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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattctgcatgtttttctcttctctactatataaagcatcattttccacggttccatgtcctctactcccccacatttaaatggtaaaaaagctaa...

Basic information

species Zea mays
transcript GRMZM2G087212_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 5'ss of exon 9
GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattctgcatgtttttctcttctctactatataaagcatcattttccacggttccatgtcctctactcccccacatttaaatggtaaaaaagctaa---------------------------------------------
 ||||||||||||||||| |||||||| ||||||||||| |||||||||||||| |||||||||||||||||||| ||||| ||||||||||| |||||| ||||  || | |   | || |        |    | |  | ||| ||  | |  ||   |  | |   |    || ||||| |  ||   ||                                               
ACGAGGAGCTATCATCACGACCTTCATCGTGTGCTACGCCCTTACATCTTTCATTTCTGGATATGTTAGTGGTGGCCTCTACTCAAGGAATGGCGgtatgtttctatatatatagtttttgttgttggacttgcccgttttattctactatcc--tgaaatagattattcagttttgaaatgtttcaatttctgtgtttcttatctactgttcactgaatccatttctgatccatggcag

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 9
GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattctgcatgtttttctcttctctactatataaagcatcattttccacggttccatgtcctctactcccccacatttaaatggtaaaaaagctaa
 |||||||| ||  |||||||||||||||| ||||| ||||| ||||||||||| ||||| ||||| ||||| ||  | || ||| | ||||| |||| || | |||||   | | |  |   |  |   |   |      | ||  |   |  |||     ||   ||   | | ||| |   |          
ACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGGgtaagaatttgcattgatctttgctacatgtttgtttgggtgcttctctctccctctgaatga---ttataaccgtgcttataattttcag---------

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA05G30210.1 (Glycine max), 5'ss of exon 9
GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattctgcatgtttttctcttctctactatataaagcatcattttccacggttccatgtcc-tctactcccccacattt-aaatggtaaaaaagctaa----------------
||||||||| ||  |||| || ||||||||||| || ||||| ||||||||||| ||||| ||||| ||||| ||  | || ||| | ||||| |||| |  ||| | | |  || |||             ||| ||   |||    || |   | ||  ||| |||       |||  |||| | |   | ||||                
GCGAGGAGCCATTGTCACTACTTTCATTGTGTGTTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGGATGTACTCACGAAATGGGGgtaagtatcttctt-taattttctgtatattcgctccaagtatg--tttgggtggctttgtctcagtcttctctttttggttttgaatgattatgcaactaatttttatgtttgttag

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 9
GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattctgcatgtttttctcttctctactatataaagcatcattttccacggttccatgtcctctactcccccacatttaaatggtaaaaaagctaa----------
 |||||||| ||  |||||||||||||||| ||||| ||||| ||||||||||| ||||| ||||| ||||| ||  | || ||| | ||||| |||| ||||| ||||   | | |  |   |  | | |  |   |   |||    |  ||  | ||     ||| | | |      ||  | |    ||| |          
ACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGGATGTACTCACGTAATGGGGgtaagattc-gcattgatctatgctacatgttctcttga-tgtttgtttaggtgcctctctctctctctctctctctctgaatgattatgactgtgcttatcattttcag

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G13370.1 (Glycine max), 5'ss of exon 9
GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattctgcatgtttttctcttctctactatataaagcatcattttccacggttccatgtcc-tctactcccccacattt-aaatggtaaaaaagctaa------------------
||||||||| |||||||| || ||||||||||| || ||||| |||||||| || ||||| ||||| ||||| ||  | || ||| | ||||| |||| || ||| | | |  || |||    |         || ||   |||    || |   | ||  ||| ||||      |||  |||| | |   | |||                   
GCGAGGAGCCATCATCACTACTTTCATTGTGTGTTATGCTCTCACATCTTTTATTTCTGGTTATGTGAGTGGGGGGATGTACTCACGAAATGGGGgtaagaatcttctt-taattttctgtattttcgctcctagtatg--tttgggtggctttgtctcagtcttctccttttggttttgaatgattatgtaactattttttatctgtttgttag

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ15096 (Selaginella moellendorffii), 5'ss of exon 9
GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattctgcatgtttttctcttctctactatataaagcatcattttccacggttccatgtcctctactcccccacatttaaatggtaaaaaagctaa
||| ||||| ||  | |||||||||||||| |||||||||||||| || |||||||| || ||||| ||||| ||  | || ||  | || | ||||| |       ||| || |  ||    | ||        ||     || |||| ||    |                                      
GCGGGGAGCAATAGTGACAACCTTCATTGTATGCTACGCTCTTACGTCATTCATCTCCGGTTATGTCAGTGGCGGGTTTTACTCGCGAAACGATGgtaggta-----atgcttctacctgtggtgct------gacaatcccttacacgctttggag--------------------------------------

upper sequence: GRMZM2G087212_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ37593 (Selaginella moellendorffii), 5'ss of exon 9
GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattctgcatgtttttctcttctctactatataaagcatcattttccacggttccatgtcctctactcccccacatttaaatggtaaaaaagctaa
||| ||||| ||  | |||||||||||||| |||||||||||||| || |||||||| || ||||||||||| ||  | || ||  | || | ||||| | |  ||| | |   | |  |    || ||      ||   |||    | |                                             
GCGGGGAGCAATAGTGACAACCTTCATTGTATGCTACGCTCTTACGTCATTCATCTCCGGTTATGTTAGTGGCGGGTTTTACTCGCGAAACGATGgta-ggtaatgcttctacctgtggtgctaacaatcccttacacgctttggagcag---------------------------------------------

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|32930509|gb|CF035321.1|CF035321
EST:     ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG                         GAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCT
genomic: ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattct ... atcgtggcagGAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCT
EST: gi|32933279|gb|CF038091.1|CF038091
EST:     ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG                         GAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCT
genomic: ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattct ... atcgtggcagGAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCT
EST: gi|33094118|gb|CF054112.1|CF054112
EST:     ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG                         GAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCT
genomic: ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattct ... atcgtggcagGAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCT
EST: gi|71428339|gb|DR809389.1|DR809389
EST:     ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG                         GAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCT
genomic: ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattct ... atcgtggcagGAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCT
EST: gi|32932276|gb|CF037088.1|CF037088
EST:     ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG                         GAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCT
genomic: ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattct ... atcgtggcagGAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCT
EST: gi|15199064|gb|BI423636.1|BI423636
EST:     ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG                         GAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTT
genomic: ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattct ... atcgtggcagGAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTT
EST: gi|32930445|gb|CF035257.1|CF035257
EST:     ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG                         GAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCT
genomic: ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattct ... atcgtggcagGAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCT
EST: gi|32932743|gb|CF037555.1|CF037555
EST:     ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG                         GAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCT
genomic: ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattct ... atcgtggcagGAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCT
EST: gi|32930966|gb|CF035778.1|CF035778
EST:     ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG                         GAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCT
genomic: ATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattct ... atcgtggcagGAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCT

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: 18 (upstream exon), 49 (downstream exon)
Score: 191

GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattct ... atcgtggcagGAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCTTGTGTTTCTCGATTGGATTGTTGTTAAACACTATTGCTATCTTCTACCG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 121

GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattct ... atcgtggcagGAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCTTGTGTTTCTCGATTGGATTGTTGTTAAACACTATTGCTATCTTCTACCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 141

GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattct ... atcgtggcagGAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCTTGTGTTTCTCGATTGGATTGTTGTTAAACACTATTGCTATCTTCTACCG


Block sizes: 18 (upstream exon), 49 (downstream exon)
Score: 252

GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattct ... atcgtggcagGAAAAAACTGGATAAAGGCTATGATCCTTACAGCATCACTTTTTCCATTCTTGTGTTTCTCGATTGGATTGTTGTTAAACACTATTGCTATCTTCTACCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTGgtatgattctgcatgtttttctcttctctactatataaagcatcattttccacggttccatgtcctctactcccccacatttaaatggtaaaaaagctaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaaaaaa