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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgatactgcatgaacaacaaaaaggatatgtggattttactatctagatggtgttgtcaaatgtcatcatttataggctccttc...

Basic information

species Zea mays
transcript GRMZM2G368908_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 5'ss of exon 5
AATGCTACACAGAAA-AGTCAGAAGGTATTTGTCCATGTTCCTTCAG-AAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgatactgcatgaacaacaaaaaggatatgtggattttactatctagatggtgttgtcaaatgtcatcatttataggctccttc-
|||||||| || ||| ||||| ||||| ||||| ||||||||||||| |||| ||||| || || ||||||||||| |||| | ||   | ||||| |  | |  | | || |   | | | | || ||||| | |  || |     | || |  |    | |    ||      ||  
AATGCTACTCAAAAACAGTCAAAAGGTGTTTGTTCATGTTCCTTCAGCAAATAGCTGCCCACGAGGTTGAGGAAATCGgtatgtctgtctcatctgtttttactaggaaaa-agggatgctttatgtattttgcaagttacagataatagttagcttgtttgagcggtaaatatattaa

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA11G34980.1 (Glycine max), 5'ss of exon 5
AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgatactgcatgaacaacaaaaaggatatgtggattttactatctagatggtgttgtcaaatgtcatcatttataggctccttc--------------------------------------------------------------------------
||||| || || |||||||| || || ||||| ||||| || ||||| |||||||||||||||||||||||||| ||||   | ||    ||    | || |  |||           |   |   ||||  | | ||  | || |  |  ||  |    || |  |   || |                                                                            
AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatgccattc----aatgtaaaaactggtcttttttttcttatgttttgtt-tttattttgtttgattcaaaatttctatatgaaaattcttaattttatccataccattgtgtaacctgtttctcctgttttttgtttttttttaaattcttcttacctttgtgcag

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA20G03160.1 (Glycine max), 5'ss of exon 5
----------------AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgatactgcatgaacaacaaaaaggatatgtggattttactatctagatggtgttgtcaaatgtcatcat-----ttataggctccttc---------------------------------------------------------
                ||||| || || |||||||| ||||||||| | ||||| || ||||| |||||| || ||||||||||||||||  ||| | | ||   ||   ||     ||  |            |||||    |||| ||| | | |  || |   |||| ||   ||     ||||    |   ||                                                         
TTTATTCTGTGTACATAATGCCACTCAAAAAAGTCAAAAGGTATTTATACATGTGCCATCAGAGATTGCTACTAATGAAGTTGAGGAAATATgtatgtcatgcc-attcaatgtaaaattgatgtatttcttcttatgttttgttta-tattttgtt--tgattcaaaatttctatatgaaaattatgaattttatccatacaattgtgtaaccagtttctcttgtttttttaattcttcttacctttgtgcag

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA18G03360.1 (Glycine max), 5'ss of exon 5
-AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg----ttgatctgatactg-------------catgaacaacaaaaaggatatgtggattttactatctagatggtgttgtcaaatgtcatc------att-tataggctccttc----------------------------------
 ||||| || || |||||||| ||||| ||||| ||||| || ||||| |||||||||||||||||||||||||| ||||   | ||    |  || | | ||||              |||        | |   | | ||  |   | | |||| |||    |    ||| | |||      ||| | ||  |   |||                                  
GAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAggtatttcatgccattcaatgtaaaactgatgtttttcttcttatgttttgtttatattttgtttgattcaaaatttctatatgaaaattctgaattttatccatacaattgtgtaaccagtttctcctgttttttttaattcttcttacctttgtgca

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 5
AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgta------------agacttgttgatctgat-actgcatgaac-------aacaaaaaggatatgtggatt----ttactatctagatggtgttgtcaaatgt-----catcatttataggctccttc--
|||||||| |||||||| ||||| || || || |||||  || ||||||||||||||||||||||||||||||| ||||            | |   |||  | |||| | | ||| | |       |     || || |||||  ||    ||  | |   || | | || | | |  |     | |||||  |   ||  | |  
AATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATTGCTGCTCATGAAGTTGAGGAAATCGgtatgtccaaaagggaaaacagttcttttgatgatttcatcatctcggttgagttttaaagaaatgtgttttgtgattgttctgaggaagattttctgacacttacctgcgtcattcttgttcttgtacag

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 5
AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagact--------------------tgttgatctgata-ctgcat---gaacaacaaaaaggatatgtggattttactatctagatggtgttgtcaaatgtcatcatttataggctccttc---------------------------------
|||||||| |||||||| ||  |||| ||||| || || ||| |||||||||| ||||||||||||||||||||||||| | ||                    || |  | ||||  |   ||     |  | || || |||  | | |||||  | | |  |   || |  | |      ||| |      || |||                                  
AATGCTACCCAGAAAAGCCAACAGGTTTTTGTACACGTGCCTACAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtatgtctacatggggaaacaaatcctttgatagtttgatttccttatttcagagcataagaatgatgagggaatttttttttttgta-aatgcttccgaggaaactcaatggagtccttcttgcttcgcttacgccagttggttggtcttgaacag

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 5
AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg--ttga------tctgatactgca-tgaacaacaaaaaggatatgtggattttactatctagatggtgttgtcaaatgtcatcatttataggctccttc-------------------------------------------
|||||||| |||||||| |||||||| ||||||||||| || || |||||||||||||||||||||||||||||||||| | | ||    ||      ||| ||  | |  | | |||           | |   | ||   | || || | ||       |  | |||||  ||    | | |                                            
AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtatgtcatgagccgaaaagcttcttattttcctcttagcaatgctttttccctttccgtattctgaacttgaagatgcaaattgactttatcatgaattatttacctttttgaaccttcagtaattaacttcatgtgtcacctttccctag

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv02s0025g01490.t01 (Vitis vinifera), 5'ss of exon 5
AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgatactgcatgaacaacaaaaaggata--tgtggattttactatctagatggtgttgtcaaatgtca--tcatttataggctccttc---------------------------------------------
||||| || |||||||| ||||| || ||||||||  | ||||| |||||||||||||||||||||||||||||||||| | |  | |||     ||||   |   |    | |||  |   | |   |||| ||||   ||       | || |  | |  | || ||| |  |  ||                                              
AATGCCACTCAGAAAAGCCAGAAAGTTTTTGTCCACATACCTTCTGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtatgtcaagctgaaaaactacttattttcctcttagaagtgttcctttcccttttcctattctgaactcaaagacacaattgaatttatatatggattgtttaactttgaatctttaatgataaacttcctacatcacctgccaatag

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|149042715|gb|EE047230.2|EE047230
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTTTTAGGGACGTAAAGGACACAACCATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTG
EST: gi|32930134|gb|CF034946.1|CF034946
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTG
EST: gi|148973687|gb|EE024808.2|EE024808
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTG

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 248

AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 210

AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 146

AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTGCTACAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgatactgcatgaacaacaaaaaggatatgtggattttactatctagatggtgttgtcaaatgtcatcatttataggctccttc

- - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT