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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACAgtaagtagcttgtcctgttaatagtcttgtcctgttaatagtctactctgcgtgatgcctcagcaaaactgagttggattgctatggtttgcag

Basic information

species Zea mays
transcript GRMZM2G052880_T01
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052880_T01 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os02g25580.2 (Oryza sativa), 5'ss of exon 16
TTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACAgtaagtagcttgtcctgttaatagtcttgtcctgttaatagtctactctgcgtgatgcctcagcaaaactgagttggattgctatggtttgcag
||||||||||  ||||||||| |||||||||| ||||| ||  |||| |||||||||||||| || ||||||||||||||||||||||| |||||||  || |  ||||  || |||  |||||  ||   || |||  || |      |||  | |           ||||||  |  |||||
TTACGTGCTGTGCACAAGCTTACATCCAAGCTAAAGCGGGAAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACGgtaagtactttatattgtttctaatctcatcctg--aaagctcgact--gcatagcttttcaagata-----------ttgctactgcctgcag
















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|211275799|gb|FL433157.1|FL433157
EST:     ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACA                         AAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG
genomic: ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACAgtaagtagct ... tggtttgcagAAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG
EST: gi|60345833|gb|DN212806.1|DN212806
EST:     ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACA                         AAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG
genomic: ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACAgtaagtagct ... tggtttgcagAAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG
EST: gi|60398850|gb|DN231666.1|DN231666
EST:     ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACA                         AAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG
genomic: ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACAgtaagtagct ... tggtttgcagAAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG
EST: gi|50336914|gb|CO532040.1|CO532040
EST:     ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACA                         AAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG
genomic: ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACAgtaagtagct ... tggtttgcagAAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG
EST: gi|76911270|gb|DV164216.1|DV164216
EST:     ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACA                         AAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG
genomic: ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACAgtaagtagct ... tggtttgcagAAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG
EST: gi|6827451|gb|AW331094.1|AW331094
EST:     ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACA                         AAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG
genomic: ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACAgtaagtagct ... tggtttgcagAAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG
EST: gi|76908403|gb|DV162923.1|DV162923
EST:     ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACA                         AAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG
genomic: ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACAgtaagtagct ... tggtttgcagAAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG
EST: gi|6194629|gb|AW146733.1|AW146733
EST:     ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACA                         AAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG
genomic: ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACAgtaagtagct ... tggtttgcagAAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG
EST: gi|211447144|gb|FL470093.1|FL470093
EST:     ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACA                         AAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG
genomic: ACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACAgtaagtagct ... tggtttgcagAAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTG

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), 47 (downstream exon)
Score: 135

TTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACAgtaagtagct ... tggtttgcagAAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTGTAAATGGTGTCCGCCCACACGGAGTGTAACCTTTTATTTTCTCTGTTCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 275

TTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACAgtaagtagct ... tggtttgcagAAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTGTAAATGGTGTCCGCCCACACGGAGTGTAACCTTTTATTTTCTCTGTTCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 211

TTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACAgtaagtagct ... tggtttgcagAAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTGTAAATGGTGTCCGCCCACACGGAGTGTAACCTTTTATTTTCTCTGTTCT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 144

TTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACAgtaagtagct ... tggtttgcagAAATTAAAGTTGATGTCAGTAGAAGAATTGACACTTGATGACCTTCAGCTGTAAATGGTGTCCGCCCACACGGAGTGTAACCTTTTATTTTCTCTGTTCT