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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgtttattttctaatttaattgttatcgagttgttgtacctgccctcacatcaaaatctgagtattgtttgcctaagtaaaccttctcactctgtatatatctcgggcatatttcccaatgggtgtttttgttgatgagcagaggttttggctatctaaactcagaagtcctgttgtgcag

Basic information

species Zea mays
transcript GRMZM2G035150_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035150_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g64219.1 (Oryza sativa), 5'ss of exon 8
TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgtttattttctaatttaattgttatcgagttgttgtacctgccctcacatcaaaatctgagtattgtttgcctaagtaaaccttctcactctgtatatatctcgggcatatttcccaatgggtgtttttgttgatgagcagaggttttggctatctaaactcagaagtcctgttgtgcag
|| ||||||||||| |||||||||||||||||||||||||| || || ||||| || |||||||||||| |||||||   |||||||||  ||| ||||| ||||   ||| ||  || ||||  |||      |  || | |  |     |||| |      ||  | |  | |  | |||  ||   |                                                                                
TATGGTGTAAAGATTTTCATCCTGACATCATTCAGAGATACTTGCTACATTGAAATCCTTCCTGTTGTTCAGAAATCAGAAAGAGgtaacctttcttttcaaattatgttgctactgaattgtattactgaaattagcaactactt----atattatccagtcaaacatagatgcaga-tcttcatcagt--------------------------------------------------------------------------------
















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|74235678|gb|DT643592.1|DT643592
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|78092883|gb|DV521257.1|DV521257
EST:     AGATACATGTTATATTGAGATTTTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|4804174|gb|AI666040.1|AI666040
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|32808275|gb|CD960509.1|CD960509
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCGGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|76289426|gb|DV028994.1|DV028994
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|71427953|gb|DR809003.1|DR809003
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|113633600|gb|DW792172.1|DW792172
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGC
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGC
EST: gi|32793686|gb|CD945922.1|CD945922
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|86466720|gb|DY233090.1|DY233090
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|71427180|gb|DR808230.1|DR808230
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|50324081|gb|CO519207.1|CO519207
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|50331811|gb|CO526937.1|CO526937
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|78080763|gb|DV509175.1|DV509175
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|24462661|gb|BM660192.1|BM660192
EST:     CTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: CTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|50327716|gb|CO522842.1|CO522842
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG

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: 41 (upstream exon), 49 (downstream exon)
Score: 30

TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG


Block sizes: 29 (upstream exon), 49 (downstream exon)
Score: 9

TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 27

TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 44

TACGGTGTAAAGATCTTCATCCTGACATCATTCAGAGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG