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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGGAAGGTATTGCCTAATGGACCTGTTGTGATTTCACCTGATGGTTTATTTCCGTCATTGTACCGGGAAGgtaacatcatctctccaatatttacatatccatattcttctattatgacttgctgaataatgattagccttcactgaactactaggatggtctgtataat...

Basic information

species Oryza sativa
transcript LOC_Os05g38710.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38710.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G099481_T01 (Zea mays), 5'ss of exon 7
GATGGGAAGGTATTGCCTAATGGACCTGTTGTGATTTCACCTGATGGTTTATTTCCGTCATTGTACCGGGAAGgtaacatcatctctccaat-atttacatatc--catattcttctattatgacttgctgaataatgattagccttcactgaact----actaggatggtctgtataat-------------------------------------------------------------------------------------
|||||||| | | | || ||||| |||||||| |||||||||||||| || ||||| ||| | ||||| |||||| ||||  | | | || | | ||  ||     |||| |  |  | |||||||||    |   ||||| ||| |  |   | |    | ||   ||| || |    |                                                                                     
GATGGGAAAGCACTACCCAATGGGCCTGTTGTAATTTCACCTGATGGCTTGTTTCCTTCACTCTACCGAGAAGgtgacattttgtttgcagttagttgtatcctgacatagttgttcactatgacttggactaatttgatttgccatatcaatattttccagtaatgtggcctctggcttcatagaaaatcaactgctaatggcttaaaataatgctgctgttattgattttaagcatgatctaatattcctctgtttttcttag

upper sequence: LOC_Os05g38710.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA13G19730.1 (Glycine max), 5'ss of exon 7
GATGGGAAGGTATTGCCTAATGGACCTGTTGTGATTTCACCTGATGGTTTATTTCCGTCATTGTACCGGGAAGgtaa--catcatctctccaatatttacatatccatattcttctattatgacttgctgaataatgattagccttcactgaactactaggatggtctgtataat-
||||| ||    || || ||||||||||| || || ||||||||||| |||||||| ||| | ||||| ||||||    || |      |  | |||           || || | ||  || ||   |   | ||  ||||  |  |    | | |       |    |  |   
GATGGAAAAACCTTACCAAATGGACCTGTGGTTATCTCACCTGATGGATTATTTCCCTCACTTTACCGTGAAGgtggggcacctctaacctgagattagttgtgatggatactgcaatgttgtctatgtagttgattgttagaataaa---gatttcactttctgctaatgcaccc

upper sequence: LOC_Os05g38710.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA19G35930.1 (Glycine max), 5'ss of exon 9
GATGGGAAGGTATTGCCTAATGGACCTGTTGTGATTTCACCTGATGGTTTATTTCCGTCATTGTACCGGGAAGgtaacatcatctctccaatatttacata-tccatattcttctattatgacttgctgaataatgattagccttcactgaactactaggatggtctgtataat-----
||||| |||   || || |||||||||||||| |||||||||||||| |||||||| ||  | ||||| |||||| | | ||  | |  ||| |     || |  |  ||    |  |||  |    | | |  |   ||| |     ||| | |   ||||| |    |  |      
GATGGCAAGACCTTACCGAATGGACCTGTTGTTATTTCACCTGATGGATTATTTCCCTCTCTTTACCGAGAAGgtgaga-cactttt--aatgtgagagtaattaaggttgaattggtattgcaattttagtt-tatgtagtcaattgtgagccat--ggatgatgataacgacttctc

upper sequence: LOC_Os05g38710.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA10G05320.1 (Glycine max), 5'ss of exon 7
GATGGGAAGGTATTGCCTAATGGACCTGTTGTGATTTCACCTGATGGTTTATTTCCGTCATTGTACCGGGAAGgtaacatcatctctccaatatttacatatccatattcttctattatgacttgctgaata-atgattagccttcactgaactactaggatggtc--tgtataat-
||||| ||    || || |||||||||||||| || ||||||||||| |||||||| ||  | ||||| ||||||     || ||||  ||  |     ||    |  |    || |   |  || ||   |  |    ||   |   ||   || ||      ||  | | |  | 
GATGGAAAAACCTTACCAAATGGACCTGTTGTTATATCACCTGATGGATTATTTCCCTCGCTTTACCGAGAAGgtgg-ggcacctct--aacctgagattagttgtgatgga-tactgcaatatgttgttcatgtagccagttattgatgttataataaagatttcactttttgctt

upper sequence: LOC_Os05g38710.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv08s0040g02800.t01 (Vitis vinifera), 5'ss of exon 6
GATGGGAAGGTATTGCCTAATGGACCTGTTGTGATTTCACCTGATGGTTTATTTCCGTCATTGTACCGGGAAGgtaacatcatctctccaatatttacatatccatattcttctattatgacttgctgaataatgattagccttcactgaactactag-gatggtc-tgtataat---------
||||| || |  || |||||||| ||| |||| |||||||||||||| |||||||| ||||| ||||| |||||| | ||| | ||||     |||  |||   ||  | | ||| |   | |    ||    || ||   ||||||  || |||     || ||  | |||| |         
GATGGAAAAGCTTTACCTAATGGGCCTATTGTTATTTCACCTGATGGGTTATTTCCTTCATTATACCGAGAAGgtgagatc-tttctc-----tttggata---attgtttgctacttctaatcatcgatc--tgctttagcttcacataaataccgtcaatagttatttatagttctaggtcc

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|42592169|gb|CK738655.1|CK738655
EST:     CGTCATTGTACCGGGAAG                         TTATACGAAGAGCACCACATGAGTTTAAGATTGCATGTCTGGAG
genomic: CGTCATTGTACCGGGAAGgtaacatcat ... ttcttctcagTTATACGAAGAGCACCACATGAGTTTAAGATTGCATGTCTGGAG
EST: gi|86595618|gb|CI272594.1|CI272594
EST:     ACCTGTTGTGATTTCACCTGATGGTTTATTTCCGTCATTGTACCGGGAAG                         TTATACGAAGAGCACCACATGAGTTTAAGATTGCATGTCTGGAG
genomic: ACCTGTTGTGATTTCACCTGATGGTTTATTTCCGTCATTGTACCGGGAAGgtaacatcat ... ttcttctcagTTATACGAAGAGCACCACATGAGTTTAAGATTGCATGTCTGGAG

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: 66 (upstream exon), 74 (downstream exon)
Score: 20

GATGGGAAGGTATTGCCTAATGGACCTGTTGTGATTTCACCTGATGGTTTATTTCCGTCATTGTACCGGGAAGgtaacatcat ... ttcttctcagTTATACGAAGAGCACCACATGAGTTTAAGATTGCATGTCTGGAG




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