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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttcatgcctactcgtttcagcattattgtcgatgctgttacagccagctaaatgtgtatctccaagtttgttctttgtatatccaccagctcacatgcttctgccacttctgttctgcag

Basic information

species Zea mays
transcript GRMZM5G835235_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835235_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g14860.3 (Oryza sativa), 5'ss of exon 11
GAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtt-tcatgcctactcgt-ttcagcattattgtcgatgct-gttacagccagctaaatgtgtatctccaagtttgttctttgtatatccacc---agctcacatgctt----ctgccacttctgttctgcag-------------------------------------------
|| || ||||| |||||||||||||| ||||||||||| |||||| |||| ||||| |||||||||||  |||| || || ||||||||||||||||| |||| ||| | |  | |  ||   || | | || |||    | |  |||| ||   | | ||   |   || |||  |||||||   ||| |||      | || |||   |     |||| | |  |    | | |                                           
GAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCTCGCCTTCCGAATGGCCGCTTTTTGCCTCCTCTCTTCAACTTCAAGCCTCATGgtaagttgtgaaacatgatcacatttatccttgttgatattaccagttaaagtttgttcaagcaggcacttcaa--ttgttctggttatttccgttgtaaacttacaatttgggagctgcaagtcataactttctgatatgatcagctacttacgttgcccctttcttgtttcttgcag

upper sequence: GRMZM5G835235_T02 (Zea mays), 5'ss of exon 10
lower sequence: EFJ10962 (Selaginella moellendorffii), 5'ss of exon 11
GAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttcatgcctactcgtttcagcattattgtcgatgctgttacagccagctaaatgtgtatctccaagtttgttctttgtatatccaccagctcacatgcttctgccacttctgttctgcag
|| |||||||  |||||||||||||| ||| | || |||||||| ||||| ||||||||||| ||    || ||||| || | ||| |||||||     |||  ||  | || || |   ||  |    | |      ||  ||  | |     |   ||   |                                                              
GAAGCGCTTGCACACCCATTCTTTGATGAGTTGCGGGATCCTAACACTCGACTTCCAAATGGTCGTCCGCTACCACCTCTGTACAATTTCAAGCAATTGGgtgagtgcc-tgtctccagcttctattcctttcaggcttgaagtcgc-gttttttcgttgcacag-------------------------------------------------------------

upper sequence: GRMZM5G835235_T02 (Zea mays), 5'ss of exon 10
lower sequence: EFJ04915 (Selaginella moellendorffii), 5'ss of exon 11
GAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttcatgcctactcgtttcagcattattgtcgatgctgttacagccagctaaatgtgtatctccaagtttgttctttgtatatccaccagctcacatgcttctgccacttctgttctgcag
|| |||||||  |||||||||||||| ||| | || |||||||| ||||| ||||||||||| ||    || ||||| || | ||| |||||||     |||  ||  | || || ||  ||  |    | |      ||  ||  |       |   ||   |                                                              
GAAGCGCTTGCACACCCATTCTTTGATGAGTTGCGGGATCCTAACACTCGACTTCCAAATGGTCGTCCGCTACCACCTCTGTACAATTTCAAGCAATTGGgtgagtgcc-tgtctcctgcttctattcctttcaggcttgaagtcgcgttt--ttcgttgcacag-------------------------------------------------------------

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|20337055|gb|BQ172685.1|BQ172685
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|4621641|gb|AI612474.1|AI612474
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|33092593|gb|CF052587.1|CF052587
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|211246876|gb|FL472897.1|FL472897
EST:     TTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|30087357|gb|CB885563.1|CB885563
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|32865480|gb|CF005162.1|CF005162
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|60395660|gb|DN228530.1|DN228530
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAGATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|18172726|gb|BM348114.1|BM348114
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|28986914|gb|CB351371.1|CB351371
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|4647428|gb|AI622503.1|AI622503
EST:     TTCCCAAATGGCCGCTTCCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TT-CCAAATGGCCGCTT-CCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|21331244|gb|BQ486625.1|BQ486625
EST:     TCTTCCAAATGGCCGCTTCCTGCCGCCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|32928745|gb|CF033557.1|CF033557
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|60348494|gb|DN215467.1|DN215467
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|78544269|gb|DV621767.1|DV621767
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|32916889|gb|CF021701.1|CF021701
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|211497820|gb|FL217204.1|FL217204
EST:     AAATGGCCGCTTCCTGCCACCCCTTTKCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: AAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|16379449|gb|BI992951.1|BI992951
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|5740140|gb|AI947830.1|AI947830
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|4621640|gb|AI612473.1|AI612473
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|32865498|gb|CF005180.1|CF005180
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|29129738|gb|CB380442.1|CB380442
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|18170275|gb|BM340115.1|BM340115
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
EST: gi|23357521|gb|BU645170.1|BU645170
EST:     TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACG                         AATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG
genomic: TCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATG

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), 48 (downstream exon)
Score: 266

GAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATGCGAAGAAGCAATGCTCTTATGTTGGATCGTGAGATGACCGTGCCTTGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 207

GAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATGCGAAGAAGCAATGCTCTTATGTTGGATCGTGAGATGACCGTGCCTTGGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 379

GAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATGCGAAGAAGCAATGCTCTTATGTTGGATCGTGAGATGACCGTGCCTTGGG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 141

GAGGCGCTTGTCCACCCATTCTTTGACGAGCTTCGAGATCCTAATACTCGTCTTCCAAATGGCCGCTTCCTGCCACCCCTTTTCAACTTCAAGCCTCACGgtatgtttca ... tgttctgcagAATTGAAAGGAGTCCCAGCAGACATTGTTGCGAAATTGGTTCCAGAACATGCGAAGAAGCAATGCTCTTATGTTGGATCGTGAGATGACCGTGCCTTGGG