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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttttgcatgacaagttctgcttttttctatccttcaacatcaattgcatatatcatactcattaagtcaagtgttccagGTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTG

Basic information

species Zea mays
transcript GRMZM2G078711_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078711_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g01070.3 (Oryza sativa), 3'ss of exon 3
gttttttgcatgacaagttctgcttttttctatccttcaacatcaattgcatatatcatactcattaagtcaagtgttccagGTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTG
|| |    |  | ||  |  | || |  |  |||  |  |   |      || || |  |||   | |   || | ||  |||||||| ||||||||||||| || ||| | ||||| |  |||||||| |||||||||||||| || ||||||||||| |
gtctcccactcgtcatctcttactgtacttcatcgctggatggctccatgat-taacccact-gctcatctaactatt--agGTCAATCATCTCAGAGAGGACCTCCAACTTTTGTCCAGGTCAAATCAAGTTGCTATTGTCACCGTCGATGGTAGACCAG
















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|32840160|gb|CD979841.1|CD979841
EST:     AGGATGGGCCGTCGACCAGCAGGCCACATACTTCTGAGTTGTTGTCCCAG                         GTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTT
genomic: AAGATGGGCCGTCGACCAGCAGGCCACATACTTCTGAGTTGTTGACCCAGgttttttgca ... agtgttccagGTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTT
EST: gi|32838724|gb|CD978405.1|CD978405
EST:     AGGATGGGCCGTCGACCAGCAGGCCACATACTTCTGAGTTGTTGTCCCAG                         GTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTT
genomic: AAGATGGGCCGTCGACCAGCAGGCCACATACTTCTGAGTTGTTGACCCAGgttttttgca ... agtgttccagGTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTT
EST: gi|78105202|gb|DV523620.1|DV523620
EST:     AAGATGGGCCGTCGACCAGCAGGCCACATACTTCTGAGTTGTTGACCCAG                         GTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTT
genomic: AAGATGGGCCGTCGACCAGCAGGCCACATACTTCTGAGTTGTTGACCCAGgttttttgca ... agtgttccagGTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTT
EST: gi|76017583|gb|DT944753.1|DT944753
EST:     AAGATGGGCCGTCGACCAGCAGGCCACATACTTCTGAGTTGTTGACCCAG                         GTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTT
genomic: AAGATGGGCCGTCGACCAGCAGGCCACATACTTCTGAGTTGTTGACCCAGgttttttgca ... agtgttccagGTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTT
EST: gi|76015767|gb|DT942937.1|DT942937
EST:     AAGATGGGCCGTCGACCAGCAGGCCACATACTTCTGAGTTGTTGACCCAG                         GTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTT
genomic: AAGATGGGCCGTCGACCAGCAGGCCACATACTTCTGAGTTGTTGACCCAGgttttttgca ... agtgttccagGTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTT
EST: gi|211421421|gb|FL071937.1|FL071937
EST:     AGGATGGGCCGTCGACCAGCAGGCCACATACTTCTGAGTTGTTGTCCCAG                         GTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTT
genomic: AAGATGGGCCGTCGACCAGCAGGCCACATACTTCTGAGTTGTTGACCCAGgttttttgca ... agtgttccagGTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTT

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), 47 (downstream exon)
Score: 60

TTCTTGACCAAGAGTTCAAAGCAAGGCAAAGATGGGCCGTCGACCAGCAGGCCACATACTTCTGAGTTGTTGACCCAGgttttttgca ... agtgttccagGTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

TTCTTGACCAAGAGTTCAAAGCAAGGCAAAGATGGGCCGTCGACCAGCAGGCCACATACTTCTGAGTTGTTGACCCAGgttttttgca ... agtgttccagGTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTG


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

TTCTTGACCAAGAGTTCAAAGCAAGGCAAAGATGGGCCGTCGACCAGCAGGCCACATACTTCTGAGTTGTTGACCCAGgttttttgca ... agtgttccagGTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 67

TTCTTGACCAAGAGTTCAAAGCAAGGCAAAGATGGGCCGTCGACCAGCAGGCCACATACTTCTGAGTTGTTGACCCAGgttttttgca ... agtgttccagGTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctatccttcaacatcaattgcatatatcatactcattaagtcaagtgttccagGTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTG
                       atatatcata  TA-rich tract