Sequence
atgc intronic sequence ATGC exonic sequencegttagttgtctactgatgtcattcttcagctattgtaagatgctcaatcataatccccctagctgttcttctttacagGCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTACAGAGACATGGCCTTAGCTGTGAAAAATCCCTGCCATCTCAACATGGCCG
Basic information
species | Oryza sativa |
transcript | LOC_Os12g05090.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g05090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G133624_T01 (Zea mays), 3'ss of exon 5
gttagttgtctactg-atgtcattcttcagctattgtaagatgctcaatcataatccc-cctagctgttcttctttacagGCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTACAGAGACATGGCCTTAGCTGTGAAAAATCCCTGCCATCTCAACATGGCCG
|||||| | | || | | | | | | | || | || | || | | | | | ||||||| | ||||||| |||||||||||||| |||||||||||||||||||| ||||| |||||||||||||||||||| |||||||||||||| ||||||||||| ||||| |
gttagtagcatgctatactttggacatta-ttgtagttatcagcatattctgatttcagtcgacctgttctcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTACAGAGACATGGCCTTGGCTGTGAAAAATCCATGCCATCTCAATATGGCTG
upper sequence: LOC_Os12g05090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G01080.1 (Glycine max), 3'ss of exon 5
---------------------------------------------gttagttgtctactgatgt-cattcttcagctattgtaagatgctcaatcataatccccctagctgttcttctttacagGCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTACAGAGACATGGCCTTAGCTGTGAAAAATCCCTGCCATCTCAACATGGCCG
||| | || | || | |||| |||| | | | | | || | | | | | ||||| ||||| |||||||| ||||| ||||| |||||||| || |||||||||||||| ||||| ||||| | || || || ||||| |||||||| |||||||| |
gttacacacttatgtttcttgtgctcttcttaataattcttcgctgttcttaatccatggaaatatcttctctttttattttgggttatttga-caaatttgtgattgtcttggttcttgtcagGCCATTGCATATATGGGAGATGACTTCATGTTCCAGTTGTTTGGGAAGTATAGAGATATGGCTCTGGCAGTAAAGAATCCATGCCATCTTAACATGGCAG
upper sequence: LOC_Os12g05090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G36250.1 (Glycine max), 3'ss of exon 6
-----------------------------------gttagttgtctactga--tgtcattcttcagctattgt---aagatgctcaatcataatccccctagctgttcttctttacagGCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTACAGAGACATGGCCTTAGCTGTGAAAAATCCCTGCCATCTCAACATGGCCG
|| | | | || | || |||||| |||| | | || | | || | | | | | ||||| ||||| || ||||| ||||| ||||| |||||||| || |||||||||||||| ||||| ||||| | ||||| || ||||| |||||||| |||||||| |
gttacacacttatgtttcttgtgctcttctacataattcttaacccatggaaatttctttcttctcttattattttgggttgtttga-caaatttgtggttgtcttggttcttgtcagGCCATAGCATATATGGGAGATGACTTCATGTTCCAGTTGTTTGGGAAGTATAGAGATATGGCTCTGGCTGTAAAGAATCCATGCCATCTTAACATGGCAG
upper sequence: LOC_Os12g05090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G21640.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------------------------------gttagttgt--ctactgatgtcattcttcagctattgtaagatgctcaatcataatccccctagctgttcttct-ttacagGCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTACAGAGACATGGCCTTAGCTGTGAAAAATCCCTGCCATCTCAACATGGCCG
| || | || ||| ||| ||| |||| | | | | | ||| | || || ||||| || |||||||||||||| ||||| |||||||| ||| |||||||||| || ||||| ||||| || ||||| || |||||||| ||||| || |
gttatgcatctctctctatctctatctctctttccaacaattacggtcaaagtttaggttttcaggcatacttagtga-gtctgctcgaggctcttgtgtcttctttcggcttttgattagtcatggttttgctgtttcagGCCATAGCATACATGGGGGACGATTTTATGTTTCAGCTGTATGGGAAGTACCAGGATATGGCTTTAGCAGTTAAAAACCCATGCCATCTTAACATAGCAG
upper sequence: LOC_Os12g05090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv13s0064g00580.t01 (Vitis vinifera), 3'ss of exon 6
--------gttagttgtctactgatgtcattcttcagctattgta-agatgctcaatcataatccccctagctgttcttctttac-agGCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTACAGAGACATGGCCTTAGCTGTGAAAAATCCCTGCCATCTCAACATGGCCG
|| | || || | | || | || | |||| || | | | || | || || || |||| || ||||| ||||| ||||| |||||||| || ||||||||||||||| | |||||||| || |||||||| ||||| ||||| || |||||||| |
gttacatacttgctcctcagtcaatattggtgttttgagtttatgcagattttcttcctcttttgacaaagtccctttttttaaccagGCCATAGCATATATGGGAGATGACTTCATGTTCCAGTTGTTTGGGAAGTACCGTGACATGGCTTTGGCTGTGAAGAATCCATGCCACCTTAACATGGCAG
upper sequence: LOC_Os12g05090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S364_48V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------gttagttgtctactgatgtcattcttcagctattgtaagatgctcaa-tcataatccccctagctgttcttctttacagGCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTACAGAGACATGGCCTTAGCTGTGAAAAATCCCTGCCATCTCAACATGGCCG
| || | | | || ||| || | | | |||| | |||| || | || ||| || ||||| | || |||||||| ||||| |||||||||||| | ||||| |||||| ||||||||| | || || |||||||| || ||||||||| | ||
catttttggggcaaaagcgaattttgaggaagacatttaggttattgttgggtgttgtcactccaatcaagttctaattccgcgagtggttgg--ttggtagGCACTCGCTTACATGGGTGATGACTTCATGTTTCAACTCTTTGGCAAGTACCACGACATGGCCATTGCAGTAAAAAATCCGTGTCATCTCAACCTTGCTAMapped 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|86495605|gb|CI138238.1|CI138238EST: AATATTTCAAAGAAAAGAAGTTCGAGGAGGCTATGCAGCAATATGAAATG GCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTAC
genomic: AATATTTCAAAGAAAAGAAGTTCGAGGAGGCTATGCAGCAATATGAAATGgttagttgtc ... ttctttacagGCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTAC
EST:
gi|58693080|gb|CK081767.1|CK081767EST: AATATTTCAAAGAAAAGAAG-TCGAGGAGGCTATGCAGCAATATGAAATG GCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTAC
genomic: AATATTTCAAAGAAAAGAAGTTCGAGGAGGCTATGCAGCAATATGAAATGgttagttgtc ... ttctttacagGCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTAC
EST:
gi|24208446|gb|AU225473.1|AU225473EST: AATATTTCAAAGAAAAGAAGTTCGAGGAGGCTATGCAGCAATATGAAATG GCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTAC
genomic: AATATTTCAAAGAAAAGAAGTTCGAGGAGGCTATGCAGCAATATGAAATGgttagttgtc ... ttctttacagGCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTAC
EST:
gi|58688118|gb|CK076805.1|CK076805EST: AATATTTCAAAGAAAAGAAGTTCGAGGAGGCTATGCAGCAATATGAAATG GCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTAC
genomic: AATATTTCAAAGAAAAGAAGTTCGAGGAGGCTATGCAGCAATATGAAATGgttagttgtc ... ttctttacagGCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTAC
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
72 (upstream exon),
69 (downstream exon)
Score:
8AGTGGAAGAAAGGATTGAAGCAGCAGACAGGAGGAAGATTGAAGGCAATGAATATTTCAAAGAAAAGAAGTTCGAGGAGGCTATGCAGCAATATGAAATGgttagttgtc ... ttctttacagGCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTACAGAGACATGGCCTTAGCTGTGAAAAATCCCTGCCATCTCAACATGGCCG
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcagctattgtaagatgctcaatcataatccccctagctgttcttctttacagGCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTACAGAGACATGGCCTTAGCTGTGAAAAATCCCTGCCATCTCAACATGGCCG
tccccctagctgttct CT-rich tract
aatcataat TA-rich tract