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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGGgtaactatatatgtttcactcagtgagcataaaattgcgctaattgtttttcaggcactcctattaacataaatatgtattttcttactctaaaacacacag

Basic information

species Zea mays
transcript GRMZM2G044457_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044457_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os05g41120.1 (Oryza sativa), 5'ss of exon 8
ATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGGgtaactatatatgtttcactcagtgagcataaaatt--------gcgctaattgtttt--tcaggcactcctattaaca-----taaatatgtattttcttactctaaaacacacag----------
|| || ||||||||||| |||||||| |||||||||||||||||||||||||| |||||||||||||||||  |  |||  | |  |||| |||||||| ||||        || || ||| |  |  | |   | | || ||  ||     ||  | ||||   || |   |||| | |               
ATCACACACAAAATAAATAAACTGTCTTTTGGGACAGAATTCCCTGGTGTTGTTAATCCACTTGATGGgtacgtccatagctctagctcattgagcatataattatagccttgcacttattctcctagttatatatttcttttttcaatttttatctttgtaccctcatgtcctaacaaatttcatgaacgtcag

upper sequence: GRMZM2G044457_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv12s0178g00020.t01 (Vitis vinifera), 5'ss of exon 8
ATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGGgtaactatatatgtttcactcagtgagcataa--aattgcgctaattgtttttcaggcactcctattaacataaatatgtattttcttactctaaaacacacag
|| |  ||||  || || ||| |  | |||||     | |||||||||||||| ||||| |||||||||||||||  |     ||   ||  |   || |   ||   | ||||| |   |      ||| ||  || | |   || |  ||  |||  |   ||  |   |
ATAAGTCACAGGATCAATAAATTAGCTTTTGGAGACCATTTCCCTGGTGTTGTAAATCCCCTTGATGGgtaactactttctcctcttgca-cggctatcactgatacagttaattatgcctt---ttctcttaaaaagaaattgatatggttggttaaacattaatcctttg
















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|149111501|gb|EE295004.2|EE295004
EST:     GGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGG                         TGCTCAGTGGACACAGCCAGCTTCAGATGGGACATACCAGTATTTCATAAA
genomic: GGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGGgtaactatat ... aaacacacagTGCTCAGTGGACACAGCCAGCTTCAGATGGGACATACCAGTATTTCATAAA
EST: gi|60346135|gb|DN213108.1|DN213108
EST:     TGTTGTCAATCCACTTGATGG                         TGCTCAGTGGACACAGCCAGCTTCAGATGGGACATACCAGTATTTCATAAA
genomic: TGTTGTCAATCCACTTGATGGgtaactatat ... aaacacacagTGCTCAGTGGACACAGCCAGCTTCAGATGGGACATACCAGTATTTCATAAA
EST: gi|149027083|gb|EE046394.2|EE046394
EST:     GTCAATCCACTTGATGG                         TGCTCAGTGGACACAGCCAGCTTCAGATGGGACATACCAGTATTTCATAAA
genomic: GTCAATCCACTTGATGGgtaactatat ... aaacacacagTGCTCAGTGGACACAGCCAGCTTCAGATGGGACATACCAGTATTTCATAAA
EST: gi|211162555|gb|FL361310.1|FL361310
EST:     AAACTGTCCTTTGGGACAGAATTTCCTGGTGTTGTCAATCCACTTGATGG                         TGCTCAGTGGACACAGCCAGCTTCAGATGGGACATACCAGTATTTCATAAA
genomic: AAACTGTCCTTTGGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGGgtaactatat ... aaacacacagTGCTCAGTGGACACAGCCAGCTTCAGATGGGACATACCAGTATTTCATAAA
EST: gi|211541072|gb|FL347103.1|FL347103
EST:     AAACTGTCCTTTGGGACAGAATTTCCTGGTGTTGTCAATCCACTTGATGG                         TGCTCAGTGGACACAGCCAGCTTCAGATGGGACATACCAGTATTTCATAAA
genomic: AAACTGTCCTTTGGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGGgtaactatat ... aaacacacagTGCTCAGTGGACACAGCCAGCTTCAGATGGGACATACCAGTATTTCATAAA

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: 48 (upstream exon), 46 (downstream exon)
Score: 67

ATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGGgtaactatat ... aaacacacagTGCTCAGTGGACACAGCCAGCTTCAGATGGGACATACCAGTATTTCATAAAA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 104

ATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGGgtaactatat ... aaacacacagTGCTCAGTGGACACAGCCAGCTTCAGATGGGACATACCAGTATTTCATAAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 159

ATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGGgtaactatat ... aaacacacagTGCTCAGTGGACACAGCCAGCTTCAGATGGGACATACCAGTATTTCATAAAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 123

ATTACCCACAAAATAAACAAACTGTCCTTTGGGACAGAATTCCCTGGTGTTGTCAATCCACTTGATGGgtaactatat ... aaacacacagTGCTCAGTGGACACAGCCAGCTTCAGATGGGACATACCAGTATTTCATAAAA