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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacatcatgtagaaactattcatcaagcacatatgcatccattcctttatttggctgactttggtcttcatttacttgatag

Basic information

species Zea mays
transcript GRMZM2G018837_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018837_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g08120.1 (Oryza sativa), 5'ss of exon 3
TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacatcatgtagaaactattcatcaagcacatatgcatc----cattcctttatttggctgactttggtcttcatttacttgatag-----------------------------------------------------------------------------------------------
||||||||||||||| |||||||||||||||||||||||||| ||||||||| |||||||||||||||||||||| |||||||||      || || | |   | ||||  |  |  ||       |  ||||| |    |   ||| |  |   |||| |  |                                                                                                  
TGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTGgtaagaacaa-----agcaattctcttttaagcggaattctattatcatgtcgctttactctctttttttttgcataggtttattctagcatgctactgtctacatttatatgttccttcactactgttaattatttcttgcacttagttacattcggttatatatattctctgtatacatactag

upper sequence: GRMZM2G018837_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA15G07330.2 (Glycine max), 5'ss of exon 3
TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacatca-------tgtagaaactattca--tcaagcacatatgcatccattcctttatttggctgactttggtcttcatttacttgatag----
||| |||||||||||  | |||||||| ||||||||||  || || |||||| |||| || |||||||||||||| ||||||| || |       ||| | |   |||    ||  | |    |  ||  |||  || |  |       | |     ||| | | |||||      
TGTAATTGTTGAAGCCCTGAAGGTGGACAGTCTGCAGAAACTTTGTTCATCACTGGAGCCTATTCTTCGTAGAGTTgtaagaaaattaagttcattgtggtattgatttgcttctgggaggactatattgattatttgaaattatcacttgtaccgatcaatcaattgattatccc

upper sequence: GRMZM2G018837_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA17G07290.1 (Glycine max), 5'ss of exon 4
TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacatcatgtagaaactattcatcaagcacata-tgc-atccattcctttatttggctgactt-tggtcttcatttacttgatag----------
||| ||||| |||||  | |||||||| ||| |||||| ||| |||||||| || ||||| |||||||||||||| ||||||   |    | || |||| |     |  |  |  ||| ||  | |  | | |||| |   ||| |  | ||  | |    | ||           
TGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTTgtaagacagttggcttgacactactttctcactattttctgctatatacttttctttttgacatgcttatttttttggtgtgggggctatgcattctacg

upper sequence: GRMZM2G018837_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA13G01160.1 (Glycine max), 5'ss of exon 3
TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacatcatgtagaaactattcatcaagcacatatgcatccattcc-----tttatttggctgactttggt--ct----tcatttacttgatag---
||| ||||| |||||  | |||||||| ||| |||||| ||| |||||||| || ||||| |||||||||||||| ||||||   |    |  | ||||||  ||    | |||    ||  ||        |||| |   ||  || ||   ||    | ||  | |  | |    
TGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTTgtaagacatttggcttcacactattt-tctgctatatacttttctttttgacatgcttatctttttggtttggggaactggggttatgcattctacaaagt

upper sequence: GRMZM2G018837_T04 (Zea mays), 5'ss of exon 3
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 5'ss of exon 2
TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaaga------acatcatgtagaaa--------ctattcatcaagcacatatgcatccattcctttatttggctgactttggtcttcatttacttgatag
||| || ||||||||  | |||||||||||||||||||  || ||||||||||||||||| |||||||| ||||| ||||||      || || | ||   |        || |   | ||| |  || |    ||  | | | |||        ||| | ||  |||   | ||  
TGTAATAGTTGAAGCTCTGAAGGTGGATAGTCTGCAGAAACTTTGCTCATCATTGGAACCTATTCTTCGGAGAGTTgtaagataaataacctcttatatggatttctttactttctgtgaagaatttaggataacagccttctgttttttgtttgttgttttttttttgggtaatt-

upper sequence: GRMZM2G018837_T04 (Zea mays), 5'ss of exon 3
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 5'ss of exon 4
TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaaga------acatcatgtagaaa--------ctattcatcaagcacatatgcatccattcctttatttggctgactttggtcttcatttacttgatag
||| || ||||||||  | |||||||||||||||||||  || ||||||||||||||||| |||||||| ||||| ||||||      || || | ||   |        || |   | ||| |  || |    ||  | | | |||        ||| | ||  |||   | ||  
TGTAATAGTTGAAGCTCTGAAGGTGGATAGTCTGCAGAAACTTTGCTCATCATTGGAACCTATTCTTCGGAGAGTTgtaagataaataacctcttatatggatttctttactttctgtgaagaatttaggatagcagccttctgttttttgtttgttgttttttttttgggtaatt-

upper sequence: GRMZM2G018837_T04 (Zea mays), 5'ss of exon 3
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 5'ss of exon 2
TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaaga-acatcatgtagaaactattcatcaagcacatatgcatccattcctttatt----tggctgactttggtct----tcatttacttgatag----
||| || || |||||  | |||||||||||||||||||  || |||||||| |||||||| |||||||||||||| |||||| | |   | |  |  |||    ||    | ||||   |    ||   ||||    || ||||||    | |    |||  || |||||      
TGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTTgtaagatagactttatgtactctaccactctgttaaatatttttttcctctcatattgagatgactgactgccatttaatgtcaaatatttgatgaacat

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|149075355|gb|EE163864.2|EE163864
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|211057553|gb|FL294376.1|FL294376
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGTGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|211057556|gb|FL294379.1|FL294379
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGCGCACCGCGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|211057557|gb|FL294380.1|FL294380
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|26557412|gb|CA829647.1|CA829647
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|211054587|gb|FL294369.1|FL294369
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|76937510|gb|DV175167.1|DV175167
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|149000276|gb|EE037432.2|EE037432
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|76910443|gb|DV163876.1|DV163876
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|211057550|gb|FL294373.1|FL294373
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|211054585|gb|FL294367.1|FL294367
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGTGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|211057551|gb|FL294374.1|FL294374
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGTGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|148974485|gb|EE025268.2|EE025268
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|148956501|gb|EC902338.2|EC902338
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|211054577|gb|FL294359.1|FL294359
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGTGCGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|149014700|gb|EE044372.2|EE044372
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|211057549|gb|FL294372.1|FL294372
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGTGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|211054583|gb|FL294365.1|FL294365
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGCGCACTGTGCAAACTTGGCCCTGCAACAAT
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAAT
EST: gi|37420242|gb|CF647811.1|CF647811
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|211054586|gb|FL294368.1|FL294368
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
EST: gi|76015275|gb|DT942445.1|DT942445
EST:     ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA                         GTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC
genomic: ATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATC

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: 177

TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 143

TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 148

TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 78

TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacat ... tacttgatagGTCAGTGAAGAAGTGGAGCGCGCACTGGGCAAACTTGGCCCTGCAACAATCGGTGGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTAgtaagaacatcatgtagaaactattcatcaagcacatatgcatccattcctttatttggctgactttggtcttcatttacttgatag

- - - - - - - - - - - - - - -  CTGCAG