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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGGAAGAAGGAGGCGGGCTCATGAAGACGCTGTGGCTCGGCTCGCTCTTCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcctgacgtgagattgggtgacagagcgttcgggatatgttttttttgtgtgtatctgaatatctgattattagattttatcttgagatggta...

Basic information

species Zea mays
transcript GRMZM2G174107_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174107_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g25624.2 (Oryza sativa), 5'ss of exon 1
GGCGGAAGAAGGAGGCGGGCTCATGAAGACGCTGTGGCTCGGCTCGCTCTTCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcctgacgtgagattgggtgacagagcgttcgggat------atgttttttttgtgtgtatctgaatatctgattattagattttatcttgagatggta
|| ||| || | | |||| |||   |||||||||  ||||||| |||| ||||| || |||||||| ||||||||||||||||||||||| |||||||||||||| |      | |  |||  ||     |||   | | ||       ||| |    |  | ||||  ||  ||  |    || ||| ||||| |          
GGAGGAGGAGGAAAGCGGCCTCGCCAAGACGCTGCAGCTCGGCGCGCTGTTCGGGCTGTGGTACCTCTTCAACATCTACTTCAACATCTACAACAAGCAGgtgagcaagtgagcttatgatctggctcttgagtaattgtgaattaaaaatgctggaatgctttgtaattgtgtagattcggatcagagtttatttcaca------

upper sequence: GRMZM2G174107_T01 (Zea mays), 5'ss of exon 1
lower sequence: EDP02676 (Chlamydomonas reinhardtii), 5'ss of exon 2
GGCGGAAGAAGGAGGCGGGCTCATGAAGACGCTGTGGCTCGGCTCGCTCTTCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcctgacgtgagattgggtgacagagcg---ttcgggatatgttttttttgtgtgtatctgaatatctgattatt---agattttatcttgagatggta---------------------------------------
 || | ||    | | | | | ||| ||||| ||  ||| |||||  | ||||    |||||||     |||||||  ||||||||||||||||||||||||   |  ||   |   |       | |||   |     ||   |    | |       |   | | |     | |   |     | | |  | ||    | | |                                        
-GCAGCAGCCACACG-GAGATGATGCAGACGTTGGTGCTGGGCTCCATGTTCGCGGGCTGGTACGCAGCCAACATCGCCTTCAACATCTATAACAAGCAGgtacttgcccgacccacatcacaactcacaagcccagcctcccaacccctctcacacacgcccaccggggcccccggccacctggaaaatccacctcagcaggctttaaccaaccctctatttctgtttccttgcacttgcacag

upper sequence: GRMZM2G174107_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ27053 (Selaginella moellendorffii), 5'ss of exon 1
GGCGGAAGAAGGAGGCGGGCTCATGAAGACGCTGTGGCTCGGCTCGCTCTTCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtga-gtatcctgacgtgagattgggtgacagagcgttcgggatatgttttttttgtgtgtatctgaa-tatctgattattagattttatcttgagatggta
|   |||   ||  ||| | | |||   || ||   ||| || |||||||||||  | |||||||| ||||||||||||||||||||||||||||||||||    || || |  |||    ||   |  ||         |||| |  | || || | |  ||      ||  |  | | ||||  || |  |      |  
GCAAGAATCCGGCAGCGCGATGATGCGCACACTCCAGCTGGGATCGCTCTTCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGgcattgtttcttctcgttttcttttctc-caccttagctaggatcttctcttgttttctccatgcatgctactttctaactagaacttgtgatttctcag--

upper sequence: GRMZM2G174107_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ05868 (Selaginella moellendorffii), 5'ss of exon 1
GGCGGAAGAAGGAGGCGGGCTCATGAAGACGCTGTGGCTCGGCTCGCTCTTCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtga-gtatcctgacgtgagattgggtgacagagcgttcgggatatgttttttttgtgtgtatctgaa-tatctgattattagattttatcttgagatggta
|   |||   ||  ||| | | |||   |||||   ||| || |||||||||||  | |||||||| ||||||||||||||||||||||||||||||||||    || || |  |||    ||   |  ||         |||| | || || || | |  ||      ||  |  | | ||||  |||| |          
GCAAGAATCCGGCAGCGCGATGATGCGCACGCTCCAGCTGGGATCGCTCTTCGGATTGTGGTACCTCTTCAACATCTACTTCAACATCTATAACAAGCAGgcattgtttcttctcgttttcttttctc-caccatagctaggatcttttcttgttttctccatgcatgctactttctaactagaacttatttctcag-----

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|93017132|gb|EB642652.1|EB642652
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|13198536|gb|BG354370.1|BG354370
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|148965579|gb|EE016409.2|EE016409
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|149072176|gb|EE160417.2|EE160417
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|149110186|gb|EE294002.2|EE294002
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|13178099|gb|BG349357.1|BG349357
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGGTTTCCCATACCCTATAAACATCACAGAAGTT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTT
EST: gi|211399728|gb|FL235706.1|FL235706
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|78180316|gb|DV550689.1|DV550689
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|148964314|gb|EC905711.2|EC905711
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|149078331|gb|EE167099.2|EE167099
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|149098082|gb|EE184035.2|EE184035
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|148972203|gb|EE023080.2|EE023080
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|211302374|gb|FL235688.1|FL235688
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTNG
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTT-CCCATACCCTATAAACATCACAGAAGTTCAATTT-G
EST: gi|13558927|gb|BG550282.1|BG550282
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|211302372|gb|FL235686.1|FL235686
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|148950588|gb|EC896170.2|EC896170
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|149082156|gb|EE171337.2|EE171337
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|211399721|gb|FL235699.1|FL235699
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|211399724|gb|FL235702.1|FL235702
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAGGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|211302370|gb|FL235684.1|FL235684
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCCATACC-TATAAACATCACAGAAGTTCAATTTGC
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCC-ATACCCTATAAACATCACAGAAGTTCAATTTGC
EST: gi|148937401|gb|EC881581.2|EC881581
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|211399718|gb|FL235696.1|FL235696
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|211399730|gb|FL235708.1|FL235708
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAG
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAG
EST: gi|12047010|gb|BF729149.1|BF729149
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|211402267|gb|FL235711.1|FL235711
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
EST: gi|13150722|gb|BG321044.1|BG321044
EST:     TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAG                         GTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT
genomic: TCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCT

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: 45 (upstream exon), 48 (downstream exon)
Score: 39

GGCGGAAGAAGGAGGCGGGCTCATGAAGACGCTGTGGCTCGGCTCGCTCTTCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCTGTCGGAACTGTAGCAGCTCTGTTCATGTGGATCACTGGTATTATTAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 330

GGCGGAAGAAGGAGGCGGGCTCATGAAGACGCTGTGGCTCGGCTCGCTCTTCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCTGTCGGAACTGTAGCAGCTCTGTTCATGTGGATCACTGGTATTATTAAGA


Block sizes: 22 (upstream exon), 47 (downstream exon)
Score: 3

GGCGGAAGAAGGAGGCGGGCTCATGAAGACGCTGTGGCTCGGCTCGCTCTTCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCTGTCGGAACTGTAGCAGCTCTGTTCATGTGGATCACTGGTATTATTAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

GGCGGAAGAAGGAGGCGGGCTCATGAAGACGCTGTGGCTCGGCTCGCTCTTCGGCCTCTGGTACCTGTTCAACATCTACTTCAACATCTATAACAAGCAGgtgagtatcc ... tatgtgacagGTACTCAAGGTTTTCCCATACCCTATAAACATCACAGAAGTTCAATTTGCTGTCGGAACTGTAGCAGCTCTGTTCATGTGGATCACTGGTATTATTAAGA