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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGAACAACTGGTGGACATCGGTTGTCAATGGGTTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattttatgtgcatatgctactggtttgatgcttgcagaaacatagtttgtgattgcaatataacaagttgctcaaatgcag

Basic information

species Zea mays
transcript GRMZM5G852968_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G852968_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os09g36450.1 (Oryza sativa), 5'ss of exon 5
TGCAGAACAACTGGTGGACATCGGTTGTCAATGGGTTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattttatgtgcatatgctactggtttgat-gcttgcagaaacata-gtttgtgattgcaatataacaagttgc---tcaaatgcag---------------------------------------------------------------------------
||| || ||| |||||||||| || || ||||||||||||||||| || ||||||||||||||| | ||||||||| ||||  |||| |    | |||   || |||||||||| ||| | | |  |  |    |    ||||   |||  | || |  ||  |      || |||                                                                            
TGCGGAGCAATTGGTGGACATTGGCTGCCAATGGGTTATTCTTGGGCATTCAGAGCGTAGACATGTCATTGGTGAAGATGATCAGgtaagcgctatatacacagatgctactggattggtagttctctcacttgtccacttgtccatgctgt-tagcctgtaacattctgaaggcacctttgagatgcatgattgctgttgacatgcagtagttctgattgggattgtgacataccatgtttataaatgcag

upper sequence: GRMZM5G852968_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA13G20930.1 (Glycine max), 5'ss of exon 5
TGCAGAACAACTGGTGGACATCGGTTGTCAATGGGTTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattttatgtgcatatgctactggtttgatgct-tgcagaaacatagtttgt----gattgcaat--ataacaagttgctcaaatgcag--------------
||  || |||||    ||| | || ||  | ||||||||||||||||| || ||||| |||||| | ||||| |||||||| |||||||  |||||      |  | |||  |   |  | || || |  |  ||  |||||    |||   |||  |||| || |     ||    ||              
TGTGGAGCAACTAAAAGACCTTGGCTGCAAGTGGGTTATTCTTGGACATTCTGAGCGAAGACATGTAATTGGAGAAAATGATGAGgtgaaaattttggagataatttctatagtagttttcctatggaccagtattatttgtaaaagatgaaaatgtataataattataataaccaaagattgcaaactccag

upper sequence: GRMZM5G852968_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA10G06740.1 (Glycine max), 5'ss of exon 5
TGCAGAACAACTGGTGGACATCGGTTGTCAATGGGTTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattttatgtgcatatgctactggtttgatgcttgcaga--aacatagtttgt----gattgcaat--ataacaagttgctcaaatgcag----------
||  || |||||    ||| | || ||  | ||||||||||||||||| || ||||| |||||| | ||||| |||||||| |||||||  |||||      |  | ||| | ||    | | |   ||  |  ||  |||||    |||   |||  |||| |   |   | ||    |          
TGTGGAGCAACTAAAAGACCTTGGCTGCAAGTGGGTTATTCTTGGACATTCTGAGCGAAGACATGTAATTGGAGAAAATGATGAGgtgaaaattttggagataccttcta-tagtagttttcctagggaccagtattctttgtaaaagatgaaaatgtataatatactaaccgaagattgcaaactccag

upper sequence: GRMZM5G852968_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA19G36990.2 (Glycine max), 5'ss of exon 5
TGCAGAACAACTGGTGGACATCGGTTGTCAATGGGTTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattttatgtgcat-atgctactggtttgatgcttgcaga-aacatagtt--tgtgattgcaata--taacaagttgctcaaatgcag---------------------
 || ||||||||    ||  | || ||  | |||||| |||||||||| || ||||| |||||||||||||| |||||||| ||||| |      |     ||| ||  | ||    |     |   ||| || ||  ||  | |  |||||| |  |   || |   | | ||                         
CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaatccagacatcatttttctacagtagctttgctagagaatatgattagtatatttgcaagagatgctaaatatttaagatattaactgaacattgtcaattccag

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|71757354|gb|DR955291.1|DR955291
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|101387332|gb|EB815682.1|EB815682
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|71319071|gb|DR796286.1|DR796286
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|76014692|gb|DT941862.1|DT941862
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|149089024|gb|EE178175.2|EE178175
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|50337624|gb|CO532750.1|CO532750
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|60344413|gb|DN211386.1|DN211386
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|78089192|gb|DV517576.1|DV517576
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|71439314|gb|DR820364.1|DR820364
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|148949372|gb|EC894828.2|EC894828
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|148990724|gb|EE032131.2|EE032131
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|211138817|gb|FL315878.1|FL315878
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAAGAAG-CTGCATATGCATTGAGCCAAAATGTTAAGGT-AT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAA-GAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTAT
EST: gi|149101112|gb|EE187218.2|EE187218
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGT
EST: gi|71301510|gb|DR786796.1|DR786796
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|71436978|gb|DR818028.1|DR818028
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|148987083|gb|EE030908.2|EE030908
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|148945255|gb|EC890464.2|EC890464
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|91877369|gb|EB407326.1|EB407326
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|148942891|gb|EC887934.2|EC887934
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|91049452|gb|EB159870.1|EB159870
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|78089320|gb|DV517694.1|DV517694
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|149111298|gb|EE294796.2|EE294796
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|45567946|gb|CK985826.1|CK985826
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|76011527|gb|DT938697.1|DT938697
EST:     TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
EST: gi|78089191|gb|DV517575.1|DV517575
EST:     GTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG                         TTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT
genomic: TTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATT

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: 78

TGCAGAACAACTGGTGGACATCGGTTGTCAATGGGTTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTTCTGGAAGAGAGGGAAGCAGGGAAAACTTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 558

TGCAGAACAACTGGTGGACATCGGTTGTCAATGGGTTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTTCTGGAAGAGAGGGAAGCAGGGAAAACTTTTG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 132

TGCAGAACAACTGGTGGACATCGGTTGTCAATGGGTTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTTCTGGAAGAGAGGGAAGCAGGGAAAACTTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 301

TGCAGAACAACTGGTGGACATCGGTTGTCAATGGGTTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattt ... tcaaatgcagTTTATTGGGAAGAAGGCTGCATATGCATTGAGCCAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTTCTGGAAGAGAGGGAAGCAGGGAAAACTTTTG