtctaaattttagttgtttgggtaatggttctctctacaagagcaag-ccataaacgtatga-atcccctcacMapped 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|42793914|gb|AB117813.1|AB117813EST: TGGTATTCCTTTCAAAGTGGATGCTATCATTGCTAACCCTCCAGCATATG GACATACTCATGTGGCAGAGGCACTAAAAGTACCTATTCATATATTCTTTA
genomic: TGGTATTCCTTTCAAAGTGGATGCTATCATTGCTAACCCTCCAGCATATGgtcagtatat ... gattattcagGACATACTCATGTGGCAGAGGCACTAAAAGTACCTATTCATATATTCTTTA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAAATTATATTCTCTTTGCTACCTGCGTGCAAGGAGCCTGATCCTGACACTGGTATTCCTTTCAAAGTGGATGCTATCATTGCTAACCCTCCAGCATATGgtcagtatatcttaccagctttggattgatttcttgcgctttgctttactttctctctaccttacaagtgtaactccaagtttgtttattatatgctcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA