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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaattaccagcgcttataattgtaataaaattgtactccctccattttttatttgtcgcgttttagtttaaaaatgaactagcgggcgacaaatattcgagaacggaaggagtataaatttaatagtaaggcatgtttgagaaagtcttacattggtaactctgacttctgatatggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG

Basic information

species Zea mays
transcript GRMZM2G082976_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082976_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g63520.1 (Oryza sativa), 3'ss of exon 3
gtatggaattaccagcgcttataattgtaataaaattgtactccctccattttttatttgtcgcgttttagtttaaaaatgaactagcgggcgacaaatattcgagaacggaaggagtataaatttaatagt--aaggcatgtttgagaaagtcttacattggtaactctgacttctgatatggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG
                          |||  | | | ||||   |   ||  ||  ||| | |  || ||    |    |      || ||  |||||| || | ||      ||  | | ||  || |  |    ||    |      ||||      || |||| ||     |||  |||||      |||||||||| ||||||||||||||||| ||||| |||||||||||  ||||  ||||||||||||| ||||| || ||||| |||
--------------------------gtacgagattagtacaagcattatacttggtttttggttttctacaccatcgttaggggtgcagg--acaaatcttagggattttctgggctctgaaaatagtcttcttgggtgcatacttagaagttgagttttagtaattcc----tctcgtatggacctgcagGTTTATGTATGGAGCAAGCACAATCCCTTCATTCATATGAGCTTCTTGGGTTTGTTCACCTTTACTGCTGCTTATTTACCTTGG

upper sequence: GRMZM2G082976_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv10s0116g00010.t01 (Vitis vinifera), 3'ss of exon 1
gtatggaattaccagcgcttataattgtaataaaattgtactccctccattttttatttgtcgcgttttagtttaaaaatgaactagcgggcgacaaatattcgagaacggaaggagtataaatttaatagtaaggcatgtttgagaaagtcttacattggtaactctgacttctgatatggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG
                                                                   ||||||   || |   ||    |   ||| |||   ||      |  |  || |    |  | | ||    |||||  | | |||||      || ||||||  || |  | | | |    |||||||||| ||||||||||| |||||||| ||||||||||| ||  ||||||| || ||||| || || || ||| | ||||||
------------------------------------------------------------------gttagtt---aatttttct--ttgctcacacatagaagatgttttattggttacagtcattgt-gcaacaactgtttt-ggatgtctt------gttactctg-tttttcctgttgtac---agGTTTATGTGTGGAGCAAGCAAAATCCTTTTATCCATATGAGTTTCTTGGGCCTCTTTACCTTCACAGCGGCCTACCTTCCATGG
















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|37379052|gb|CF626253.1|CF626253
EST:     AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACGTTTATGATG                         GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
EST: gi|42491916|gb|CK700962.1|CK700962
EST:     AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATG                         GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
EST: gi|37378913|gb|CF626178.1|CF626178
EST:     ACGTTTATGATG                         GTTTATGTATGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
genomic: ACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
EST: gi|78543826|gb|DV621324.1|DV621324
EST:     AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATG                         GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
EST: gi|88754119|gb|DY538260.1|DY538260
EST:     AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATG                         GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
EST: gi|26457330|gb|CA828913.1|CA828913
EST:     AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATG                         GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
EST: gi|31353782|gb|CD438139.1|CD438139
EST:     AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATG                         GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGC

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: 47 (upstream exon), 49 (downstream exon)
Score: 113

TGTCCTAACTAGCATTGTTCTGATTGGAGGGATGATACCTTACATTTCCGAGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

TGTCCTAACTAGCATTGTTCTGATTGGAGGGATGATACCTTACATTTCCGAGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 90

TGTCCTAACTAGCATTGTTCTGATTGGAGGGATGATACCTTACATTTCCGAGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 288

TGTCCTAACTAGCATTGTTCTGATTGGAGGGATGATACCTTACATTTCCGAGACATTTGCCAGAATTCTGTTCCTGAGCAATTCATTGACGTTTATGATGgtatggaatt ... ggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgtttgagaaagtcttacattggtaactctgacttctgatatggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG
                 ttacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggaattaccagcgcttataattgtaataaaattgtactccctccattttttatttgtcgcgttttagtttaaaaatgaactagcgggcgacaaatattcgagaacggaaggagtataaatttaatagtaaggcatgtttgagaaagtcttacattggtaactctgacttctgatatggcatgttagGTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT