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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgctatgttattgaccatgaaattttctcctagctgttactgactcctaaactcttttgaattatccaaaccgaaacatatag

Basic information

species Zea mays
transcript GRMZM2G015869_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015869_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g18110.1 (Oryza sativa), 5'ss of exon 3
ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgctatgt-tattgaccatgaaattttctcctagctgttactgactcctaaactcttttgaattatccaaaccgaaacatatag
||||||||||| || |||||||||||||| |||||  | || || || || |||||||| |||||| |||||||||||||||| || ||||||||||    |  | |||  ||||       || |  |  || |  | |  ||  | |||    |  | ||| ||               
ATGATTCCTGTCGCGGCAAATGATGTTGCCTTTTCTGTACACGCGGTTGCCTTGACAGCTTTTACCCTTTTTCAAGTATTCATCTACGAGgttagttaaacagctgtatgaaccacagttacttattttcactctgtcagtatctgatacttcagtacaatatacag--------------

upper sequence: GRMZM2G015869_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA16G07090.1 (Glycine max), 5'ss of exon 1
ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgctatgttattgaccat----gaaattttctcctagctgtt------actgactcctaaactcttttgaattatccaaaccgaaacatatag
||||| |||||||||||||||||||||||||| ||  | ||||||||     |||||||  ||||  | || ||  |    || ||||| || ||  || |||||  ||  | |     |||  ||  || |   ||||      ||||| | ||  | | |  |||| |     |         | |||
ATGATACCTGTTGCTGCAAATGATGTTGCTTTCTCGATCCATGCTGTTCTGCTGACAGCAATTACATTGTTCCAGATTGCAATCTATGAAgtaagcatgatatgtatttctctagttgagaatgttgttcttttttgttctgtggactgaattctcgattttgctgaacttagtgattgttttgttgtag

upper sequence: GRMZM2G015869_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA16G07110.1 (Glycine max), 5'ss of exon 3
ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgctatgttattgaccat----gaaattttctcctagctgtt------actgactcctaaactcttttgaattatccaaaccgaaacatatag
||||| |||||||||||||||||||||||||| ||  | ||||||||   | |||||||  ||||  | || ||  |    || ||||| || ||  || |||||  ||  | |     |||  ||  || |   ||||      ||||| | ||  | | |  |||| |     |         | |||
ATGATACCTGTTGCTGCAAATGATGTTGCTTTCTCGATCCATGCTGTTCTACTGACAGCAATTACATTGTTCCAGATTGCAATCTATGAAgtaagcatgatatgtatttctctagttgagaatgttgttcttttttgttctgtggactgaattctcgattttgctgaacttagtgattgttttgttgtag

upper sequence: GRMZM2G015869_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv14s0219g00120.t01 (Vitis vinifera), 5'ss of exon 3
ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgt---tagtttgctatgttattgaccatgaaattttctcctagctgtta----ctgactccta--aactcttttgaattatccaaaccgaaacatatag-------------------
||||| ||||| |||||||||||||||||||| ||| | ||||||||    |||||||| |||||  | |||||| |    || ||||||||   | ||||| | |  | |   |  | |||||||||  |     |||    || | | ||   ||||  |||| |   || |     |||  | ||                    
ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGgtaagtggtttgttcttctctgatcagtcaaattttcttgttttgtttaaattcttagtgctgtcaacttctttgtagagtcaattttcaaat-tttatttgttgatgttttttgcag

upper sequence: GRMZM2G015869_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv14s0219g00130.t01 (Vitis vinifera), 5'ss of exon 3
ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagt---ttgctatgttattgaccatgaaattt---tctcctagctgttactgactcctaaactcttttgaattatccaaaccgaaacatatag----------------------
||||| ||||| |||||||||||||||||||| ||| | |||||||| |  |||| ||| |||||    || ||| |    || |||||||| |||   ||| |   |   ||| ||   |||||   |    | |  ||  |||  |  |  |||  |||  |   || ||     |  | ||                        
ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTGTCTTGATAGCATTTACTTGGTTCCAAATTGCAATCTATGAGgtaagtgatttgtttcttctctgatcactcaatttgtgttggtttgaagtctctgtgtgatccacttctttatagagtcaaatatatattaaattttgtctgttgatgttttgtacag

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|50329144|gb|CO524270.1|CO524270
EST:     ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG                         CGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
genomic: ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgc ... aaacatatagCGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
EST: gi|37420119|gb|CF647747.1|CF647747
EST:     ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG                         CGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
genomic: ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgc ... aaacatatagCGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
EST: gi|78084914|gb|DV513307.1|DV513307
EST:     ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG                         CGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
genomic: ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgc ... aaacatatagCGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
EST: gi|211284538|gb|FL301650.1|FL301650
EST:     ATTCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG                         CGAGGAACACAGAAAGTCTCCAAAGTTTTGCATATCAATTTCTGCTATTGT
genomic: ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgc ... aaacatatagCGAGGAACACAGAAAGTCTCCAAAGTTT-GCATATCAATTTCTGCTATTGT
EST: gi|50334359|gb|CO529485.1|CO529485
EST:     ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG                         CGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
genomic: ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgc ... aaacatatagCGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
EST: gi|32918962|gb|CF023774.1|CF023774
EST:     ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG                         CGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
genomic: ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgc ... aaacatatagCGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
EST: gi|211284537|gb|FL301649.1|FL301649
EST:     ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG                         CGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTG
genomic: ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgc ... aaacatatagCGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTG
EST: gi|211284534|gb|FL301646.1|FL301646
EST:     ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG                         CGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
genomic: ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgc ... aaacatatagCGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
EST: gi|211284540|gb|FL301652.1|FL301652
EST:     ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG                         CGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
genomic: ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgc ... aaacatatagCGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
EST: gi|78084875|gb|DV513268.1|DV513268
EST:     ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG                         CGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
genomic: ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgc ... aaacatatagCGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
EST: gi|71772025|gb|DR969962.1|DR969962
EST:     ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG                         CGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
genomic: ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgc ... aaacatatagCGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
EST: gi|9732652|gb|BE511404.1|BE511404
EST:     ATGCTGTAGCATTGACAGCCTTTACCGCTTTTCAAGTATTCATATATGAG                         CGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC
genomic: ATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgc ... aaacatatagCGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTC

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), 43 (downstream exon)
Score: 15

ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgc ... aaacatatagCGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTCTGGATCGCCGCTCTTGTTTGCCTCATTATTGCTTGGCCAAAAAGTGACT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 72

ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgc ... aaacatatagCGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTCTGGATCGCCGCTCTTGTTTGCCTCATTATTGCTTGGCCAAAAAGTGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgc ... aaacatatagCGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTCTGGATCGCCGCTCTTGTTTGCCTCATTATTGCTTGGCCAAAAAGTGACT


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 21

ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgc ... aaacatatagCGAGGAACACAGAAAGTCTCCAAAGTTTGCATATCAATTTCTGCTATTGTCTGGATCGCCGCTCTTGTTTGCCTCATTATTGCTTGGCCAAAAAGTGACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAGgttagtttgctatgttattgaccatgaaattttctcctagctgttactgactcctaaactcttttgaattatccaaaccgaaacatatag

- - - - - - - - - - - - - - - - - - - - ATGCTG