Sequence
atgc intronic sequence ATGC exonic sequencegtagtcctaattacccatcttttggtgattgaactgagaagttcagatccataatgagaataaagtcatcacatactacttatttggaaataatttcacattgatgttttagtgtaatccatgcattttgttaaatgatccatttcaccagGTGAAATACAAGAATATGACGCCTTCTACAGCTTTTGAGCATGTGCGGTCTAAAAGGGCTCGAGTGTTGCTGACTCGTTCTCAATGGAGG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05870.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05870.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G863550_T01 (Zea mays), 3'ss of exon 4
--------------------gtagtcctaattacccatcttttggtgattgaactgagaagttcagatccataatgagaataaa-gtcatcacatactacttatttggaaataatttcacattgatgttttagtgtaatccatgcattttgttaaatgatccattt-caccagGTGAAATACAAGAATATGACGCCTTCTACAGCTTTTGAGCATGTGCGGTCTAAAAGGGCTCGAGTGTTGCTGACTCGTTCTCAATGGAGG
| || | || | | | | ||| ||||||| ||||| | ||||||||||| ||| || || |||||||| | |||||| ||||| |||| ||| | | |||||||| || | | | | |||| || ||||| ||||||||||||||||| ||| || ||||||| |||||||| ||||||||||||||||||||| || |||| | ||| ||||||| |
gtaaatttaattatttatctcttgttaagaataataacatgctagaacctgagctgagaacttcag-ttcataatgagaagaaaagttatagcatactacctgcttggaatgggtttcaaattg-tgtcaggg-gcaatccatgttttatcgtggttcttaaattttcatcagGTCAAATACAAGAATATGACACCTGCTGCAGCTTTCGAGCATGTACGGTCTAAAAGGGCTCGAGTGCTGTTGACACATTCGCAATGGAAG
upper sequence: LOC_Os06g05870.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G863550_T02 (Zea mays), 3'ss of exon 4
--------------------gtagtcctaattacccatcttttggtgattgaactgagaagttcagatccataatgagaataaa-gtcatcacatactacttatttggaaataatttcacattgatgttttagtgtaatccatgcattttgttaaatgatccattt-caccagGTGAAATACAAGAATATGACGCCTTCTACAGCTTTTGAGCATGTGCGGTCTAAAAGGGCTCGAGTGTTGCTGACTCGTTCTCAATGGAGG----------
| || | || | | | | ||| ||||||| ||||| | ||||||||||| ||| || || |||||||| | |||||| ||||| |||| ||| | | |||||||| || | | | | |||| || ||||| ||||||||||||||||| ||| || ||||||| |||||||| ||||||||||||||||||||| || |||| | ||| ||||||| |
gtaaatttaattatttatctcttgttaagaataataacatgctagaacctgagctgagaacttcag-ttcataatgagaagaaaagttatagcatactacctgcttggaatgggtttcaaattg-tgtcaggg-gcaatccatgttttatcgtggttcttaaattttcatcagGTCAAATACAAGAATATGACACCTGCTGCAGCTTTCGAGCATGTACGGTCTAAAAGGGCTCGAGTGCTGTTGACACATTCGCAATGGAAGGTACTGAAAAMapped 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|58693134|gb|CK081821.1|CK081821EST: ATTGCAAAGCTGGGAGGGGCAGGAGTACAACTATTGTCTTGTGTTATCTG GTGAAATACAAGAATATGACGCCTTCTACAGCTTTTGAGCATGTGCGGTCT
genomic: ATTGCAAAGCTGGAAGGGGCAGGAGTACAACTATTGTCTTGTGTTATCTGgtagtcctaa ... atttcaccagGTGAAATACAAGAATATGACGCCTTCTACAGCTTTTGAGCATGTGCGGTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacattgatgttttagtgtaatccatgcattttgttaaatgatccatttcaccagGTGAAATACAAGAATATGACGCCTTCTACAGCTTTTGAGCATGTGCGGTCTAAAAGGGCTCGAGTGTTGCTGACTCGTTCTCAATGGAGG
cattgat putative branch site (score: 4)
tccatttc putative PPT
attttgttaaatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtcctaattacccatcttttggtgattgaactgagaagttcagatccataatgagaataaagtcatcacatactacttatttggaaataatttcacattgatgttttagtgtaatccatgcattttgttaaatgatccatttcaccagGTGAAATACAAGAATATGACGCCTTCTACAGCTTTTGAGCATGTGCGGTCTAAAAGGGCTCGAGTGTTGCTGACTCGTTCTCAATGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG