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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttattttgtattttgtcctgggtactttccctcctgtctttttctccggttacattatgtactgttgtcttgtgagttgtgacaagtcttctct...

Basic information

species Zea mays
transcript GRMZM5G814700_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G814700_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 5'ss of exon 14
AGCCCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttattttgtattttgtcctgggtactttccctcctgtctttttctccggttacattatgtactgttgtcttgtga-gttgtgaca-agtcttctct-
||| || |||||||| ||||||||||| |||||||||||||||||||| ||||||||||||||||| ||||| || ||||||||||||||||||||||||||||| |  || | | | |    ||     || || |||      | |      | || ||   ||        |   |||   |  |||| ||| | || | 
AGCTCTTATTGCTCACTTCCAGAACTCCAGTTTGATGAATGAGGACAAGCGCTGCCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAGgtatgatctttctctctctctctct---ctctctctctctctctctctctcgttgataaatggagttaaagcagcagatgacacttggacacagtttgctgtt

upper sequence: GRMZM5G814700_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G01040.1 (Glycine max), 5'ss of exon 14
AGCCCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttattttgtattttgtc-ctgggtactttccctc--ctgtctttttctccggttacattatgtactgttgtcttgtgagttgtgacaagtcttctct
  | || |||||||||||||||||||| ||  |||||||||| |||||||| ||||| || || || |||||  ||||||| || ||||| || |||| ||||     |  || | || | |   |  | |||||   |   |||  | ||     ||| | |  ||  |    | | || |    | || ||          
TTCTCTTATTGCTCATTTCCAGAACTCAAGCCTGATGAATGAAGACAAACGTTGCCGTCCTATTCTCTTCCATACAGATGGCCCAAATGCTGGTGATCCGgtaaatcaagcttttgttctttagttaagaactttgtattatctgattcttctggtggtgataaaattgatcaatatttttttgtctctg-cag---------

upper sequence: GRMZM5G814700_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT5G07290.1 (Arabidopsis thaliana), 5'ss of exon 13
AGCCCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttattttgtattttgtcctgggtactttccctcctgtctttttctccggttacattatgtactgttgtcttgtgagttgtg-acaagtcttctct
||| || ||||| |||||||||||||| ||||||||||| || |||||||| ||| | || || || |||||| | | |||||| ||||| || ||||||||| |        |   |   |         | | |   || |    |  | | ||| ||     |  | |  ||| || |||| || |       |  | 
AGCTCTTATTGCCCATTTCCAGAACTCAAGTTTGATGAACGAAGACAAACGTTGCAGGCCTATTCTCTTCCACACTGCTGGTCCAAATGCTGGTGATCAGgtaaggaagacaagggctcaattgatatccttattcaaactataacctctttctgttgcaagtaatcatatcatctggt-agttatgtattcactatagcg

upper sequence: GRMZM5G814700_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT5G61960.2 (Arabidopsis thaliana), 5'ss of exon 13
AGCCCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtat-gctta---ttttgta---ttttgtcctgggtactttccctcctgtcttttt-ctccggttacattatgtactgttgtcttgtgagttgtgacaagtcttctct-----------------------------------------
||| || ||||| |||||||||||||| || || ||||| || |||||||| ||||| || || || |||||| | |||||||| ||||| || |||||||||  | |||    ||  ||   ||  ||| ||  |  || || |  |   | |   || |  | || | | ||    ||   || |    |  ||  |||                                                
AGCTCTTATTGCCCATTTCCAGAACTCAAGCTTAATGAACGAAGACAAACGTTGCCGACCTATTCTCTTCCACACTGATGGTCCAAATGCTGGTGATCAGgtaaagattaaagcttcatacaattccgtcttgtttggttcccattatccatatgcacttccttcacttcaagtgtgatttcattatatcataagattagtgagtaaaagaagattcatatgatttcctttgttgttatatcaccacag

upper sequence: GRMZM5G814700_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv00s0239g00110.t01 (Vitis vinifera), 5'ss of exon 4
AGCCCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttattttgtattttgtcctgggtactttccctcctgtctttttctccggttacattatgtactgttgtcttgtgagttgtgacaagtcttctct-----
 || || | |||||||||||| ||||| || |||||||||||||| ||||  |||||||| || || || ||  |  ||||||| |||||||| ||||||||| |   || |   ||   ||     || || |   |  |   | ||| | |   |   | ||| ||| ||    | ||| |  |   |   |||  ||     
TGCTCTTACTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACATTGCCGCCCTATTCTATTTCATACTAATGGTCCAAATGCAGGTGATCAGgtaggac-atctgacataaagt---atgttctctattttgttattctttatactaattggtaatg-actattaatgtatgattacttgtatacctttccttgata

upper sequence: GRMZM5G814700_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 5'ss of exon 14
AGCCCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatg-cttattttgtattttgtcctgggtactttccctcctgtctttttctccggttacattatgtactgttgtct--tgtgagttgtgacaagtcttctct
 || || |||||||||||||| ||||| || |||||||||||||| ||||| |||||||| || || || ||  | |||||||| |||||||| ||||||||| | | | |    ||   | |  |   || |||       |   |    |         ||    | | || | |  | | | | || |  | | ||    
TGCTCTTATTGCTCATTTCCAAAACTCGAGCTTGATGAATGAGGATAAACGTTGCCGCCCTATTCTATTTCATACTGATGGTCCAAATGCAGGTGATCAGgtaggacatctgacataaagtatgttctctattttgttgttggatctcggatgtaaacctgtttaagaatattctttattctaattggtaatgactatta---

upper sequence: GRMZM5G814700_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv01s0150g00090.t01 (Vitis vinifera), 5'ss of exon 15
AGCCCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttatttt---gtattttgtcctgggtactttc-cctcctgtctttttctccggttacattatgtactgttgtcttgtgagttgtgacaagtcttctct
 || || ||||| |||||||||||||| ||  ||||||||||||| || || || || ||||| || |||||  | |||||||| |||||||| |||||||||||   || |     || ||      | | ||| |   |   | |   |||  | ||  |         |      ||||    |   | |||         
TGCTCTCATTGCCCATTTCCAGAACTCAAGCCTGATGAATGAGGATAAGCGATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAGgtatgaggatctctacatacttcacatagaggactctaatcagttatacatttacctggacaagaggaaatccagaaacttgaagataaaggcaacctaa----

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|22542340|gb|BU092793.1|BU092793
EST:     GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
EST: gi|32837722|gb|CD977400.1|CD977400
EST:     GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
EST: gi|33095731|gb|CF055725.1|CF055725
EST:     GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
EST: gi|67013397|gb|CO442146.1|CO442146
EST:     GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
EST: gi|74235606|gb|DT643520.1|DT643520
EST:     GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
EST: gi|26558461|gb|CA830696.1|CA830696
EST:     GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
EST: gi|71307207|gb|DR789770.1|DR789770
EST:     GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
EST: gi|86471732|gb|DY238102.1|DY238102
EST:     GCTGCCGCCCCATATTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGACCCAGGTCGGGGAGATCCCGG
genomic: GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
EST: gi|71772001|gb|DR969938.1|DR969938
EST:     GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
EST: gi|211347381|gb|FL343898.1|FL343898
EST:     GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
EST: gi|33093066|gb|CF053060.1|CF053060
EST:     GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
EST: gi|76925720|gb|DV170563.1|DV170563
EST:     CCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCAGGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: CCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
EST: gi|33092822|gb|CF052816.1|CF052816
EST:     GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
EST: gi|67015508|gb|CO444257.1|CO444257
EST:     CTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: CTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
EST: gi|33091257|gb|CF051251.1|CF051251
EST:     GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG

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: 572

AGCCCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGGACTTCTTCGGGTGAAGAAAATCACCATGACATCCAGACAGTCTTGACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 553

AGCCCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGGACTTCTTCGGGTGAAGAAAATCACCATGACATCCAGACAGTCTTGACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 708

AGCCCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGGACTTCTTCGGGTGAAGAAAATCACCATGACATCCAGACAGTCTTGACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 557

AGCCCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGGACTTCTTCGGGTGAAGAAAATCACCATGACATCCAGACAGTCTTGACCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttattttgtattttgtcctgggtactttccctcctgtctttttctccggttacattatgtactgttgtcttgtgagttgtgacaagtcttctct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccctcct