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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatcgtgaggcctctgatgtttcctaattactgttacctagtcttaagatgttaacatatctctctcctttttctcag

Basic information

species Oryza sativa
transcript LOC_Os07g42950.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G851698_T02 (Zea mays), 5'ss of exon 3
GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaa-tatcgtgaggcctc------tgatgtttcctaattactgtt-acctagtcttaagatgttaacatatctctctcctttttctcag
 ||||| |||| ||||   |||||||| |||||||||||||| ||||||||||| ||||||| | |  ||    ||       ||||   | |    || || | |  |  |  | |  | |     |       | ||||||  |||
ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCTGGGTGAGgtaaattttctgctttcttatttcttgatccatgccccctattgctgatttcatacttaattataggtgtgatgtgtttcttttttgcag

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G054136_T09 (Zea mays), 5'ss of exon 3
GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatc----gtgaggcctctgatgtttcctaattactgtt-acctagtcttaagatgttaacat-atctctctcctttttct-cag
|||||| |||| ||||   ||||| || |||||||||||||| ||||||||||| |||||||  |      |||    | |  || | | | | |  || | |  |  |  | | || |     | || | | || || || | |||
GCGTGCCTTTTATGACCGAAGGATATCCCAGGAGGTCAGTGGTGATGCTCTGGGTGAGgtaaactttgggatgacttatttcttgatccatgactcttgctgatttcatacttaaatataggtgtgatatgtttctttgttttgcag

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G054136_T05 (Zea mays), 5'ss of exon 3
GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatc----gtgaggcctctgatgtttcctaattactgtt-acctagtcttaagatgttaacat-atctctctcctttttct-cag-----------
|||||| |||| ||||   ||||| || |||||||||||||| ||||||||||| |||||||  |      |||    | |  || | | | | |  || | |  |  |  | | || |     | || | | || || || | |||           
GCGTGCCTTTTATGACCGAAGGATATCCCAGGAGGTCAGTGGTGATGCTCTGGGTGAGgtaaactttgggatgacttatttcttgatccatgactcttgctgatttcatacttaaatataggtgtgatatgtttctttgttttgcaggagttcaaggg

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G054136_T01 (Zea mays), 5'ss of exon 3
GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatc----gtgaggcctctgatgtttcctaa---ttactgttacctagtcttaagatgttaacat-atctctctcctttttct-cag
|||||| |||| ||||   ||||| || |||||||||||||| ||||||||||| |||||||  |     ||||    | |  || | | | |   || ||| |  |     | || || |     | || | | || || || | |||
GCGTGCCTTTTATGACCGAAGGATATCCCAGGAGGTCAGTGGTGATGCTCTGGGTGAGgtaaactttggggtgacttatttcttgatccatgactcttgctgatttcatacttaaaaatataggtgtgatatgtttctttgttttgcag

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA07G31840.3 (Glycine max), 5'ss of exon 2
------------------------------------------GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatcgtgaggcctctgatgtttcctaattactgt---tacctagtctt---aagatgttaacatatc-tctctcctttttctcag--------------
                                           || |||||||  |||||||||||||| ||||||||   ||| ||||||||||| ||||||   |||| || |     || ||     ||   |||   | |||| | ||         |||| | ||  ||| |     |    |               
GGACCAACCTCTGTTATTGTATTCTTATGCTATATATTGCAGTCGAGCATTTTGGGACAAGAGGATCTCCCAGGAGGTTCTTGGTGATGCTCTGGGTGAGgtatgctcgttag-ctggaaatcttattatatctgtgtctgttcctattttttgtggagcattaagaaatgatctattaacctctataactttgccactgaag

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA07G31840.2 (Glycine max), 5'ss of exon 3
GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatcgtgaggcctctgatgtttcctaattactgt---tacctagtctt---aagatgttaacatatc-tctctcctttttctcag--------------
 || |||||||  |||||||||||||| ||||||||   ||| ||||||||||| ||||||   |||| || |     || ||     ||   |||   | |||| | ||         |||| | ||  ||| |     |    |               
TCGAGCATTTTGGGACAAGAGGATCTCCCAGGAGGTTCTTGGTGATGCTCTGGGTGAGgtatgctcgttag-ctggaaatcttattatatctgtgtctgttcctattttttgtggagcattaagaaatgatctattaacctctataactttgccactgaag

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA18G26190.1 (Glycine max), 5'ss of exon 2
GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatcgtgag------gcctctgatgtttcctaattactgttacctagtcttaagatgttaacatatctctctcctttttctcag-------
 || |||||||  |||||||||||||| ||||||||||| || ||||| || || ||||||   || | ||       |||   |||  ||||    | | || |  | | || |    ||| |   || |  || |  |  |  |       
ACGAGCATTTTGGGACAAGAGGATCTCACAGGAGGTCAGCGGAGATGCACTTGGTGAGgtatgctctttagctgctaaccttaaatgcatcctctcaatttttgctgaatttttaatgattatctattcaccttcatgctcttttgccaacag

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT4G31700.1 (Arabidopsis thaliana), 5'ss of exon 3
GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatcgtgaggcctctgatgttt-cctaattactgttac--ctagtcttaagatgttaacatatctctctcctttttctcag---------------
 ||||| ||||  |||||||| |||||||| || |||||||| |||||| |||||||||||        |    ||| |  ||   ||||| | ||| |    |||  ||  || |   | ||     | |  | ||| | |                
ACGTGCGTTTTACGACAAGAGAATCTCTCAAGAAGTCAGTGGAGATGCTTTGGGCGAGgtacagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaagc--agatgatgatgttttgtttatgaattgttgttattgcag

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 5'ss of exon 3
GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatcgtgaggcctctg-atgtttcctaattactgttacctagtcttaagatgt-taacatatctctctcctt-tttctcag--------
 || ||||||||||||||||||||||| |||||||||||||| ||||| || || |||||||     |        |      | || || | ||  || | || ||  |  | | |||||| | | | |  || ||| |  |        
TCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCTCGGAGAGgtaagcatttaccattgttatgcaatgccaaaattctactatc-agactagatttatataacatttatttttgtttgtttgtttgtgtgacag

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 5'ss of exon 3
GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatcgtgaggcctctgatgtttc--ctaattactgttacctagtcttaagatgttaacatatctctctcctttttctcag
||| ||||||||||||||||||||||| |||||||||||||| ||||| ||||| ||||||  ||  ||   |   |  | ||      | || |  ||   |||   | |  | || |  |||||    | | |||  |||
GCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACTGGGTGAGgtatgattttgttactattcttcttaggataacttgccctttgttaggaatgatttattgatgtatcttaagcgtgtttgacag

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 5'ss of exon 3
GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatcgtgaggcctctgatgtttcctaattac----tgttacctagtcttaagatgttaacatatctctctcctttttctcag
 || ||||||| ||||||||||||||| |||||||||| ||| ||||| |||||||||||| |  | |     ||||  |    | || |||     | ||   |  |||    ||  ||  | |  | ||  ||  ||| |||
CCGAGCATTTTATGACAAGAGGATCTCACAGGAGGTCAATGGGGATGCACTGGGCGAGgta-tgccttttctgctcttctcccacttatttatctcatattgtttgatctactaatcatacaaaacatgtcatctgcttcacag

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|29682891|gb|CB679166.1|CB679166
EST:     TTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAG                         GAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGT
genomic: TTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatcgt ... tttttctcagGAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGT
EST: gi|218498560|gb|FG955781.1|FG955781
EST:     GGCGATGCTCTGGGCGAG                         GAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGT
genomic: GGCGATGCTCTGGGCGAGgtaatatcgt ... tttttctcagGAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGT
EST: gi|58675684|gb|CK064371.1|CK064371
EST:     TTTTTGACAAGAGGATCTCTCAGGAGGTCGGTGGCGATGCTCTGGGCGAG                         GAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGT
genomic: TTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatcgt ... tttttctcagGAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGT
EST: gi|58605263|gb|CK033296.1|CK033296
EST:     TTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGTGCGAG                         GAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCA
genomic: TTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGG-GCGAGgtaatatcgt ... tttttctcagGAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCA
EST: gi|58680867|gb|CK069554.1|CK069554
EST:     TTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAG                         GAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGT
genomic: TTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatcgt ... tttttctcagGAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGT
EST: gi|218490056|gb|FG943987.1|FG943987
EST:     TTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAG                         GAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGT
genomic: TTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatcgt ... tttttctcagGAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGT
EST: gi|218494399|gb|FG963390.1|FG963390
EST:     TTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAG                         GAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGT
genomic: TTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatcgt ... tttttctcagGAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGT
EST: gi|218479219|gb|FG969099.1|FG969099
EST:     TTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAG                         GAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGT
genomic: TTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatcgt ... tttttctcagGAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGT

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: 58 (upstream exon), 75 (downstream exon)
Score: 251

GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatcgt ... tttttctcagGAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGTTTCCCTATGAAGCAGGGAGTGCTCACTGCTGGACGTGTCCGCCTTCTTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAGgtaatatcgtgaggcctctgatgtttcctaattactgttacctagtcttaagatgttaacatatctctctcctttttctcag

- - - - - - - - AAGAGG
- - - - - - - -  AGAGGA
- - - - - - - - - GAGGAT