Sequence
atgc intronic sequence ATGC exonic sequenceCAGGGAGTGAAAAATTTGTTTTCTTGCTTTCGACTAGGGCAGGTGGTCTTGGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtccttttcaaatcgtaattttttctcattctacaatttgtgaagttaaaggttatggttatttggtttcacag
Basic information
species | Oryza sativa |
transcript | LOC_Os05g05780.1 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 11
CAGGGAGTGAAAAATTTGTTTTCTTGCTTTCGACTAGGGCAGGTGGTCTTGGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtc-cttttcaaatcgtaattttttctcattctacaatttgtgaagttaaaggttatggttatttggtttcacag-
|||| |||||||| ||||||||||| ||||| |||||||||||||| ||||| || || | || |||||||||||||| ||||||||||||| || ||||||| || | | || | | ||| | | | | | || |||| ||| | | || | || || | |
CAGGAAGTGAAAAGTTTGTTTTCTTACTTTCAACTAGGGCAGGTGGCCTTGGTATCAACTTGGCCACTGCTGATGTTGTGGTTCTTTATGACAGCGATTGgtatgagactatgctaaacttgattctgttgcttaccctaaga-atgaatctaatgcctctgttatttctgtgcctccag
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 8
CAGGGAGTGAAAAATTTGTTTTCTTGCTTTCGACTAGGGCAGGTGGTCTTGGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtccttttcaaatcgtaattttttctcattctacaatttgtgaagttaaaggttatggttatttggtttcacag-----------------
|||| ||||| || ||||||||||| ||||| |||||||||||||| ||||| || || | || |||||||||||||| |||| |||||||| || ||||||| ||| || ||| ||| | | || ||| | | ||| || ||| | ||
CAGGAAGTGAGAAGTTTGTTTTCTTACTTTCAACTAGGGCAGGTGGCCTTGGTATCAACTTGGCCACTGCTGATGTTGTGGTTCTCTATGACAGCGATTGgtatgcgactttgttatgctaaatttagttttgttgcttataccctaagcatgaagccatgaaccttatgttcc-tagtacttctgtgcctccag
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA15G10370.1 (Glycine max), 5'ss of exon 11
CAGGGAGTGAAAAATTTGTTTTCTTGCTTTCGACTAGGGCAGGTGGTCTTGGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtccttttcaaatcgtaattttttc--tcattctaca---atttgtg---aagttaaa--ggttatggttatttggtttcacag---
|||| ||||| |||||||| |||||| | || ||| | || || |||||||| || ||||||||||||||||||||||| ||||| || || |||||||||| || |||||| | || || || ||| | || ||| || ||| | | |||||| | | ||| |||
CAGGAAGTGAGAAATTTGTCTTCTTGTTATCAACTCGTGCTGGAGGTCTTGGTATTAATCTTGCTACTGCTGATGTTGTCATTCTGTACGATAGTGACTGgtcagt--atttcaagtagttatggactcagccatctgatttatatctgtaccaaaattattttgttgatggttggt-gcttttacaacag
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA07G38050.2 (Glycine max), 5'ss of exon 11
CAGGGAGTGAAAAATTTGTTTTCTTGCTTTCGACTAGGGCAGGTGGTCTTGGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgt--atgtccttttcaaatcgtaattttttctcattctacaatttgtgaagttaaaggtt-atggttatttggtttcacag--------------------
|||| |||||||||||||| |||||| | || ||| | || || || ||||| || ||||||||||||||||||||||| |||||||||||||||||||||| | | ||| | | | | | | | || |||| | | | ||| ||| || ||| ||| |
CAGGAAGTGAAAAATTTGTCTTCTTGTTATCTACTCGTGCTGGAGGCCTTGGCATTAATCTTGCTACTGCTGATGTTGTCATTCTTTATGACAGTGACTGgttagtattcttgttgattgtcagcagccttctaacttgca----gtgatgccataagttcatgactaattgtttttgttgataattggtggttataacag
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 11
CAGGGAGTGAAAAATTTGTTTTCTTGCTTTCGACTAGGGCAGGTGGTCTTGGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtccttttcaaatcgtaattttttctcattctacaatttgtgaagtta----aaggttatggttatttggtttcacag--------------------
|||| |||||||||||||| |||||||| || ||| | || || || ||||| || ||||||||||| ||||||||||||||||||||||||||||||||| | | | |||| || | ||| | | || ||| | | ||| | ||| || || ||| |
CAGGAAGTGAAAAATTTGTCTTCTTGCTATCTACTCGCGCTGGAGGCCTTGGCATTAATCTTGCTACAGCTGATGTTGTTATTCTTTATGACAGTGACTGgcaag---tattcatattg--attgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttttgttgataattggtggttataacag
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 11
CAGGGAGTGAAAAATTTGTTTTCTTGCTTTCGACTAGGGCAGGTGGTCTTGGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtcctttt--caaatcgtaattttttctcattctaca-atttgtg---aagttaaa--ggttatggttatttggtttcacag---
|||| ||||| |||||||| |||||| | || ||| | || || |||||||| || ||||||||||||||||||||||| ||||| || || |||||||||| || || | | | || | || | | || ||| || ||| | | |||||| | | ||| |||
CAGGAAGTGAGAAATTTGTCTTCTTGTTATCAACTCGTGCTGGAGGTCTTGGTATTAATCTTGCTACTGCTGATGTTGTCATTCTGTACGATAGTGACTGgtcagtatttctagtagttttgaacacagccatgttatttatatctgtacccaaattattttgttgatggttggt-gcttttacaacag
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 5'ss of exon 11
CAGGGAGTGAAAAATTTGTTTTCTTGCTTTCGACTAGGGCAGGTGGTCTTGGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtccttttcaaatcgtaattttttctcattctacaatttgtgaagttaaaggttatggttatttggtttcacag
|||| ||||| ||||||||||||||| | || ||||| || || || ||||| || |||||||||||||| |||||||| || ||||| || ||||| ||||| ||| | | | | | | | || | | | ||| | | | || | | | |||
CAGGAAGTGAGAAATTTGTTTTCTTGTTATCTACTAGAGCTGGAGGGCTTGGTATCAATCTTGCTACTGCAGATGTTGTGATCCTTTACGATAGTGATTGgtaagtctctcatcattgtccactgtagtttatgaactttctcttcacgtttgacgagtctggcatat--tctggcag
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 5'ss of exon 11
CAGGGAGTGAAAAATTTGTTTTCTTGCTTTCGACTAGGGCAGGTGGTCTTGGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtccttttcaa-----atcgtaattttt-----tctcattctacaatttgtgaagttaaagg-ttatggttatttggtttcacag
|||| ||||| ||||| ||||||||| | || ||||| || || || ||||| || |||||||||||||| |||||||| || || ||||| ||||||||||| | | ||| || ||||||| | | | || || | ||| || || ||||||
CAGGAAGTGAGAAATTCGTTTTCTTGTTATCCACTAGAGCTGGAGGACTTGGTATCAATCTTGCTACTGCAGATGTTGTGATCCTCTATGATAGTGACTGgtaaggctctttttgtgtccattgtaatttatgagtgttttcttttatgcctaatgaggtgggtggattatggcag-------------
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 11
CAGGGAGTGAAAAATTTGTTTTCTTGCTTTCGACTAGGGCAGGTGGTCTTGGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtccttttcaaatcgtaattttttctcattctacaat--ttgtgaa--gttaaaggttatggttatttggtttcacag---------------
| || ||||| |||||||| ||||| || || ||||| || || |||||||| || |||||||||||||| |||||||| || ||||||||||||||||||| | || || | | | || ||| || || || ||| | | ||| |||| | | | || ||||| |
CCGGAAGTGAGAAATTTGTGTTCTTACTGTCAACTAGAGCTGGAGGTCTTGGTATCAATCTTGCTACTGCAGATGTTGTCATCCTTTATGACAGTGACTGgtgagcatttctccatttttttttctttttc-ttttagaatgctagggaattgttatattatttaccaatctggttgatctctttattgcaccgtag
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 11
lower sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 11
CAGGGAGTGAAAAATTTGTTTTCTTGCTTTCGACTAGGGCAGGTGGTCTTGGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtccttttcaaatcgtaattttttctcattc-tacaatttgtgaagttaaaggttatggttatttggtttcacag
||| ||||| || ||| | |||||||||||||| | || || |||||||| || ||| | |||||||| ||| | |||||||| ||||||||||||||||| ||| | |||| |||| | | | ||| ||| ||| | | |
AAGGAAGTGAGAAGTTTATATTCTTGCTTTCGACCCGAGCCGGCGGTCTTGGTATCAATTTGGCTACTGCCGATATCGTTATTCTCTATGACAGTGACTGgtaat---------aataatgatttgttctgagtggcatgtttttagaaattat--gctgcag----------------
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 11
lower sequence: EFJ31365 (Selaginella moellendorffii), 5'ss of exon 11
CAGGGAGTGAAAAATTTGTTTTCTTGCTTTCGACTAGGGCAGGTGGTCTTGGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtccttttcaaatcgtaattttttctcattctacaatttgtgaagttaaaggttatggttatttggtttcacag
||| ||||| || ||| | |||||||||||||| | || || |||||||| || ||| | |||||||| ||| | |||||||| ||||||||||||||||| | | | |||| |||| | | ||| ||| ||| | | |
AAGGAAGTGAGAAGTTTATATTCTTGCTTTCGACCCGAGCCGGCGGTCTTGGCATCAATTTGGCTACTGCCGATATCGTTATTCTCTATGACAGTGACTGgtaat---------agtaatgatttgttctgagtggcatgttttagaaattat--gctgcag----------------Mapped 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|58692379|gb|CK081066.1|CK081066EST: TGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTG GAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGCACATAGAATTGGTCA
genomic: -GGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtcctt ... ggtttcacagGAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGCACATAGAATTGGTCA
EST:
gi|58668270|gb|CK056956.1|CK056956EST: GGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTG GAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGC
genomic: GGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtcctt ... ggtttcacagGAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGC
EST:
gi|58691699|gb|CK080386.1|CK080386EST: GGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTG GAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGCACATAGAATTGGTCA
genomic: GGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtcctt ... ggtttcacagGAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGCACATAGAATTGGTCA
EST:
gi|58694226|gb|CK082913.1|CK082913EST: GGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTG GAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGCACATAGAATTGGTCA
genomic: GGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtcctt ... ggtttcacagGAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGCACATAGAATTGGTCA
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:
74 (upstream exon),
73 (downstream exon)
Score:
50CAGGGAGTGAAAAATTTGTTTTCTTGCTTTCGACTAGGGCAGGTGGTCTTGGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtcctt ... ggtttcacagGAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGCACATAGAATTGGTCAAAAGAAAGAAGTTCAAGTTTTTCGTTTCTGCACTGAG
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAGGGAGTGAAAAATTTGTTTTCTTGCTTTCGACTAGGGCAGGTGGTCTTGGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtccttttcaaatcgtaattttttctcattctacaatttgtgaagttaaaggttatggttatttggtttcacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT