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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgctcccatgttggacccatacatcctgcagcaagtaatttgctttctttgtctggaaatattattccccagaccccacccgtgggagcttcca...

Basic information

species Zea mays
transcript GRMZM2G164352_T05
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G10000.1 (Glycine max), 5'ss of exon 3
GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgctcccatgttggacccatacatcctgcagcaagtaatttgctttct-ttgtctggaaatattattccccagaccccacccgtgggagcttcca
 || ||  | |||||||| || ||||| || || || |||||||||||||| |||||||| || ||||| |||||||| ||||| |||||||| || |||||   |||  |    ||   || |  | |   |  |   ||  ||| |   | | |  ||   |   ||| |    |  || | |     ||||  |    
TCGGCTACTTGCTGTTGAGGGTTGTGCAGCTCTGGGAAAATTGTTGGAACCTCAAGATTGTGTGGCACATATTCTTCCTGTCATAGTCAATTTTTCTCAGgtttgttggccattagtaatacactgatactatatatgtagagattagagatatatcctccatatccattttgtggccaacactaatgaggggatgtctt-

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA02G10790.1 (Glycine max), 5'ss of exon 4
GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgctcccatgttggacccatacatcctgcagcaagtaatttgctttctttgtctggaaata-ttattccccagaccccacccgtgggagcttcca----
  |  |||||||||| || || |||||||| ||||| ||| || |||| |||||||||||| |  |||| || || || || |||||||| ||||| |||||  |||  |  || ||   |   ||||     |     |  || ||  ||| | ||  |    ||  |||   |     |   | |  | | |   | ||    
TAGATTGTTGGCTGTGGAGGGTTGTGCTGCTCTTGGGAAACTGCTGGAGCCACAAGATTGCATCACACATATACTACCGGTTATTGTCAACTTCTCGCAGgtgtatttttagca-gtgaaa--tatactgttagttatcatcaaattaatttttctgcttcattatgcttaaaactattgctttatc--tagtaatgttcagttt

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA20G24790.1 (Glycine max), 5'ss of exon 4
GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgctcccatgttggacccatacatcctgcagcaagta-atttgctttctttgtctggaaatattattccccagaccccacccgtgggagcttcca
  |  |||||||||| || ||||||||||| ||||| ||  ||||||| ||||||||||| || ||||| || || || || ||||| || |||||||||||||||       |   |  |   ||| ||        |  || || |   |  |  |     |  |  |  |     ||           | |   |   
CAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGTTAACTTCTCCCAGgtacatgataggaactgtatatatatatatatatatatatatatatatatataatgagagacaagcttctgatatttggaataggaaaacagaacgataa-

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 4
GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgctcccat--gttggacccatacatcctgcagcaagta-atttgctttctttgtctggaaatattattccccagaccccacccgtgggagcttcca
  |  |||||||||| || ||||||||||| ||||| ||  ||||||| ||||||||||| || ||||| || || || || ||||| || |||||||||||||||       |   | |  |   ||| ||       ||   | |  |   | ||   |   || || |        | | |  |    |   |   |   
CAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGTTAACTTCTCCCAGgtacatgataggaactggatatatatatatatatacacacacacacagatatatactagcttctgatatttggaataggaaaacagaatgataaaacagt---

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA09G31760.1 (Glycine max), 5'ss of exon 4
GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgctcccatgttggacccatacatcctgcagcaagtaatttgctttctttgtctggaaatattattccccagaccccacccgtgggagcttcca---------
 || ||  | |||||||| || ||||| || || || |||||||||||||| ||||||||||| ||||| |||||||| ||||| |||||||| || |||||   |||  |    ||   ||  |||||        |   || | |   |     | || ||  ||| ||   ||| | ||     ||||      | |         
TCGGCTACTTGCTGTTGAGGGTTGTGCAGCTCTGGGGAAATTGTTGGAACCTCAAGATTGCGTGGCACATATTCTTCCTGTCATAGTCAATTTTTCTCAGgtttgttggccattagtaatactgataca--------ctgatactatatatgtagagactagaggtat-atcttccatatccattttgtggccaacactaatgagagga

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA02G10790.2 (Glycine max), 5'ss of exon 4
-------------GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgctcccatgttggacccatacatcctgcagcaagtaatttgctttctttgtctggaaatattattccccagaccccacccgtgggagcttcca
               |  |||||||||| || || |||||||| ||||| ||| || |||| |||||||||||| |  |||| || || || || |||||||| ||||| |||||  |||  |  || ||   |   ||||     |     |  || ||  ||| | ||  |      ||||| |   | ||     |              
ATCAAGACTCTGTTAGATTGTTGGCTGTGGAGGGTTGTGCTGCTCTTGGGAAACTGCTGGAGCCACAAGATTGCATCACACATATACTACCGgttattgtcaacttctcgcaggtgtatttttagca-gtgaaa--tatactgttagttatcatcaaattaatttttctgctt-----cattatgcttaaaactattgct-------------

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 4
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 5'ss of exon 3
GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgctcccatgttggacccatacatcctgcagcaagtaatttgctttctttgtctggaaatattattccccagaccccacccgtgggagcttcca
  |  | ||||| ||||| || |||||||| ||||| ||||||||||| || || ||||| ||   |||||||||||| || ||||| |||||||| |||||              ||    |  ||     |   ||   | || | |    |||    | ||   ||| ||     ||     |  || |        
TAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCTCAGGATTGTGTCCAACACATTCTTCCCGTGATTGTTAATTTCTCGCAGgtg------------attatgtctgtaggcttttatgctgatgatctaca---tttaaaagaaatgcttaatctttgtactttttcactgagcag-----

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 4
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 5'ss of exon 4
GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgctcc-catgttggacccatacatcctgcag-caagtaatttgctttctttgtctgg-aaatat-tat----tccccagaccccacccgtgggagcttcca----
  |  | ||||||||||| || |||||||| ||||| ||||||||||| || || || || || |||||||||||||| || |||||||||||||| |||||| ||   |       |  ||   | | || ||   |   ||   | ||       |||  || | |||| |||    | |     |   |    |     |||  |    
TAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGTCAATTTCTCGCAGgtaaataaatgtgtgaatatgataaaaaaattctattgatgagctttatgggaaagctgtaaggcagatatgtatgagctgctttatcttgatttttttcgtctttgagcag

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 4
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 4
GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattg---ctcccatgttggacccatacatcctgcagcaagtaatttgct-ttctttgtctggaaatattattccccagaccccacccgtgggagcttcca-------------------------------
| | || |||||||||||||| ||||| || ||||| || ||||||||||| || ||||| || |||| |||| | || || ||||| |||||||| |||||  ||||    |    | ||  |  |||  ||  | |||  | |  | |||| |||  ||| |  || | | ||     | | |   |   |  ||  ||                                  
GAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAAAGTTGTTGGAACCTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGTTAATTTCTCTCAGgtgaattgagctttgtttttttcattcatggatttttcagttaattgtctgctgttccatgttt--aattttcatcggtaaaagcttgctgttctgatgtttttctatggtgtttgtattgatttctgagagcag

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 4
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 5'ss of exon 5
GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgctcccatgttggacccatacatc-----ctgcagcaagtaatttgctttctt-tgtctggaaatattattc-cccagaccccacccgtgggagcttcca
  |  | ||||||||||| || ||||| || || || ||  |||||||||| |||||||| |||||||| |||||||| || ||||| |||||||| |||||||||  |    | ||||||    |  |||      |    | |   ||||||||  |  | | |  || | |  ||   |   | |  |   ||   ||      
TAGGTTATTGGCTGTTGAGGGTTGTGCAGCTCTCGGAAAGCTGTTGGAACCTCAAGATTGTGTAGCACATATTCTTCCCGTAATTGTGAATTTCTCTCAGgtacat--ccataaagttggatatgttaatcaacatttatttccatggatttgcttattcatattttaaagtttctttgatcttcatcttatgtgttcaagt-----

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|33091965|gb|CF051959.1|CF051959
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|32940030|gb|CF044849.1|CF044849
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|32831601|gb|CD971279.1|CD971279
EST:     CACAAGATTGCGTA-CACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|211403483|gb|FL417168.1|FL417168
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|32938569|gb|CF043388.1|CF043388
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|22935744|gb|BU572019.1|BU572019
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|32830645|gb|CD970323.1|CD970323
EST:     CACAAGATTGCGTA-CNCACATTCTTCCAGTCATTGTCAATTTCTCC-AG                         GATAAATCATGGCGTGTTCGTTATATGGTTGCCAANTCAAT-ATATGAGCT
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAA-TCAATTATATGAGCT
EST: gi|31349427|gb|CD433784.1|CD433784
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|211356091|gb|FL413289.1|FL413289
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTA
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTA
EST: gi|32847343|gb|CD987024.1|CD987024
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|211150174|gb|FL390449.1|FL390449
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|31353403|gb|CD437760.1|CD437760
EST:     ACAAGATTGCGTAGCACACATTCTTCCAGTCATTTGTCA-TTTCTCCCAG                         GATAAATCATGGCGTGTT
genomic: ACAAGATTGCGTAGCACACATTCTTCCAGTCATT-GTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTT
EST: gi|32829962|gb|CD969640.1|CD969640
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|32851452|gb|CD991133.1|CD991133
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|31356642|gb|CD440999.1|CD440999
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|21088918|gb|BQ401231.1|BQ401231
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATA
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATA
EST: gi|211520937|gb|FL382784.1|FL382784
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|31355734|gb|CD440091.1|CD440091
EST:     TTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATCGTGTGTTCGTTATATGGTCGCCAATCAATTATATGAGCTC
genomic: TTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC

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: 364

GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 255

GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG