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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttttaatctgacagtggttgtctctttcagtcatagttggtagtattaacagttgaccaggttattgcccatatatgctgtttttattgtata...

Basic information

species Zea mays
transcript GRMZM2G143330_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143330_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os08g21660.2 (Oryza sativa), 5'ss of exon 6
ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttttaat-ctgacagtggttgtctctttcagtcatagttggtagtattaacagttgaccaggttattgcc-catatatgctgtttttattgtata---
|||||||||||||||||||||||||||||||| |||||||| |||||||| ||  |||||||||||||||||||||||||||||| || ||||| |    | | ||  |  | ||| | |   |    || | ||     ||||  || || || ||  || | ||   |||||  |  ||    
ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattcttaatacatgtatttgtatttacgttctgcccctgcactta-tgttc----ttgattagctttttcccatatttgtgtgctttttgctcaatgatt

upper sequence: GRMZM2G143330_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g16660.1 (Oryza sativa), 5'ss of exon 6
ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttttaatctgacagtggttgtctctttcagtcatagttg-gtagtattaacagttgaccaggttattgcccatatatgctgtttttattgtata-
|||||||||||||||||||||||||| ||||| |||||||| |||||||| ||  ||||||||||||||||||| |||||||||| || |||||      ||  |  | | |    |  ||| ||  ||  ||  | |        | ||| | |   |  | |    ||  ||||   |  
ATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAGgtaatattcttaatacatgtgtaatattatatgaatgctatatttatgttctaccaccg--cacttatgttctcgattagctttttgtttcatattactttg

upper sequence: GRMZM2G143330_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA09G36870.2 (Glycine max), 5'ss of exon 4
ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttttaatctgacagtggttgtctctttcagtcatagt-tggtagtattaacagttgac--caggttattgcccatatatgctgtttttattgtata-
||| | ||||| |||||||| ||||| ||||| || ||||| ||||||||||| ||||| ||||| ||||||||    |||||  || | |  |||     |   | |   |||   ||||    |  |  |||| |  |    |  | | |  |||   | ||   |     |  || | |  
ATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCACTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGGTATgttctctgttcttcacctcccttttgttttgcttcatgacatacttttattcaatgaaaccttccgttcgttggagaaattgacaaccatgcttatgtta

upper sequence: GRMZM2G143330_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA09G36870.1 (Glycine max), 5'ss of exon 4
ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttttaatctgacagtggttgtctctttcagtcatagttggtagtattaa-cagttgaccaggttattgcccatatatgctgtttttattgtata-
||| | ||||| |||||||| ||||| ||||| || ||||| ||||||||||| ||||| ||||| ||||||||    |||||  || | |  |||     |   | |   |||   ||||      || | |||  || |  | |      ||      | |   ||       ||  || 
ATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCACTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatgttctctgttcttcacctcccttttgttttgcttcatgac--atacttttattcaatgaaaccttccgttcgttggagaaattgacaaccatgcttat

upper sequence: GRMZM2G143330_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA12G00510.1 (Glycine max), 5'ss of exon 4
ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttttaatctgacagtggttgtctctttcagtcatagt-tggtagtattaacagttgac--caggttattgcccatatatgctgtttttattgtata
||| | ||||| |||||||| ||||| ||||| |||||||| ||||||||||| ||||| ||||| ||||||||    ||||   ||   |  |||     |   | |    ||   |||||   |  |  |||| |  |   ||  | | |  |||   | ||   |     |  || |   
ATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtgtattcactgttcttcacctcccttttgtgttgcatcataacatacttttattcaatgaaaacttccgttcgttggagaaattgacaaccatgcttat---

upper sequence: GRMZM2G143330_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA01G03610.2 (Glycine max), 5'ss of exon 7
ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttttaatctgacagtggttgtctctttcagtcatagttggtagtattaacagttgac-caggttattgcccatatatgctgtttttattgtata--
||| | ||||| |||||||| ||||| |||||||||||||| ||||||||||| ||||| ||||| ||||||||    |||||  || | |  |||   | |   | |    ||   ||||      || | |||    ||||  |    | |||     || || ||     ||||   |  
ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctgtgttcttcaactcccttttatattttatcatgac--atacttttattctttgaaaccttctgttgtttg-atttgttggagaaattgacaacc

upper sequence: GRMZM2G143330_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT2G46290.1 (Arabidopsis thaliana), 5'ss of exon 8
ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttttaa-tctgacagtggttgtctctttcagtcat-agttggtagtattaacagttgaccaggttattgcccatatatgctgtttttattgtata-----
||| ||||||||||||||||||| || ||||| |||||||| || ||||||||||||||||| | ||||||||||  |||||||  |    || | |||   || |||  |  | || || | ||||| |   | |    |||    ||| | |||    |   || | |||  | |||||      
ATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAGgtaaactaacaaaatttgattttgattgattgatacaatcctcagttgatgagagt----gttttttaggct-ttgttgctgagtgttttttggaatgtattttcag

upper sequence: GRMZM2G143330_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT2G46280.3 (Arabidopsis thaliana), 5'ss of exon 6
ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt--taatctgacagtggttgtctctttcagtcatagt-tggtagtattaacagttgaccaggttattgcccatatatgctgttttt--attgtata------
||| |||||||||||||||||||||| ||||| |||||||| || || |||||||||||||| ||||||||||||  ||||||| ||      | |  ||   || |||  |    || || |    || |    ||   |||       ||| | || |    |    |||| |  | ||||||      
ATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAGgtaaattaacaacatttggattttgattgattgacacaatcctcacatgatgaggttttgagt---gtgtgttttggctctctcactgagtttgtggaatgtatatttcag

upper sequence: GRMZM2G143330_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S28_21V6.2 (Physcomitrella patens), 5'ss of exon 2
ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaattttt-----ttaatctgacagtggttgtctctttcagtcatagttggtagtat-taacagttgaccaggttattgcccatatatgctgtttttattgtata
|||||  ||||||||||||||||||| || || |||||||| || ||||||||| | |  ||||||||||| ||  ||||||   ||||     ||| | |    |    |||     | |||  |  ||||   ||| ||  ||||      | | || |||| |||| |   | ||| |     
ATTTTCGAAGAGGAAATTGGTGGTGTGAAGGGCCATTTTGGACCTATTAATGCTCTAGTTTTTAATCCTGACGGAAGGAGgttcgttttggattttattttctgcgcatgtgttgggataagtagtttttggacatatgtataagtttggatagatgtttccca-atatccctctcttact-----

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|7119030|gb|AW497573.1|AW497573
EST:     GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGCTGCATCATTTTGATTC
genomic: GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
EST: gi|71760667|gb|DR958604.1|DR958604
EST:     GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
genomic: GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
EST: gi|7238210|gb|AW573477.1|AW573477
EST:     GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGCTGCATCATTTTGATTC
genomic: GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
EST: gi|211472837|gb|FL449625.1|FL449625
EST:     CCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
genomic: CCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
EST: gi|101401499|gb|EB822429.1|EB822429
EST:     GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTT
genomic: GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
EST: gi|78086971|gb|DV515364.1|DV515364
EST:     GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
genomic: GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
EST: gi|113648032|gb|DW806291.1|DW806291
EST:     TTTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
genomic: TTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
EST: gi|32825463|gb|CD965185.1|CD965185
EST:     TAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGCTGCATCATTTTGATTC
genomic: TAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
EST: gi|74242276|gb|DT650190.1|DT650190
EST:     GGCATTTAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
genomic: GGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
EST: gi|74243657|gb|DT651571.1|DT651571
EST:     GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
genomic: GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
EST: gi|78087876|gb|DV516269.1|DV516269
EST:     GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGGGGAG                         CTTTTCAAGTGGTGGTGAAGAGGGATATGTAAGGTTGCATCATTTTGATTC
genomic: GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
EST: gi|78119407|gb|DV537791.1|DV537791
EST:     GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
genomic: GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
EST: gi|37374667|gb|CF623711.1|CF623711
EST:     GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGCTGCATCATTTTGATTC
genomic: GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
EST: gi|60353275|gb|DN220248.1|DN220248
EST:     GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
genomic: GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
EST: gi|166703791|gb|EG200912.1|EG200912
EST:     GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGG
genomic: GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGG
EST: gi|32937077|gb|CF041896.1|CF041896
EST:     GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGCTGCATCATTTTGATTC
genomic: GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
EST: gi|91872572|gb|EB402529.1|EB402529
EST:     GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTT
genomic: GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
EST: gi|71301121|gb|DR786593.1|DR786593
EST:     GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
genomic: GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
EST: gi|31909651|gb|CD651025.1|CD651025
EST:     GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC
genomic: GGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTC

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: 48 (upstream exon), 49 (downstream exon)
Score: 287

ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 254

ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 166

ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 182

ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttt ... ttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAATCAGAG