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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggctgggagtcttctgtttatcttctgttttagcgagtttttctttacatggtattcctcgtactacccattcttcgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCAAGGGGCTTGATGTCATTCAGCAAGCACAATCTGGTACAGGAAAGACAGC

Basic information

species Zea mays
transcript GRMZM2G027995_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027995_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g48750.1 (Oryza sativa), 3'ss of exon 3
gtaggctgggagtcttctgtttatcttctgttttagcgagtttttctttacatggtattcctcgtactacccattcttcgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCAAGGGGCTTGATGTCATTCAGCAAGCACAATCTGGTACAGGAAAGACAGC
||||| | | |||| || || | ||| | | | || | || ||||| || || | || || | | | ||||||| ||||| || || || |||||||| || || ||||| || ||||||||||| |||||||| ||||||||||| || || || ||||||||||| ||
gtaggtttataatctttcgt--gctttttttttgtgtgtttgccatttgaactgttattcatcagac--ctttttttttgttttatagGTTTCGAGAAGCCTTCAGCCATTCAGCAAAGGGGTATTGTCCCTTTCTGCAAGGGTCTTGATGTGATTCAGCAAGCTCAGTCAGGAACAGGAAAGACTGC

upper sequence: GRMZM2G027995_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S136_29V6.4 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------------------------------------------------------------gtaggctgggagtcttctgtttatcttctgttttagcgagtttttctttacatggtattcctcgtactacccattcttcgatgt--gtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCAAGGGGCTTGATGTCATTCAGCAAGCACAATCTGGTACAGGAAAGACAGC
|||||| | | | ||| || ||| | | | | | | || | |||||| || || | || | | |||||||||||| |||||||| ||||| ||| | || ||||| ||||| |||||| || ||||| ||||||||||||||||| || || || ||||| ||
gtaaggtcttcacctaatttcattgatattctaatcgaatgcaattcatttattcatttatacataagttactcctccttgggcgcatttttttagtaggcacgca-ttatcttcatagtttccttccaataggttataacattgcgatccattcctactagcttaattttgttaatttttgcagGTTTTGAGAAGCCATCTGCTATTCAACAGCGTGGTATTGTACCCTTTACCAAGGGCCTCGATGTTATTCAGCAAGCACAATCAGGGACTGGCAAGACTGC

upper sequence: GRMZM2G027995_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S31_150V6.5 (Physcomitrella patens), 3'ss of exon 3
------gtaggctgggagtcttctgtttatcttctgttttagcgagtttttctttacatggtattcctcgtacta--cccattct--tcga--tgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCAAGGGGCTTGATGTCATTCAGCAAGCACAATCTGGTACAGGAAAGACAGC
|| |||| | | || | | | | || |||| || | | | | ||| | |||||| | || ||| |||||||||||| |||||||| || || ||| | ||||| ||||||||| |||||| |||||||||||||| ||||| || ||||| || || ||||||||
ttgcatgttttgtgggtgcttgtggtgttcgtagtttcctaccgagaaccaattgaaccgcactctgctgctctaatctcattctggttgacctgtacagGTTTTGAGAAGCCATCTGCTATCCAACAGCGTGGAATCGTTCCCTTCACCAAGGGTCTTGATGTCATTCAACAAGCCCAGTCTGGAACTGGCAAGACAGC

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|211082279|gb|FL286148.1|FL286148
EST:     TGATGACATGGGCCTTCAAGAGAATCTTTTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|211079538|gb|FL286131.1|FL286131
EST:     TGATGACATGGGCCTTCAAGAGAATCTTTTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|8368624|gb|BE051569.1|BE051569
EST:     GATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGC
genomic: GATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGC-ATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGC
EST: gi|31354357|gb|CD438714.1|CD438714
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|31357673|gb|CD442030.1|CD442030
EST:     CCATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|32851137|gb|CD990818.1|CD990818
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|67041361|gb|CO467616.1|CO467616
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|211288318|gb|FL286178.1|FL286178
EST:     TGATGACATGGGCCTTCAAGAGAATCTTTTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|211294754|gb|FL286234.1|FL286234
EST:     GATGGACATGGGCCTTCAAGAGAATCTTTTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: GATG-ACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|67031983|gb|CO460732.1|CO460732
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|28931273|gb|CB334634.1|CB334634
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|31354677|gb|CD439034.1|CD439034
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|32933416|gb|CF038228.1|CF038228
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|31351797|gb|CD436154.1|CD436154
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|31359138|gb|CD443495.1|CD443495
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|22715433|gb|BU197760.1|BU197760
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|211290464|gb|FL286197.1|FL286197
EST:     TGATGACATGGGCCTTCAAGAGAATCTTTTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|211082280|gb|FL286149.1|FL286149
EST:     TGATGACATGGGCCTTCAAGAGAATCTTTTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|14646056|gb|BI180245.1|BI180245
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|29946169|gb|CB816014.1|CB816014
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|20811047|gb|BQ295525.1|BQ295525
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|31356525|gb|CD440882.1|CD440882
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTTTT
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|31349540|gb|CD433897.1|CD433897
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|8368623|gb|BE051568.1|BE051568
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|32933398|gb|CF038210.1|CF038210
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATACATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|30306982|gb|CD001655.1|CD001655
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|31353577|gb|CD437934.1|CD437934
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCATTTTTTATGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|32851113|gb|CD990794.1|CD990794
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
EST: gi|67017759|gb|CO446508.1|CO446508
EST:     TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCA

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), 49 (downstream exon)
Score: 778

GGTGAGACTGAGGAGTTCTTCACTTCATATGATGAAGTTTTTGAAAGTTTTGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCAAGGGGCTTGATGTCATTCAGCAAGCACAATCTGGTACAGGAAAGACAGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 818

GGTGAGACTGAGGAGTTCTTCACTTCATATGATGAAGTTTTTGAAAGTTTTGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCAAGGGGCTTGATGTCATTCAGCAAGCACAATCTGGTACAGGAAAGACAGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 664

GGTGAGACTGAGGAGTTCTTCACTTCATATGATGAAGTTTTTGAAAGTTTTGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCAAGGGGCTTGATGTCATTCAGCAAGCACAATCTGGTACAGGAAAGACAGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 435

GGTGAGACTGAGGAGTTCTTCACTTCATATGATGAAGTTTTTGAAAGTTTTGATGACATGGGCCTTCAAGAGAATCTTCTGAGAGGCATTTATGCATATGgtaggctggg ... cgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCAAGGGGCTTGATGTCATTCAGCAAGCACAATCTGGTACAGGAAAGACAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcgagtttttctttacatggtattcctcgtactacccattcttcgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCAAGGGGCTTGATGTCATTCAGCAAGCACAATCTGGTACAGGAAAGACAGC
                                    cccattcttc  CT-rich tract
 tttttcttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggctgggagtcttctgtttatcttctgttttagcgagtttttctttacatggtattcctcgtactacccattcttcgatgtgtagGTTTTGAGAAACCATCTGCAATTCAGCAGAGAGGAATTGTTCCCTTCTGCAAGGGGCTTGATGTCATTCAGCAAGCACAATCTGGTACAGGAAAGACAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG