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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGCTGTACAAGGACTACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgcttcgctccgtttcggaacaccccgtttcctcttgttcagcttcggtccttttactagggcgttgctttgtgctttctccggactggaatgaa...

Basic information

species Zea mays
transcript GRMZM2G150616_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G150616_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G40800.1 (Glycine max), 5'ss of exon 2
ATCTGCTGTACAAGGACTACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgcttcgctccgtttcggaacacccc-gtttcctcttgttcagcttcggtccttttactagggcgttgctttgtgctt-tctccggactggaatgaa
|||| |||| |||||| || |||| |||||||||||||||| |||| || ||||| |||| ||| || |||||   ||   |   |||        |   |     | || ||  | ||   |     ||   ||    || |||||  || | | | ||      | | 
ATCTTCTGTTCAAGGATTATCAGAATGACCACAAGTTCACCATCACCACTTACACTTCCACTGGAGTGgtaaggttttatttatttttttatttgtctttgaagtatatttttttgtttaaatttgactat--ggaaaatgttttgtttttgttttcagatattcgttat

upper sequence: GRMZM2G150616_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA18G49070.1 (Glycine max), 5'ss of exon 2
ATCTGCTGTACAAGGACTACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgcttcgctccgtttcggaacaccccgtttcctcttgttcagcttcggtccttttactagggcgttgctttgtgctt------tct-ccggactggaatgaa
 |||||||| |||||||||||| | |||||| ||||||||| |||| |||||| |  | | ||| || || |||| ||   |   |||   ||  |  |  ||  | | |  ||    |  | | |  | | ||   ||| |||||  ||      |||      || |  ||||
-TCTGCTGTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACCACCTACTCACCGACTGGAGTTGtgagtgttt---tttattt---aatccttcaatttttgtggcacaaacacaatgcatggaatgggtatttgttttgttattggatgttctatttagcttgtgtgaa

upper sequence: GRMZM2G150616_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA09G37570.1 (Glycine max), 5'ss of exon 2
ATCTGCTGTACAAGGACTACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgcttcgctccgtttcggaacaccccgtttcctcttgttcagcttcggtccttttactagggcgttgctttg-tgctttctccggactggaatgaa---
||||||||| |||||||||||| | |||||| ||||||||| |||| |||||| |  ||| ||| || || |||| ||   |   ||    ||     |  ||  | | |  ||    |  | | |  | | ||   ||| |||| || |   |  |   | | |||     
ATCTGCTGTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACCACCTACTCACCCACTGGAGTTgtgagtgtttttttttttt----aatctttcaatttttgtggcacaaacacaatgcatggaatgggtatttgttttgctgttgggtttgttattggatgttctt

upper sequence: GRMZM2G150616_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA19G02380.1 (Glycine max), 5'ss of exon 2
ATCTGCTGTACAAGGACTACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgcttcgctccgtttcggaacaccccgtttcctcttgttcagcttcggtccttttactagggcgttgctttgtgctttctccggactggaatgaa--
|||| |||| |||||||||||| | |||||| ||||| ||| ||||||||||| |  ||| ||| || |||||   ||   |   || |           |||  |  |  | |   |  |     | | || |  | |||| | |   |    | || || ||      
ATCTCCTGTTCAAGGACTACCACAGTGACCAGAAGTTTACCATCACTACCTACTCACCCACTGGAGTTgtaagctatta--tttattactattattattttttaattattattattatgaggatgatgattatgatgatgctatatttctaggactgattgaaactgggt

upper sequence: GRMZM2G150616_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA13G05130.1 (Glycine max), 5'ss of exon 2
ATCTGCTGTACAAGGACTACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgcttcgctccgtttcggaacaccccgtttcctcttgttcagcttcggtccttttactagggcgttgctttgtgctttctccggactggaatgaa---
|||| || | |||||||||||| | |||||| ||||||||| ||||||||||| |  ||| ||| || |||||   ||   |    ||   |  |      ||  | || || |   |   |  | ||| ||     ||  ||   |   |    | |||||  | |    
ATCTCCTCTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACTACCTACTCACCCACTGGAGTTgtaagctatttattattattattattattattattattattatt-attattattattattattat--tattatttctaggactgattgaactgggtttattcc

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|211412244|gb|FL229030.1|FL229030
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|78121836|gb|DV540220.1|DV540220
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|211412254|gb|FL229040.1|FL229040
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGNACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|148936370|gb|EC880462.2|EC880462
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|211414795|gb|FL229043.1|FL229043
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|211412252|gb|FL229038.1|FL229038
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|149110762|gb|EE190597.2|EE190597
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|148973802|gb|EE024938.2|EE024938
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|149088362|gb|EE177462.2|EE177462
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|91050628|gb|EB161046.1|EB161046
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|116815705|gb|EC858392.1|EC858392
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|211412253|gb|FL229039.1|FL229039
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|31348886|gb|CD433243.1|CD433243
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|14204290|gb|BG837967.1|BG837967
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACCCCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|32838380|gb|CD978058.1|CD978058
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|211412247|gb|FL229033.1|FL229033
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|211412248|gb|FL229034.1|FL229034
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|211412256|gb|FL229042.1|FL229042
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         RMTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|211412243|gb|FL229029.1|FL229029
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|33104065|gb|CF064025.1|CF064025
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|211412250|gb|FL229036.1|FL229036
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|32855345|gb|CD995026.1|CD995026
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|93013107|gb|EB638627.1|EB638627
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|94473288|gb|EB702246.1|EB702246
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|211412249|gb|FL229035.1|FL229035
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|32934430|gb|CF039242.1|CF039242
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|211412245|gb|FL229031.1|FL229031
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|211412255|gb|FL229041.1|FL229041
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|211412242|gb|FL229028.1|FL229028
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
EST: gi|211061032|gb|FL204119.1|FL204119
EST:     ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC                         GCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC
genomic: ACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATC

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: 951

ATCTGCTGTACAAGGACTACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATCCAATCACAGATAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 953

ATCTGCTGTACAAGGACTACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATCCAATCACAGATAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 603

ATCTGCTGTACAAGGACTACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATCCAATCACAGATAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 818

ATCTGCTGTACAAGGACTACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTCgtaagtgctt ... tttcatgcagGCTGTAACTGCTTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATCCAATCACAGATAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACT