Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgctaagctcttatcatgtctttcacttgctccatagtacctcttgattgtttgctatttctgacaacaattcctggctttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTGCTTTCCCGTTTTGATTTACTTTTTATTGTTCTTGATCAAATGGACCCTG

Basic information

species Zea mays
transcript GRMZM2G100639_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100639_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 8
gtaagctgctaagctcttatcatgtct--ttcacttgctccatagtacctcttgattgtttgctatttctgacaacaattcctggctttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTGCTTTCCCGTTTTGATTTACTTTTTATTGTTCTTGATCAAATGGACCCTG
         |||| |||||| || |||  | | ||   |  || |          ||  ||||  ||||||| || ||||  ||||| | | ||||||||| ||||||||||||||||| ||||| || |||||||| |||||| | || || ||||||||||| |||||||||||||||||||||||||| ||||
--------gtaagttcttattatttctcgtccgctgcttttatggcgtgataatgtt-cttgcattttctgataataatttttggctgtgttacagTATGACCGTTCATTGACACCAACCAAGAACATTGGGCTTCCAGATTCATTACTCTCACGTTTTGATTTGCTTTTTATTGTTCTTGATCAAATGGATCCTG

upper sequence: GRMZM2G100639_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G08920.1 (Glycine max), 3'ss of exon 8
---------------------gtaagctgctaagctcttatcatgtctttcacttgctccatagtacctcttgattgtttgctatttctgacaacaattcctg-gctttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTGCTTTCCCGTTTTGATTTACTTTTTATTGTTCTTGATCAAATGGACCCTG
                      |  ||||  ||| |   |  |      |  ||       || |    ||| |||  ||  | |  ||     |  ||  || ||  |   ||||||||||||||||||||| ||||| || |||||||| || || || ||  ||||||| || |||||| |||||||||||||  | ||||||||||| ||||
gtaagtggcattgtgagagaaatttgctgtgaagtttaaactaccaaagttcctgatattgtactgaacctttatttatttttctaactagtggcttttattgtgcaattctacagTATGATCGTTCATTGACTCCAACCAAAAATATCGGACTCCCAGACTCCTTGCTTTCTCGATTTGATCTACTTTTTATTGTGTTGGATCAAATGGATCCTG

upper sequence: GRMZM2G100639_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 8
---------------------gtaagctgctaagctcttatcatgtctttcacttgctccatagtacctcttgattgtttgctatttctgacaacaattcctg----gctttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTGCTTTCCCGTTTTGATTTACTTTTTATTGTTCTTGATCAAATGGACCCTG
                      |  ||||  ||| |   |  |      |  ||       ||       || | | |||  | ||    | |     |  |     ||  |   ||||||||||||||||||||| ||||| || ||||| || || || || ||  ||||||| || |||||| |||| ||||||||  | ||||||||||| ||||
gtaagtggcattatgcgggaaatttgctgtgaagtttaaactaccaaagttcctgatgttgtaccgaacatttaattttttttcttctaaatagtggcttttattgtgcaattctacagTATGATCGTTCATTGACTCCAACCAAAAATATTGGACTCCCAGACTCCTTGCTTTCTCGATTTGATCTACTGTTTATTGTGTTAGATCAAATGGATCCTG

upper sequence: GRMZM2G100639_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT5G46280.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagctgctaagctcttatcatgtctttcacttgctccatagtacctcttgattgtttgctatttctgacaacaattcctggctttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTGCTTTCCCGTTTTGATTTACTTTTTATTGTTCTTGATCAAATGGACCCTG
         |||| ||| | |     ||||   |  || |      ||  ||| |  |   | ||| |   || |  | ||     |    ||||||||  | ||| |||| ||||||||||| || || ||||| ||||| |||||||| ||||||||| |||| ||||||||  | |||||||||||  |||
--------gtaagttctcaccgaagttttc--ctaatctacttactctactgactagtatttttttgtcctaatacctactcttgctcctgcagTATGACAGATCACTGACTCCAACAAAGAACATTGGACTTCCAGATTCGCTGCTTTCTCGTTTTGATCTACTGTTTATTGTGTTGGATCAAATGGATGCTG

upper sequence: GRMZM2G100639_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 8
-----------gtaagctgctaagctcttatcatgtctttcacttgctccatagtacctcttgattgtttgctatttctgac-----aacaattcctggctttatg-acagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTGCTTTCCCGTTTTGATTTACTTTTTATTGTTCTTGATCAAATGGACCCTG
            |    | ||||  |   |||  ||  | | | |  | |||| || | | | |||| |  ||   | |||           ||  ||  || ||| ||||||||| || ||||| || |||||||||||||| || ||||| || ||  |||| ||||||||||||||||| ||||| ||  | || ||||||||  |||
gtgagttttacatttattactaatataa-atccagtaatactcatattgcataataacgcatcattgctgccttaatttgattttctgctggttattgaattgatgtacagTATGACCGGTCATTAACCCCAACAAAGAATATTGGACTTCCAGACTCTTTGCTCTCCCGTTTTGATTTACTGTTTATAGTATTGGACCAAATGGATGCTG

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|60398614|gb|DN231430.1|DN231430
EST:     TAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACT                         TATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTG
genomic: TAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACTgtaagctgct ... tttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTG
EST: gi|32933016|gb|CF037828.1|CF037828
EST:     TAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACT                         TATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTG
genomic: TAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACTgtaagctgct ... tttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTG
EST: gi|5895653|gb|AW036899.1|AW036899
EST:     TAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACT                         TATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTG
genomic: TAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACTgtaagctgct ... tttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTG
EST: gi|32934580|gb|CF039392.1|CF039392
EST:     TAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACT                         TATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTG
genomic: TAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACTgtaagctgct ... tttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTG
EST: gi|32945489|gb|CF050308.1|CF050308
EST:     TAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACT                         TATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTG
genomic: TAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACTgtaagctgct ... tttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTG
EST: gi|60341724|gb|DN208697.1|DN208697
EST:     TAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACT                         TATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTG
genomic: TAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACTgtaagctgct ... tttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTG
EST: gi|32930876|gb|CF035688.1|CF035688
EST:     TAAATGCAAGATGTAGTGTAATTTCTGCAGCAAATCCAATATATGTAACT                         TATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTG
genomic: TAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACTgtaagctgct ... tttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTG
EST: gi|32933866|gb|CF038678.1|CF038678
EST:     TAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACT                         TATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTG
genomic: TAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACTgtaagctgct ... tttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTG
EST: gi|9566453|gb|BE475962.1|BE475962
EST:     TAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACT                         TATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCA
genomic: TAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACTgtaagctgct ... tttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCA

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: 319

TATGGAACAGCAAACTGTAACCATTGCAAAGGCAGGAATACATGCCTCACTAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACTgtaagctgct ... tttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTGCTTTCCCGTTTTGATTTACTTTTTATTGTTCTTGATCAAATGGACCCTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 72

TATGGAACAGCAAACTGTAACCATTGCAAAGGCAGGAATACATGCCTCACTAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACTgtaagctgct ... tttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTGCTTTCCCGTTTTGATTTACTTTTTATTGTTCTTGATCAAATGGACCCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 44

TATGGAACAGCAAACTGTAACCATTGCAAAGGCAGGAATACATGCCTCACTAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACTgtaagctgct ... tttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTGCTTTCCCGTTTTGATTTACTTTTTATTGTTCTTGATCAAATGGACCCTG


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 19

TATGGAACAGCAAACTGTAACCATTGCAAAGGCAGGAATACATGCCTCACTAAATGCAAGATGTAGTGTAATTGCTGCAGCAAATCCAATATATGGAACTgtaagctgct ... tttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTGCTTTCCCGTTTTGATTTACTTTTTATTGTTCTTGATCAAATGGACCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtacctcttgattgtttgctatttctgacaacaattcctggctttatgacagTATGATCGTTCATTGACACCAACAAAGAATATCGGGCTTCCGGATTCACTGCTTTCCCGTTTTGATTTACTTTTTATTGTTCTTGATCAAATGGACCCTG
                         ttctgac  putative branch site (score: 19)
             attgttt  TA-rich tract