Sequence
atgc intronic sequence ATGC exonic sequencegttaatttctgtctattctcatgcttcaacccttttttggtcgtcttgattcctaacaatatctcatatcttgcagGCATATACAAGTCAAATAGTAGTCATGGTGATGGTGGCCTTGGCTGTTGGATCTGATCAAATATCCACCCAAGTTAGACGTCAAGCTATCATCAGTGGTC
Basic information
species | Oryza sativa |
transcript | LOC_Os12g03720.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g03720.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G005849_T03 (Zea mays), 3'ss of exon 6
------------------------------------------------------------------------gttaatttctgtctattctcatgcttcaacccttttttggtcgtcttgat-tcctaacaatatctcata------tcttgcagGCATATACAAGTCAAATAGTAGTCATGGTGATGGTGGCCTTGGCTGTTGGATCTGATCAAATATCCACCCAAGTTAGACGTCAAGCTATCATCAGTGGTC
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gttggttggtctatataagtttttccctttgcaacgtgctccctttttttgtagctatccattgtcaccataactgaattctcatcataactgaaagaaggtacttagttttttatcctgaaatcctaacaacacctgacaatccaatcttgcagGCTTATACAAGTCAAATAGTAGCCATGGCGATGATGGCGTTGGCTATTGGGTCCGATCAGATATCTACTCAAGCTAGGAGGGACAGTATCATCAGTGGAC
upper sequence: LOC_Os12g03720.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G180155_T01 (Zea mays), 3'ss of exon 2
------------------------------------gttaatttctgtc-tattctcatgcttcaacccttttttggtcgtcttgattcctaacaatatctcata-tcttgcagGCATATACAAGTCAAATAGTAGTCATGGTGATGGTGGCCTTGGCTGTTGGATCTGATCAA----ATATCCACCCAAGTTAGACGTCAAGCTATCATCAGTGGTC
| |||| ||| || | | | | ||||| | || | |||||||| | || | | |||||||||||||||||||||||||||||| ||||||||| |||| |||||| | ||||| || ||| ||||| || | || |||| | || ||||||||||
gttggtctatataagttttccctccgttttatagctatccattttcgtcataactgaaagaaggtattcattttttttttcctgaagtcctaacagcacctgacaatcttgcagGCATATACAAGTCAAATAGTAGCAATGGTGATGATGGCGTTGGCTATCGGATCCGACCAATAATATATCTACTCGAGCTAGAAGGAAAATTATCATCAGT----
upper sequence: LOC_Os12g03720.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA09G38460.1 (Glycine max), 3'ss of exon 7
------------------------gttaatttctgtctattctca--tgcttcaacccttttttggtcgtc--ttgattcctaacaatatctcatatcttgcagGCATATACAAGTCAAATAGTAGTCATGGTGATGGTGGCCTTGGCTGTTGGATCTGATCAAATATCCACCCAAGTTAGACGTCAAGCTATCATCAGTGGTC
||| ||| | ||| | || | | ||| ||| | || | || | || | | | | || ||||||||||||||||||||||||| ||||| ||| | || | || | ||| ||| ||| || | |||| ||| | |||||||||| |||||
gtaaatgttgcatttaaggatgttgttttcttcatttcattttatattgtcttattacttgtttaaccaatgttttactctcatgcatttataac-tactgtagGCATATACAAGTCAAATAGTAGTGATGGTCATGTTAGCTCTTGCAATAGGAGGCGATACAATTTCAAATCAAGCCAGAAGAGAAGCTATCATAGATGGTCMapped 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|8857882|gb|AU095200.1|AU095200EST: GTGGAGTTCATATCAATGCTGGNTGTGAAATAGGTGTTGCTAGTACCAAG GCATATACAAGTCCAATAGTAGTCATGGTGATGGTGGCCCTTGGCTGTTGG
genomic: GTGGAGTTCATATCAATGCTGGTTGTGAGATAGGTGTTGCTAGTACCAAGgttaatttct ... tatcttgcagGCATATACAAGTCAAATAGTAGTCATGGTGATGGTGGCC-TTGGCTGTTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttcaacccttttttggtcgtcttgattcctaacaatatctcatatcttgcagGCATATACAAGTCAAATAGTAGTCATGGTGATGGTGGCCTTGGCTGTTGGATCTGATCAAATATCCACCCAAGTTAGACGTCAAGCTATCATCAGTGGTC
tcctaac putative branch site (score: 1)
taacaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaatttctgtctattctcatgcttcaacccttttttggtcgtcttgattcctaacaatatctcatatcttgcagGCATATACAAGTCAAATAGTAGTCATGGTGATGGTGGCCTTGGCTGTTGGATCTGATCAAATATCCACCCAAGTTAGACGTCAAGCTATCATCAGTGGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT