Sequence
atgc intronic sequence ATGC exonic sequence...ctcctttttcattagtacatttactgatttaggcttatggttacacatctgtcggattcacatttcactcaattctgtcatggactgtgtgtttctgtagGTACAGCAAGCGGGATTCTCTGCACCAACTCCTATCCAAGCTCAATCATGGCCAATTGCTCTTAGGAATCGTGATATTGTAGCTGTGGCGAAGACAGGTT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g07740.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g07740.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G066440_T01 (Zea mays), 3'ss of exon 5
ctcctttttcattagtacatttactgatttaggcttatggtta--cacatctgtcggattcacatttcactcaattctgtcatggactgtgtgtttctgtagGTACAGCAAGCGGGATTCTCTGCACCAACTCCTATCCAAGCTCAATCATGGCCAATTGCTCTTAGGAATCGTGATATTGTAGCTGTGGCGAAGACAGGTT
| ||| || || || | | | | || || |||| | | ||||| || ||||| |||| | ||| || | |||| | |||||| |||||||||||||||||||||||||||||||| ||||||||||||||| | | | | | ||||| ||||||||||| ||||||||||
gccttttctcgttgctatagactatagtatgaattttgttctaaacacagatataatattcagataatactcatctctg--aaggatatctaccttttccagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAGTCATGGCCAATTGCTATGAAGGGTAGGGATATAGTAGCTGTGGCAAAGACAGGTT
upper sequence: LOC_Os01g07740.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G462134_T01 (Zea mays), 3'ss of exon 2
--ctcctttttcattagtacatttactgatttaggcttatggttacacatctgtcggattcacatttcactcaattctgtcatggactgtgtgtttctgtagGTACAGCAAGCGGGATTCTCTGCACCAACTCCTATCCAAGCTCAATCATGGCCAATTGCTCTTAGGAATCGTGATATTGTAGCTGTGGCGAAGACAGGTT
| ||| || || || | || | | |||| ||||||| | | | ||||| || ||||| |||| | || || || |||| | |||||| |||||||||||||||||| ||||||||||||||||||||||||||||||| ||| ||||||||| |||||| |||||||||||||||
agcctttttctctttgctataactatattatgacttttatccttacacagatctagtattcagataatactcatctctg--aagggtatctaccttttgcagGTTCTGCAAGCAGGATTCTCTGCACCAACTTCTATCCAAGCTCAATCATGGCCAATTGCTCTAAGGGGTCGTGATATAGTAGCTATGGCGAAGACAGGTT
upper sequence: LOC_Os01g07740.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G481227_T01 (Zea mays), 3'ss of exon 2
--ctcctttttcattagtacatttactgatttaggcttatggttacacatctgtcggattcacatttcactcaattctgtcatggactgtgtgtttctgtagGTACAGCAAGCGGGATTCTCTGCACCAACTCCTATCCAAGCTCAATCATGGCCAATTGCTCTTAGGAATCGTGATATTGTAGCTGTGGCGAAGACAGGTT
| ||| || || || | || | | |||| ||||||| | | | ||||| || ||||| |||| | || || || |||| | |||||| ||||||||||||||||||||||||||||||||||||||||||||||||| ||| ||||||||| |||||| |||||||||||||||
agcctttttctctttgctataactatattatgacttttatccttacacagatctagtattcagataatactcatctctg--aagggtatctaccttttgcagGTTCTGCAAGCAGGATTCTCTGCACCAACTCCTATCCAAGCTCAATCATGGCCAATTGCTCCAAGGGGTCGTGATATAGTAGCTATGGCGAAGACAGGTTMapped 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|2310452|gb|C26607.1|C26607EST: CATTCATGACATTTCAGTCCACAGGTTTCCCTCCAGAGATTCTAAGGGAG GTACAGCAAGCGGGATTCTCTGCACCAACTCCTATCCAAGCTCAATCATGG
genomic: CATTCATGACATTTCAGTCCACAGGTTTCCCTCCAGAGATTCTAAGGGAGgtaagtgcac ... gtttctgtagGTACAGCAAGCGGGATTCTCTGCACCAACTCCTATCCAAGCTCAATCATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catctgtcggattcacatttcactcaattctgtcatggactgtgtgtttctgtagGTACAGCAAGCGGGATTCTCTGCACCAACTCCTATCCAAGCTCAATCATGGCCAATTGCTCTTAGGAATCGTGATATTGTAGCTGTGGCGAAGACAGGTT
tgtttct CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcctttttcattagtacatttactgatttaggcttatggttacacatctgtcggattcacatttcactcaattctgtcatggactgtgtgtttctgtagGTACAGCAAGCGGGATTCTCTGCACCAACTCCTATCCAAGCTCAATCATGGCCAATTGCTCTTAGGAATCGTGATATTGTAGCTGTGGCGAAGACAGGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA