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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttctttaaacaactatatgatgtatgccccttctcttatggtctgtttgctgactcagcaagccattttttgttgtgctataattgatagcaaggcaatgatgcaatccattagtggtagtacaatgtcaattgaatcttctaactcattatatttgcttggacag

Basic information

species Zea mays
transcript GRMZM5G844195_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G844195_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 5'ss of exon 11
TGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttctttaaacaactatatgatgtatgccccttctcttatg-gtctgtttgctgactcagcaagccattttttgttgtgctataattgatagcaaggcaatgatgcaatccattagtggtagtacaatgtcaattgaatcttctaactcattatatttgcttggacag
|||||||||||||||||| ||  ||||| |||||||||||||| |||| |||||||||||||| ||||| |||||||||||||||||||| |||||| ||||||| ||||||         | |  |  | | |    ||| |  |   | ||  ||     || | |    || | |  ||   | | |||  | |                                                                             
TGACATGCCAGTTGTTGGTGCAGTAACTTTATATGTATCACTTTTGACATTTACTCTCCGTGTGCATCCGGATCGGCTTGATTATGTTGATCAAGTGTTGgtaagccttcttgtgtaggggaaaaaaaatctcctaactctatagtatatgtgcatgtaatttctgtactttatatatactttctccacaatctacaaat--------------------------------------------------------------------------

upper sequence: GRMZM5G844195_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA17G37870.1 (Glycine max), 5'ss of exon 12
-TGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttctttaaacaactatatgatgtatgccccttctcttatggtctgtttgctgactcagcaagccattttttgttgtgctataattgatagcaaggcaatgatgcaatccattagtggtagtacaatgtcaattgaatcttctaactcattatatttgcttggacag
  ||||||||  | || ||||| ||| || |  |||| || ||||| || |||||||||||||| ||||| ||||| ||||||||||| |||||||| |||||| ||    || |||||   | |        ||| |||    ||||   |||    ||    || |   ||||||  | |  |||  | | | |     || | |  ||||                                                             
ACGACATGCCTATCGTGGGAGCAATAGCTTTGCATGTTTCTCTTCTTACATTTACTCTCCGTGTTCATCCGGATCGACTTGATTATGTGGACCAAGTACTggtatgttactttcaaaca-tcaca--------gcctctt----tatgagatgtggtatggacaagaattgcatttta-gcttagctgca-tcgtt--tctggaatttgtgca-------------------------------------------------------------

upper sequence: GRMZM5G844195_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA14G40270.1 (Glycine max), 5'ss of exon 11
TGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttctttaaacaactatatgatgtatgccccttctcttatggtc-tgtttgctgactcagc-aagccattttttgttgtgctataattgatagcaaggcaatgatgcaatccattagtggtagtacaatgtcaattgaatcttctaactcattatatttgcttggacag
|||||||||  |||| ||||| ||| || |  |||| || ||||| || |||||||||||||| ||||| ||||| ||||||||||| |||||||| |||||| ||    || |||||   | |   | | |      | |  ||||| | ||  |      | ||| ||||    |  |    | ||  ||||  || ||                                                                          
TGACATGCCTATTGTGGGAGCAATAGCTTTGCATGTTTCTCTTCTTACATTTACTCTCCGTGTTCATCCAGATCGACTTGATTATGTGGACCAAGTACTGgtatgttactttcaaaca-tcacaacctttttatgagatgtggtatggacatgaattgcattttagctaagctgcatcat----ttctggaatttgta-cag-------------------------------------------------------------------------

upper sequence: GRMZM5G844195_T02 (Zea mays), 5'ss of exon 12
lower sequence: AT1G75850.1 (Arabidopsis thaliana), 5'ss of exon 11
TGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttctttaaacaactatatgatgtatgccccttctcttatggtctgtttgctgactcagcaagccattttttgt-tgtgctataattgatag---caaggcaatgatgcaa--tccattagtggtagtacaatgtcaattgaatcttcta-actcattatatttgcttggacag-------------------
||| |||||  |||| ||||| || ||||| | ||| || ||| |||| ||||||||||| || ||||||||||||||||| ||||| || |||||  ||||| |  ||| ||      | ||||| | | |   | ||   | |   |    |   |  ||       |  | |    | | || |   ||| | |    ||  | || | || ||  | ||||  |     |  |   | | ||||||||  |  |  | |    ||    |    |                    
TGAGATGCCTATTGTCGGAGCTATGACTCTGTTTGTCTCTCTTTTGACTTTTACTCTCCGAGTTCATCCTGATCGGCTTGACTATGTGGATCAAGTATTGgtatggtttcctttcgttgccatatgttttctaaacttttagtcagtattgtctctgtagcttgtatctctgtctacactatatgttcagattcagattttcattgtaaaggtgtaaaatgcatttttaaagttttatgattacttgaatctggtgtagccctggcgttaaactaattattgatccgaaaactttgtag

upper sequence: GRMZM5G844195_T02 (Zea mays), 5'ss of exon 12
lower sequence: AT2G17790.1 (Arabidopsis thaliana), 5'ss of exon 10
TGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttctttaaacaactatatg-atgtatgccccttctcttatggtctgtttgctgactcagcaagccattttttgttgtgctataattgatagcaaggcaatgatgcaatccattagtggtagtacaatgtcaattgaatcttctaactcattatatttgcttggacag
 ||||||||  || |  | ||  |||| ||||||   || ||||| |  |||||||| |  || || |||||||||||||||||||  ||||||||| |||| ||| |||||  | | ||| |||  |  |||    ||  |||||      ||||    ||||       | | || |||       |  ||  | ||    | ||                                                                   
AGACATGCCTATTCTGAGTGCAGTAACCCTATATTCCTCCCTTCTCAAGTTTACTCTTCACGTTCACCCTGATCGGCTTGATTATGCGGACCAAGTGTTGgtcagttttcttatagcgactgtatttacctattgttctcttcttaactcaagtttaaatactc-------cgtcttctgtca-atgttgcttagtggcctatcgatc------------------------------------------------------------------

upper sequence: GRMZM5G844195_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 5'ss of exon 11
TGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttct-ttaaacaactatatgatgtatgccccttct-cttatggtct-gtttgctgactcagcaagccattttttgttgtgctataattgatagcaaggcaatgatgcaatccattagtggtagtacaatgtcaattgaatcttctaactcattatatttgcttggacag
||||||||| ||| ||||||| |||||| ||||||| || ||||| || |||||||| ||||| ||||||||||||||||||||||| || ||||| |||||| |||  |  ||| ||||   |      ||||  || | | |  ||||| | | |  |  |  | |  |  |  | | |    |  | |   || |                                                                              
TGACATGCCTGTTTTTGGAGCAATAACTTTATATGTCTCTCTTCTTACATTTACTCTTCGTGTTCATCCTGATCGGCTTGATTATGTGGATCAAGTACTGgtatgtccccaattatacaaagttcatgcttatgatccatttgcacatggttttgctaacgaatgctgatacacgatctataaaattttctggctgctgc----------------------------------------------------------------------------

upper sequence: GRMZM5G844195_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 5'ss of exon 11
TGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttctttaaacaactatatgatgtatgccccttctcttatggtctgtttgctgactcagcaagccattttttgttgtgctataattgatagcaaggcaatgatgcaatccattagtggtagtacaatgtcaattgaatcttctaactcattatatttgcttggacag
|||||||||  || |||||||  |||||||||||  ||| ||||| || |||||||| | ||| || |||||||||||||||||||| || ||||| |||||| || |  |||| | ||||   |           || || ||  || ||   | |    |  |      ||||||  || |   | ||   | |  ||||  || || ||    |  |                                                     
TGACATGCCTATTTTTGGAGCTGTAACTCTATATTCATCTCTTCTCACTTTTACTCTGCATGTGCACCCTGATCGGCTTGATTATGTGGATCAAGTTCTGgtatgtttcatttata-aactcctt----------tctacttttgcgggctaggttccagttttg------attttt--ttatttgaaaaccaagattaaggatatcat-cacctaagca-----------------------------------------------------

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|19058370|gb|BM737037.1|BM737037
EST:     TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTG                         GGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
genomic: TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
EST: gi|18963630|gb|BM660543.1|BM660543
EST:     TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTG                         GGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
genomic: TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
EST: gi|33094690|gb|CF054684.1|CF054684
EST:     GTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTG                         GGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
genomic: GTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
EST: gi|87153186|gb|DY397975.1|DY397975
EST:     TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTG                         GGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAGGATAGCAGG
genomic: TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
EST: gi|33094433|gb|CF054427.1|CF054427
EST:     GTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTG                         GGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
genomic: GTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
EST: gi|19058197|gb|BM736864.1|BM736864
EST:     TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTG                         GGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
genomic: TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
EST: gi|18963632|gb|BM660544.1|BM660544
EST:     TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTG                         GGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
genomic: TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
EST: gi|19057727|gb|BM736394.1|BM736394
EST:     TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTG                         GGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
genomic: TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG

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: 164

TGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGGGCAACAAAGCAAATTGTTGCACTTCTTAGTGCTCCCCTGGAAAAATATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

TGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGGGCAACAAAGCAAATTGTTGCACTTCTTAGTGCTCCCCTGGAAAAATATA


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

TGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGGGCAACAAAGCAAATTGTTGCACTTCTTAGTGCTCCCCTGGAAAAATATA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 130

TGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGGGCAACAAAGCAAATTGTTGCACTTCTTAGTGCTCCCCTGGAAAAATATA