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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctactggacaactgatggctgaatgtcttgtatcagtaagattttttttccacatccgacaccattctttttggatcaatcgggcttttaatat...

Basic information

species Zea mays
transcript GRMZM2G058498_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os08g07960.2 (Oryza sativa), 5'ss of exon 10
GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctactggacaactgatggctgaatgtcttgtatcagtaagattttttttccacatccgacaccattctttttggatcaatcgggcttttaatat---------
||||||||| | ||||| ||||| ||||||||||||||||||||||||||||| || |||||||||||||| |||||||        || |||||  ||| | ||||||   | |    |  ||| |    ||  |  |||||  ||| || | ||    |  |||  || |         
GCTTTTAGTCGGTGCCCTCTTCCTATTCCTTGCAGTACCTTCAACAGTGATGGGTCGATATTTGCTTATGCAgtaagtc--------aagtgatgcttgagtatcttgttgtactttattagtttgtgactatatgcaaccatgttttctg-accaggttgaatttagatgtattttattg

upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA02G13780.1 (Glycine max), 5'ss of exon 9
GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtct-actgg--------acaactgatggctgaatgtcttgtatcagt-aagatttttt-ttccacatccgacaccattctttttggatcaatcgggcttttaatat
||| |    || ||    |  ||||| ||||||||||| || || | |||||| ||||||||||||||||||||| || | | | |        ||||   ||  || | |  ||| |     | || |||||||  | ||  ||  |   |||||||     |  ||               
GCTATGCAAAGGTGTAGTCAGCCCATACCTTGCAGTACATTTAATAATGATGGCTCCATATTTGCTTATGCGgtatgtttcatttgctgttttcacaaaccata-cttatttacttatgcagtttaatattttttgcttcatttcttatgacattcttccataaataaggaaa----------

upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA15G05740.1 (Glycine max), 5'ss of exon 9
GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctactggacaactgatggctgaatgtcttgtatcagtaagattttttttccacatcc-gacaccattctttttggatcaatcgggcttttaatat-
||  |    ||||||  ||  || |||||||||||||||||||||| ||||||||| |||||||||||  | ||| | | ||   || | |      |    ||| || |     |   |||||  |     ||| |     | |     | |  ||||    |||||   || 
GCCATGTTGAGATGCAGCCAACCTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCAgtatgcccaccttactattctgcttttccagtcatgcacatagagcttttttcctttttgtcctggtgtaaattcaccttg--caatgcttcttttgtcata

upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA08G19260.1 (Glycine max), 5'ss of exon 9
GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctactggacaactgatggctgaatgtcttgtatcagtaagattttttttccacatccgacaccattctttttggatcaatcgggcttttaatat--
||  |    ||||||  ||| || |||||||||||||||||||||| ||||||||| |||||||||||  | ||| |   ||   || | |      |    |||||| |    ||   ||||   |      | |     | |     | |  ||||    |||||   |   
GCCATGTTGAGATGCAGCCTACCTATTCCTTGCAGTACCTTCAACAATGATGGTTCAATATTTGCTTACTCAgtatgctcaccttactattatgctttttcagtcttgcacatatagctttttccattttgtcctggtgtaaattcaccttg--caatgcttcttttgtcacac

upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA01G09290.1 (Glycine max), 5'ss of exon 9
GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctactggacaactgatggctgaatgtcttgtatcagtaagattttttttccacatccgacaccattctttttggatcaatcgggcttttaatat-----
||| |    || ||    |  ||||| ||||||||||| || || | |||||||||||||||||||||||||||| ||    |   |   |  |     ||       |||            ||||  |  |    |  ||||  || ||   || |||  |  | ||||      
GCTATGCAAAGGTGTAGTCAGCCCATACCTTGCAGTACATTTAATAATGATGGTTCCATATTTGCTTATGCGgtatgttccatttgctgtt--ttctcaaaccatacttatttacttatgcagttttatattttttgcttcatttcttatga--cactcgt-ccataaataaggaaa

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|33104196|gb|CF064156.1|CF064156
EST:     ACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG                         GTTTGCTATGACTGGAGCCATGGGGCCGAAAATCACAACCCTGCAGCTGCA
genomic: ACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
EST: gi|71310172|gb|DR791375.1|DR791375
EST:     CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG                         GTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
genomic: CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
EST: gi|5055819|gb|AI734706.1|AI734706
EST:     CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG                         GTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
genomic: CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
EST: gi|32868064|gb|CF007746.1|CF007746
EST:     TTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG                         GTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
genomic: TTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
EST: gi|32915972|gb|CF020784.1|CF020784
EST:     CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG                         GTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
genomic: CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
EST: gi|32823928|gb|CD963650.1|CD963650
EST:     CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG                         GTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
genomic: CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
EST: gi|78092604|gb|DV520978.1|DV520978
EST:     CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG                         GTTTGCTATGACGGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
genomic: CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
EST: gi|24769686|gb|CA404815.1|CA404815
EST:     CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG                         GTTTGCTATGACTGGACCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
genomic: CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
EST: gi|50339683|gb|CO534809.1|CO534809
EST:     CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG                         GTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
genomic: CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
EST: gi|71756690|gb|DR954627.1|DR954627
EST:     CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG                         GTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
genomic: CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
EST: gi|12969344|gb|BG266288.1|BG266288
EST:     CCATTCCCTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG                         GTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCGCAACCCTGCAGCTGCA
genomic: CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
EST: gi|211462818|gb|FL454180.1|FL454180
EST:     CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG                         GTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
genomic: CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
EST: gi|78023897|gb|DV492284.1|DV492284
EST:     CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG                         GTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
genomic: CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
EST: gi|67013709|gb|CO442458.1|CO442458
EST:     CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG                         GTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA
genomic: CCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCA

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), 49 (downstream exon)
Score: 128

GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 107

GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 64

GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 119

GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCGgtaagtctac ... tggaaaatagGTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG