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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgctcttttctgtaattactgggagtaattgttggttttattagcatgatcatgcatttgggtccacagtctacaactgttacaaaaataatgg...

Basic information

species Zea mays
transcript GRMZM5G877597_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G877597_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g50880.1 (Oryza sativa), 5'ss of exon 3
GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTAC-AAAAATCTAGAGAATACACAGgtaatatgctcttttctgtaattactgggagtaattgttggttttattagcatgatcatg-catttgggtccacagtctacaactgttacaaaaataatgg
 ||||| |||||||||||||| ||||| ||||||||||||||||| || ||||||||||  ||||||||| | |||||  |||| ||| ||||||| |||||||| ||||| |      ||||| |  | |       ||   ||   | | ||||||||| |  ||          | ||  |   ||||     |   ||
-TCTCTCAAACATGAAGATGCAGAGAATATAGGTTATGTGATACCCACCCCAGTTATTATGCATTTCATTCAAGACTATGAAAAGTCTGGAGAATATACAGgtaa-atgctatacaacttaattgcatgaatatgccatttacttctattgtatgatcatggcccttcttcttttcttttagtataattacctctgtttggg

upper sequence: GRMZM5G877597_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA17G09970.1 (Glycine max), 5'ss of exon 3
GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATC-TAGAGAATACACAGgtaatatgctcttttctg--taattactgggagtaattgtt----ggttttattagcatgatcatgcatttggg--tccacagtctacaac---tgttacaaaaataatgg----
 || || || ||||||||||||||||| ||||||||||| || || || |||||||| |  ||||| ||  |||| ||  | ||   | ||| ||| || ||||||||| |   | |    |||    | |   | | | ||    | |  ||| ||     |  |  | |||    |  |    ||   |    | || |  ||      |    
-TCCCTCAAGCATGAAGATGCGGAGAATATAGGTTATGTCATTCCAACGCCAGTTATCATGCATTTTATCCAGGATTATGAGAAGAATGGAGGATATACTGgtaatatggtagctacaaactaagatgtagatttcacttttacaagatgctatcagagcatttttagaattgaagttttatgcactgagatctttctttctcaatctgctgttag

upper sequence: GRMZM5G877597_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA01G16820.1 (Glycine max), 5'ss of exon 3
GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATC-TAGAGAATACACAGgta----atatgctcttttctgtaattactgggagta-attgttggttttattagcatgatcatgcatttgggtccacagtctacaactgttacaaaaataatgg
 ||||||||||||||||||| |||||| ||||| ||||| ||||| || ||||||||   |||||| ||    |||||  ||||   | | | ||| |||||||    | | | | ||||   |  ||         | |   ||    ||  ||        || |||||       |    |    ||  |  | |   |||  
-TCTCTTAAACATGAAGATGTGGAGAATATAGGATATGTAATACCCACCCCAGTTATCCTACATTTTATCCGAGACTATGAAAAGAATGGGGCATATACAGgtatctaaaaggatgttttacttctttgtctatttcatacccttctccttcctaaagaagatat-catttactcttgct-cttgtgtctact-tagaggaaat--

upper sequence: GRMZM5G877597_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA05G01930.1 (Glycine max), 5'ss of exon 3
GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATC-TAGAGAATACACAGgtaatatgctcttttctgtaattactgggagtaattgttggttttattag------catgatcat-----gcatttgggtccacagtctacaactgttacaaaaataatgg-------
 || || || ||||||||||||||||| ||||||||||| || || || |||||||| |  ||||| ||  |||| ||  | ||   | ||| ||| || ||||||||| |   |   | || ||   |  |||  | |   |||||  ||      | ||| |||     | |||  | |  |    ||   |   ||       ||   |       
-TCCCTCAAGCATGAAGATGCGGAGAATATAGGTTATGTCATTCCAACGCCAGTTATCATGCATTTTATCCAGGATTATGAGAAGAATGGAGGATATACTGgtaatatggtagcta--ggaacta--agatgtagatttcacttttacaagatgctacctgagcatttttagaattaagttttatgcactcagatctttctttctctatctgctgttag

upper sequence: GRMZM5G877597_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv17s0000g07900.t01 (Vitis vinifera), 5'ss of exon 3
GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATC-TAGAGAATACACAGgtaatatgctcttttctgtaattactgggagtaattgttggttttattagcatgatcatgcatttgggtccacagtctacaactgttacaaaaataatgg----
 |||||||||||||||||||| ||||| ||||||||||| ||||| || ||||| || |  || || ||  | || ||  | ||   | ||| ||| || |||| | |  |   || ||   | |          ||| |  | || ||       |  || |     |   ||||| ||    |||    ||  |  |      
-TCTCTTAAACATGAAGATGCAGAGAATATAGGTTATGTCATACCAACACCAGTCATCAAGCACTTTATCCAAGATTATGAGAAGAATGGAGCATATACTGgta-tgtatttgattgtggcttcaactatttcggttgataatgttcttgttggatttttgaac---agcttacagtttatctttgtgcataacttccttatgat

upper sequence: GRMZM5G877597_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv14s0066g01660.t01 (Vitis vinifera), 5'ss of exon 3
GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATC-TAGAGAATACACAGgtaatatgctcttttctgtaattactgggagtaattgttggtttta-ttagcatga-tcatgcatttgggtccacagtctacaactgttacaaaaataatgg
 || ||||||||||||||||  ||||| ||||||||||| ||||| || ||||||||||  || |||||   ||| ||  | ||   | | | ||| ||||||         | |  | |  |   |   |||   |||  ||||||  |  || || | |  |  ||      |   |||| |  ||||       |     
-TCCCTTAAACATGAAGATGTAGAGAATATAGGTTATGTCATACCAACGCCAGTTATTATGCACTTCATCCGGGATTATGAGAAGAATGGTGCATATACAGgtgcatcagagtgtagtcttgtgcttttcagtttgtgtctgttttaactctcacgagttactctctttatataattatctaaatgtgttcttg--ttggcta

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|91054928|gb|EB165346.1|EB165346
EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
EST: gi|78090489|gb|DV518863.1|DV518863
EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
EST: gi|91054929|gb|EB165347.1|EB165347
EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
EST: gi|71431610|gb|DR812660.1|DR812660
EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
EST: gi|94472958|gb|EB701916.1|EB701916
EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
EST: gi|78084750|gb|DV513143.1|DV513143
EST:     AAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: AAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
EST: gi|71311298|gb|DR791964.1|DR791964
EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
EST: gi|74246237|gb|DT654151.1|DT654151
EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
EST: gi|88748255|gb|DY532396.1|DY532396
EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACGGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgctcttttctgtaattactgggagtaattgttggttttattagcatgatcatgcatttgggtccacagtctacaactgttacaaaaataatgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaataa