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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatgaacagtcaagtgacacatgtaaaagtaatatcaaaagttctattccctgtgctattgctactttatatatgtttacttgtgcaatcttaaa...

Basic information

species Zea mays
transcript GRMZM5G824405_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA11G27410.1 (Glycine max), 5'ss of exon 20
GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatgaacagtcaagtgacacatgtaaaagtaatatcaaaagttctattccctgtgctattgctactttatat-atgtttacttgtgcaatcttaaa-
|| |||||  | ||  | ||||| |||||||||||||||||||| ||||| |||||| | || || ||| || | ||| |    |   ||    |  ||      | | | || ||  |   |  |||  ||     | |  |     | || |  |||  | ||  | | |  |  
GTTTATGAGACAGTTAATGAAGGATCTTACATAAAAATGATTGATATGGTCAGTGGGCATGGTGGACAAATACAAgtaagctcaa--tgttttatttcattgaacataattatttcggatagttcattatctagttgactagtgtaagagattacatttgatagtttattgtctata

upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA14G37520.3 (Glycine max), 5'ss of exon 14
GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatgaacagtcaagtgacacatgtaaaagtaatatcaaaagttctattccctgtgctattgctactttatatatgtttacttgtgcaatcttaaa--
|| |||||  | || |||||||| |||||||||||||||||||||||||  |||||  | || || ||| || | ||| |  |  ||| | || |    ||| |  | ||   |     |    | || | |     ||||     |||  ||   || |  ||   ||  |     
GTTTATGAGACCGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAAgtaag-gtttacatttaattatgtcat-tttatgtggcaaactgaaccattttacataaatcattgtctggttagctagtattgcaagtttgataattggta

upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA18G06770.1 (Glycine max), 5'ss of exon 16
GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatgaa----cagtcaagtgacacatgtaaaagtaatatcaaaagttctattccctgtgctattgctactttatatatgtttacttgtgcaatcttaaa
|| |||||  | ||  | ||||| |||||||||||||||||||| ||||| |||||| | || || ||| || | ||| |    |      | |  | ||   ||| | ||  ||||      |      |||  | |  | |||      |  |   | || | | || ||  |||  
GTTTATGAGACAGTTAATGAAGGATCTTACATAAAAATGATTGATATGGTCAGTGGGCATGGTGGACAAATACAAgtaagctcaatgttttatttcattgtttcat-tgaacataatcctttta-cgtagttcattatcttgttggc-tagtgcaagagattgcatttgaaagtttat-

upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA14G37520.1 (Glycine max), 5'ss of exon 22
GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatgaacagtcaagtgacacatgtaaaagtaatatcaaaagttctattccctgtgctattgctactttatatatgtttacttgtgcaatcttaaa-------
|| |||||  | || |||||||| |||||||||||||||||||||||||  |||||  | || || ||| || | ||| |  |  ||| | || |    ||| |  | ||   |     |    | || | |     ||||     |||  ||   || |  ||   ||  |          
GTTTATGAGACCGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAAGTAAG-

upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 15
GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatgaacagtcaagtgacacatgtaaaagtaatatcaaaagttctattccctgtgctattgctactttatat-atgtttacttgtgcaatcttaaa-
|| |||||  | ||  | ||||| |||||||||||||||||||| ||||| |||||| | || || ||| || | ||| |  | ||   |  | |         | || || | |  | ||||| |||  ||     | |  |     | || |  |||  | ||  | | |  |  
GTTTATGAGACAGTTAATGAAGGATCTTACATAAAAATGATTGATATGGTCAGTGGGCATGGTGGACAAATACAAgtaagc-tcaatgttttatttcattgaacataattattttggatagttc-attatctagttgactagtgtaagagattacatttgatagtttattgtctata

upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 14
GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatgaacagtcaagtgacacatgtaa--aagtaatatcaaaagttctattccctgtgctattg-ctactttatatatgtttacttgtgcaatcttaaa--
|| |||||  |||| |||||||| |||||||||||||||||||||||||  |||||  | || || ||| || | ||| |  |  ||| | || |    ||| | |  | | ||  | || | || ||   | |     |||| ||  |||     | ||| |  ||   ||  |  |  
GTTTATGAGACGGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAAgtaag-gtttacatttaattatgtcattttatgaggcaaactgaacaatttta---cataaatcattgtctggtttgctggtattt-caagtttgataattgata

upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 12
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 5'ss of exon 14
GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatgaacagtcaagtgacacatgtaaaagtaatatcaaaagttctattccctgtgctattgct-actttatatatgtttacttgtgcaatcttaaa--------------------------
|| ||||| || || ||||||||||| ||||| ||||||||||| ||||| |||||||| || || ||  || | ||| || |           ||  | ||  ||  |   | ||| | |  ||||| | | |  | ||  | ||  |||     || |   || | |   |  |                          
GTTTATGAGCCTGTAGAAGAAGGTTCGTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAAgtacgtctctgtctgtttctgtaaaattaaattggcgtttcacatgg-ctatttcatctagtcttaatcacgatatggtacttgatcggttcgactgttcatgactgttattctacttttgttgcag

upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 14
GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatgaacagtcaagtgacacatgtaaaagtaatatcaaaagttctattccctgtgctattgctactttatatatgtttacttgtgcaatcttaaa----
|| ||||| || ||||||||||| |||||||| ||||||||||| |||||| ||||  | |  || ||  || ||||| || | | |  | || |||   |   | |  |  | | ||   || | | |  |  | | |    | |  || | ||  ||| | | | || ||       
GTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTTGGTGGCCAAGATGGACAGATACAGgtaagtttcacctcttaaatgattaacagagacatgcttttaa---ttatgtact-taaggtttactaagtgcatgtttggatacatttcctattttttggttt

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|84980594|gb|DW530943.1|DW530943
EST:     CTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG                         ATTAATGACATAAGTGGTTACTTGCCTGGACGGATCGTTTTCTTCTTG
genomic: CTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatga ... tttcgtgcagATTAATGACATAAGTGGTTACTTGCCTGGACGGATCGTTTTCTTCTTG
EST: gi|211189269|gb|FL030572.1|FL030572
EST:     CTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG                         ATTAATGACATAAGTGGTTACTTGCCTGGACGGATCGTTTTCTTCTTG
genomic: CTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatga ... tttcgtgcagATTAATGACATAAGTGGTTACTTGCCTGGACGGATCGTTTTCTTCTTG
EST: gi|67010650|gb|CO439399.1|CO439399
EST:     CTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG                         ATTAATGACATAAGTGGTTACTTGCCTGGACGGATCGTTTTCTTCTTG
genomic: CTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatga ... tttcgtgcagATTAATGACATAAGTGGTTACTTGCCTGGACGGATCGTTTTCTTCTTG

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), 48 (downstream exon)
Score: 99

GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatga ... tttcgtgcagATTAATGACATAAGTGGTTACTTGCCTGGACGGATCGTTTTCTTCTTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 117

GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatga ... tttcgtgcagATTAATGACATAAGTGGTTACTTGCCTGGACGGATCGTTTTCTTCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 131

GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatga ... tttcgtgcagATTAATGACATAAGTGGTTACTTGCCTGGACGGATCGTTTTCTTCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 448

GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatga ... tttcgtgcagATTAATGACATAAGTGGTTACTTGCCTGGACGGATCGTTTTCTTCTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAGgtatgtatgaacagtcaagtgacacatgtaaaagtaatatcaaaagttctattccctgtgctattgctactttatatatgtttacttgtgcaatcttaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagtaa