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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatcttcttattgaagttgtcagacctgtacttttcaggcactcccttctaatcaataatgtacatgaatttcattgggtgaatatttggacta...

Basic information

species Zea mays
transcript GRMZM2G073774_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 5'ss of exon 11
TGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagt----tatcttcttat-tgaagttgtcagacctgtacttttcaggcactcccttctaatcaataatgtacatgaatttcattgggtgaatatttggacta
||| |||||||||||||| | ||| |||||||||||||||||||||||||| || || || ||||| |||||||||||||||||||||||  | ||||||||||||    | |  ||  || |    || |     |||  || || | ||  | | |  | ||| |     |   | |  ||   ||  |  |||||| | |  
TGTCGAACAAATCTCTGGGAGGGACCACATCCTAAATCATTTAAGCATCCCCGCTGCTTGCTTCACTCATCCAGAGATTAGTATGGTTGGGCTTACAGAGgtaagtcgggtgtaatcccatatagctttctttagtctgccctgtttatgcgttacttcttcatctact---tctgttatattttctgtcttgatatttagtc--

upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 11
TGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatcttcttattgaagttgtcagacctgtacttttcaggcactcccttctaatcaataatgtacatgaatttcattgggtgaatatttggacta-----------------------------------------------------------------------------------------------------------
 ||||||||| || ||||||| |||||| | || |||||||||||||||||||| || |||||||| ||||| ||  |||| ||||||||||| |||||||||  | ||  | |||||    ||||  ||  ||| | ||    |||     ||  ||| ||| |  |   |   ||   |  ||| ||  ||    | |                                                                                                           
GGTTGAACAAGTCACTGGAAAAGATCACGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAACTTAGCATGGTTGGATTAACAGAGgtatatcataattttatt----ttgtttgatgtgt-cattcactgcaacaatttacaatgaatgagttctctt--ttatgtgtggttaactttctctccattcttcttttccatcctcttttccttatattatttatacattaaaatttctgcctcttgtccttcacttgaattctcttgtgttgtgatcaaacttaaaatctgcag

upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA09G04270.1 (Glycine max), 5'ss of exon 6
TGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagt--tatcttcttattgaagttgtcagacctgtacttttcaggcactcccttctaatcaataatgtacatgaatttcattgggtgaatatttggacta-
 ||||||||| || ||||||  |||||| | || |||||||||||||| ||||| || |||||||| ||||| || || || |||||||||||||| ||||||  |  ||| ||||| | |  | |||     || | | |  ||  |||| |    |  |  ||  | |   || |  |   |   ||     ||   ||  
GGTTGAACAAGTCACTGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACTGAGgtatatcatattttcttttcgttgatgtttcttctcttcctc-cacccactgctgcatgtttcattct-tctgtgcacatggctaactgtcc-cttcctctgt

upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA15G15310.1 (Glycine max), 5'ss of exon 11
TGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatcttcttattgaagttgtcagacctgtacttttcaggcactcccttctaatcaataatgtacatgaatttcattgggtgaatatttggacta
 ||||||||| |  | ||||  |||||| | || |||||||||||||| ||||| || |||||||| ||||| || || || |||||||||||||||||||||  | || |  || ||    ||||      |  |   | ||    || | |  |      |  ||||||      | | ||        | ||  || 
GGTTGAACAAGTGACCGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGAGgtatatcatatattttttttttttgtttatgtttcatcctccacctgctgcttgtttcattcttctgtacagatggctaagtgtcccctcctctgttctt

upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA07G37050.1 (Glycine max), 5'ss of exon 11
TGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatcttcttattgaagttgtcagacctgtacttttcaggcactcccttctaatcaataatgtacatgaatttcattgggtgaatatttggacta-------
 ||||||||| || ||||||  |||| | | || |||||||||||||||||||| || |||||||| ||||| || || || |||||||||||||||||||||  | ||  | |||||    ||||  ||  ||| | ||    |||     ||  ||  ||| |  |   |   |    |  ||| ||  ||    | |       
GGTTGAACAAGTCACTGGAAGAGATCTCGTGCTCAATCATTTAAGCATCCCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACAGAGgtatatcataattttatt----ttgtttgatgtgt-cattcactgcaacattttacaacaaatgagttttctt--tcatgtgtggttaaccttctctccattcttct

upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 11
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 11
TGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatcttcttattgaagttgtcagacctgtacttttcaggcactccc-ttctaatcaataatgtacatgaatttcattgggtgaatatttggacta
 || || ||| || | || |  |||||  | || |||||| | ||||||||||| || ||||| || ||||| || || |||||||| ||||||||||||||||     | |||        ||    ||   ||  |||| |   | | |  | |||||  || || |   | |  || | ||    |||     |    
GGTGGAGCAAGTCACAGGTAGAGATCATGTGCTTAATCATCTTAGCATCCCAGCTGCTTGTTTTACTCATCCTGAAATAAGTATGGTGGGATTGACAGAGgtaa-----cctctagacactcttagtggattggt--ttttaaaaaattgcaatcctaatttatgatttcggtaatctttaatgc---aattcccag----

upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 11
TGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagtt---atcttcttattgaagttgtcagacctgtacttttcaggcactcccttctaatcaataatgtacatgaatttcat-tgggtgaatatttggacta-----------------------------------------------------------
|||||| ||| |  | |||||||||||  | || |||||||| |||||||||||||| |||||||| |||||||| || ||||||||||||||||| ||||||| ||   ||| ||  |||  |  || ||   |  |  |  |  |  | |   |  |  |  |  | ||   |    | |||     |  ||  |  | |                                                             
TGTTGAGCAAGTTACCGGAAAGGATCATGTGCTCAATCATTTGAGCATCCCAGCAGCTTGTTTCACTCATCCAGAAATCAGTATGGTTGGATTGACTGAGgtaaatttaaatcatccaattata--tgcca---caatgttaatatgagattagttcttggtggaataggtttgtttcctgcatgcaaattgatgctctggcagctagttctactctgtgggttctctaaactctgtttttaactgaatataaaaattcacag

upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 5'ss of exon 11
TGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagt--------tatcttcttattgaagttgtcagacctgtacttttcaggcactcccttctaatcaataatgta--catgaatttcattgggtgaatatttggacta
||||||||||||   |||||||||  |  | || |||||||| |||||||||||||| |||||||||||||| ||||| |||||||| ||  |||||||||||| |        || |  |   || |  || ||  | || ||  ||||   |||||||   |  ||     |  |  |||    |   |||  |||| ||        
TGTTGAACAAATTAGTGGAAAGGACAATGTGCTGAATCATTTGAGCATCCCAGCAGCGTGTTTCACCCATCCTGAGATCAGTATGGTGGGGCTGACAGAGgtaattctgtgctttacccacacttttatattatcttagctatatatttc---cactcccacatgttcccctcttcaaccattctctattttgtatgaaaatc-------

upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 11
lower sequence: EFJ16882 (Selaginella moellendorffii), 5'ss of exon 11
TGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatcttcttattgaagttgtcagacctgtacttttcaggcactcccttctaatcaataatgtacatgaatttcattgggtgaatatttggacta
| ||||   | |  ||||||| ||  |  ||||||| ||||||||||| |||||||| || ||||| ||||||||||| || |||  |||  |||| ||||||  |   | |  | | | ||||         |   |||  | ||| |    |  |  |  |   |                                 
TATTGAGAGACTTGCTGGAAACGACAATGTCCTAAACCATTTAAGCATACCAGCAGCTTGCTTCACACATCCAGAGATAAGCATGACTGGCATGACTGAGgtacatacgcattctctcggagtt--------cgctttttgtaagcagtgtacttcatgcgttccag---------------------------------

upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 11
lower sequence: EFJ06739 (Selaginella moellendorffii), 5'ss of exon 11
TGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatcttcttattgaagttgtcagacctgtacttttcaggcactcccttctaatcaataatgtacatgaatttcattgggtgaatatttggacta
| ||||   | |  ||||||| ||  |  ||||||| ||||||||||| ||||| || || ||||| ||||||||||| || |||  |||  |||| ||||||  |   | |  | | | | ||    | | | |         | ||| | | |    ||                                       
TATTGAGAGACTTGCTGGAAACGACAATGTCCTAAACCATTTAAGCATACCAGCCGCTTGCTTCACACATCCAGAGATAAGCATGACTGGGATGACTGAGgtacatacgcattctctcggaattc---gccttttgtaagcagtgtacttcatgcgttccag--------------------------------------

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|32944152|gb|CF048971.1|CF048971
EST:     CAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGACTGACAGAG                         CCACAAGCCAGAGAGAAGGCTGATAAAGAAGGATTTGAGATAAATGTTGTG
genomic: CAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatc ... actttctcagCCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTG
EST: gi|67029833|gb|CO458582.1|CO458582
EST:     CAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGACTGACAGAG                         CCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTG
genomic: CAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatc ... actttctcagCCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTG
EST: gi|211287326|gb|FL348627.1|FL348627
EST:     CAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGACTGACAGAG                         CCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGATAAATGTTGTG
genomic: CAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatc ... actttctcagCCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTG
EST: gi|13315813|gb|BG410365.1|BG410365
EST:     CAGCAGCATGTTTCACGCATCCAGAGATTAGTATGGTTGGATTGACAGAG                         CCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTG
genomic: CAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatc ... actttctcagCCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTG
EST: gi|31362407|gb|CD446764.1|CD446764
EST:     CAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGACTGACAGAG                         CCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTG
genomic: CAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatc ... actttctcagCCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTG
EST: gi|78075765|gb|DV504199.1|DV504199
EST:     CAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAG                         CCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTG
genomic: CAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatc ... actttctcagCCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTG
EST: gi|211284887|gb|FL322128.1|FL322128
EST:     CAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGACTGACAGAG                         CCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGATAAATGTTGTG
genomic: CAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatc ... actttctcagCCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTG
EST: gi|60340265|gb|DN207238.1|DN207238
EST:     CAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGACTGACAGAG                         CCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGATAAATGTTGTG
genomic: CAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatc ... actttctcagCCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTG
EST: gi|31353176|gb|CD437533.1|CD437533
EST:     CAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGACTGACAGAG                         CCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTG
genomic: CAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatc ... actttctcagCCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTG

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

TGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatc ... actttctcagCCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTGAAGACTAGCTTTAAGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 145

TGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatc ... actttctcagCCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTGAAGACTAGCTTTAAGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

TGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatc ... actttctcagCCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTGAAGACTAGCTTTAAGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 323

TGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGAGgtaagttatc ... actttctcagCCACAAGCCAGAGAGAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTGAAGACTAGCTTTAAGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAG