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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTTgtgagcttcctgggacctttctccatccgtgacgcttttacttctttcgtgattgttcgacacatttggttatttatgttctgtttgtttcacccacctttagtgctcacaccaaaggaatttcctttttgtgtactttcttttccacctatcatgctgtcttggtaaggaaatgttcgtctgtttctttgtattag

Basic information

species Zea mays
transcript GRMZM2G082855_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082855_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g03970.1 (Oryza sativa), 5'ss of exon 5
GATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTTgtgagcttcctgggacctttctccatccgtgacgcttttacttctttcgtgattgttcgacacatttggttatttatgttctgtttgtttcacccacctttagtgctcacaccaaaggaatttcctttttgtgtactttcttttccacctatcatgctgtcttggtaaggaaatgttcgtctgtttctttgtattag
|||||||||||||||||| ||||| ||||||||||| |||||| |||| || ||||||||||||||||| |||||||| || | | ||||| ||| |||||||||   ||||||||||| | | || || |||| | | ||| || |   ||||  |||||| ||     ||| ||                                                                                             
GATTTTGAAGAACAACCAGCTCACGGGACCCATCCCTTCCACATTGTCCCAAATTCCAAATCTCAAGACATTgtgagcctcttagtaccttactctatccgtgac-tatttacttctttgg-ggttcttggacaaactgggtgatctgacttctacttgtttaactg--tttttgt---------------------------------------------------------------------------------------------
















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|86472326|gb|DY238696.1|DY238696
EST:     ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTT                         GGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG
genomic: ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTTgtgagcttcc ... tttgtattagGGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG
EST: gi|148934014|gb|EC878019.2|EC878019
EST:     ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTT                         GGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG
genomic: ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTTgtgagcttcc ... tttgtattagGGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG
EST: gi|148940443|gb|EC885241.2|EC885241
EST:     ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTT                         GGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG
genomic: ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTTgtgagcttcc ... tttgtattagGGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG
EST: gi|149079906|gb|EE168912.2|EE168912
EST:     ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTT                         GGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG
genomic: ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTTgtgagcttcc ... tttgtattagGGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG
EST: gi|148964982|gb|EC906062.2|EC906062
EST:     ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTT                         GGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG
genomic: ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTTgtgagcttcc ... tttgtattagGGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG
EST: gi|148941048|gb|EC885905.2|EC885905
EST:     ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTT                         GGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG
genomic: ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTTgtgagcttcc ... tttgtattagGGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG
EST: gi|149096378|gb|EE182110.2|EE182110
EST:     ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTT                         GGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG
genomic: ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTTgtgagcttcc ... tttgtattagGGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG
EST: gi|101383199|gb|EB813654.1|EB813654
EST:     ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTT                         GGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG
genomic: ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTTgtgagcttcc ... tttgtattagGGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG
EST: gi|148957491|gb|EC903572.2|EC903572
EST:     ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTT                         GGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG
genomic: ACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTTgtgagcttcc ... tttgtattagGGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTG

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 626

GATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTTgtgagcttcc ... tttgtattagGGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

GATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTTgtgagcttcc ... tttgtattagGGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 486

GATTTTGAAGAACAACCAACTCACCGGACCCATCCCCTCCACACTGTCACAGATTCCAAATCTCAAGACCTTgtgagcttcc ... tttgtattagGGATCTGGCGCAGAACAAACTTACCGGCGACATCCCCAGGCTCATCTACTGGAATGAAGTACTACAATACCT