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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTTATCTTTGCTTTGAATTAGCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAGgtaacatgggcttcaagtattaaacttcttgaatgtacattactacattggtttgtgattgcatgtgcttattctaacaaagagcactctttttacgagttaacttttttctatttctttcccag

Basic information

species Zea mays
transcript GRMZM2G381933_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G381933_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g15490.3 (Oryza sativa), 5'ss of exon 11
AACTTATCTTTGCTTTGAATTAGCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAGgtaacatgggcttcaagtatta--aacttcttgaatgtacattactacattggtttgtgattgcatgtgcttattctaacaaagagcactctttttacgagttaacttttttctatttctttcccag
                            |||||||||||||| |||||||| |||||||||||||| || ||| |||||||||||||||| |||||||||||||  |||    ||| ||  |  || ||||||||| |  | | ||               |||||||  |||||||| || || |||  ||          | | ||   || |  ||| |  |||
----------------------------GCTCCTGATGAAGAGTTTGAAGAATACCTTAGTCAACTGATAGGAGACAATTACACTGGTGATCGAAATGAGgtaatctggttcgcaaatacaattaaattcttgaatatctagtgctg--------------tgcatgt--ttattctagcatagtgcaagctgca-gtattatcatttaactccacatctctttcag

upper sequence: GRMZM2G381933_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv08s0007g04980.t01 (Vitis vinifera), 5'ss of exon 12
AACTTATCTTTGCTTTGAATTAGCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAGgtaacatgggcttcaagtattaaacttcttgaatgtacattactacattggtttgtgattgcatgtgcttattctaacaaagagcactctttttacgagttaacttttttctatttctttcccag
                            || |||||||||||||||||||| || ||||| || || || ||  || ||| |||||||||||| ||||||||||  ||  ||    | |  | |  |  |   | |   ||||| |||   ||  | || ||| | | | | |         |  | | | ||   ||   ||  |||                 
----------------------------GCCCCTGATGAAGAATTTGAAGAATATCTTAGGCATCTTATAGGTGACCATTGCACTGGTGACCGGAATGAGgtaatttgttctcatggaaccacatcttattgttattt-ttactgcatccatt-ataat-gcaagggataactt--------ataattatcttgctgaaacaatctttaag--------------
















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|60359540|gb|DN226513.1|DN226513
EST:     ATGGGAAACAATTACACTGGTGACCGAAATGAG                         ATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTA
genomic: ATGGGAAACAATTACACTGGTGACCGAAATGAGgtaacatggg ... tctttcccagATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTA
EST: gi|60396268|gb|DN229137.1|DN229137
EST:     ATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAG                         ATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTA
genomic: ATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAGgtaacatggg ... tctttcccagATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTA
EST: gi|71767359|gb|DR965296.1|DR965296
EST:     ATTACTTTAGTCATCTCATGGGAAACAATTACACTGGTGACCGAAATGAG                         ATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTA
genomic: ATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAGgtaacatggg ... tctttcccagATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTA
EST: gi|60351624|gb|DN218597.1|DN218597
EST:     ACAATTACACTGGTGACCGAAATGAG                         ATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTA
genomic: ACAATTACACTGGTGACCGAAATGAGgtaacatggg ... tctttcccagATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTA
EST: gi|60394781|gb|DN227651.1|DN227651
EST:     TCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAG                         ATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTA
genomic: TCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAGgtaacatggg ... tctttcccagATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTA
EST: gi|34391288|gb|CF384516.1|CF384516
EST:     ATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAG                         ATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTA
genomic: ATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAGgtaacatggg ... tctttcccagATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTA

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: 46 (upstream exon), 49 (downstream exon)
Score: 81

AACTTATCTTTGCTTTGAATTAGCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAGgtaacatggg ... tctttcccagATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 115

AACTTATCTTTGCTTTGAATTAGCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAGgtaacatggg ... tctttcccagATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 135

AACTTATCTTTGCTTTGAATTAGCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAGgtaacatggg ... tctttcccagATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 225

AACTTATCTTTGCTTTGAATTAGCGTAGGCTCCTGATGAAGAATTTGAAGATTACCTTAGTCAACTCATGGGAAACAATTACACTGGTGACCGAAATGAGgtaacatggg ... tctttcccagATGGCACAGTTGCCAGAAGGTATTACAGAATTACTGCATCACAAAACGCTACCATTGCCATTG