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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttttgcatgcgaatttctgcttttttctatcctttaacaccaattgcatgtatcattagttcattactcatcagatcaagtgtttcagGTCAATCATCTCAGAGAGGAGCTGCAAATGTTGTCTAAATCAAATCATGTTTCCATTGTCACTGTTGATGGTAGACCTG

Basic information

species Zea mays
transcript GRMZM2G147587_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147587_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g01070.3 (Oryza sativa), 3'ss of exon 3
gttttttgcatgcgaatttctgcttttttctatcctttaacaccaattgcatgtatcattagttcattactcatcagatcaagtgtttcagGTCAATCATCTCAGAGAGGAGCTGCAAATGTTGTCTAAATCAAATCATGTTTCCATTGTCACTGTTGATGGTAGACCTG
       |  | | | |       | || || | ||| | | |    ||  |  || ||||   || | ||||||  |  |      | |||||||||||||||||||||| || ||| | ||||| |  |||||||| ||| | |||||||| || ||||||||||| |
-------gtctcccactcgtcatctcttactgtacttcatcgctggatggctccatgattaacccactgctcatctaacta------ttagGTCAATCATCTCAGAGAGGACCTCCAACTTTTGTCCAGGTCAAATCAAGTTGCTATTGTCACCGTCGATGGTAGACCAG
















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|71766303|gb|DR964240.1|DR964240
EST:     AGGATGGGCCGTCTACCAGCAGTCCACATACTGCTGAGTTGTTCAGCCAG                         GTCAATCATCTCAGAGAGGAGCTGCAAATGTTGTCTAAATCAAATCATGTT
genomic: AGGATGGGCCGTCTACCAGCAGTCCACATACTGCTGAGTTGTTCAGCCAGgttttttgca ... agtgtttcagGTCAATCATCTCAGAGAGGAGCTGCAAATGTTGTCTAAATCAAATCATGTT
EST: gi|71429464|gb|DR810514.1|DR810514
EST:     AGGATGGGCCGTCTACCAGCAGTCCACATACTGCTGAGTTGTTCAGCCAG                         GTCAATCATCTCAGAGAGGAGCTGCAAATGTTGTCTAAATCAAATCATGTT
genomic: AGGATGGGCCGTCTACCAGCAGTCCACATACTGCTGAGTTGTTCAGCCAGgttttttgca ... agtgtttcagGTCAATCATCTCAGAGAGGAGCTGCAAATGTTGTCTAAATCAAATCATGTT
EST: gi|32931585|gb|CF036397.1|CF036397
EST:     AGGATGGGCCGTCTACCAGCAGTCCACATACTGCTGAGTTGTTCAGCCAG                         GTCAATCATCTCAGAGAGGAGCTGCAAATGTTGTCTAAATCAAATCATGTT
genomic: AGGATGGGCCGTCTACCAGCAGTCCACATACTGCTGAGTTGTTCAGCCAGgttttttgca ... agtgtttcagGTCAATCATCTCAGAGAGGAGCTGCAAATGTTGTCTAAATCAAATCATGTT

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: 113

TTCTTGACCAAGAGTGCAAAGCCAGGCAAGGATGGGCCGTCTACCAGCAGTCCACATACTGCTGAGTTGTTCAGCCAGgttttttgca ... agtgtttcagGTCAATCATCTCAGAGAGGAGCTGCAAATGTTGTCTAAATCAAATCATGTTTCCATTGTCACTGTTGATGGTAGACCTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 134

TTCTTGACCAAGAGTGCAAAGCCAGGCAAGGATGGGCCGTCTACCAGCAGTCCACATACTGCTGAGTTGTTCAGCCAGgttttttgca ... agtgtttcagGTCAATCATCTCAGAGAGGAGCTGCAAATGTTGTCTAAATCAAATCATGTTTCCATTGTCACTGTTGATGGTAGACCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

TTCTTGACCAAGAGTGCAAAGCCAGGCAAGGATGGGCCGTCTACCAGCAGTCCACATACTGCTGAGTTGTTCAGCCAGgttttttgca ... agtgtttcagGTCAATCATCTCAGAGAGGAGCTGCAAATGTTGTCTAAATCAAATCATGTTTCCATTGTCACTGTTGATGGTAGACCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

TTCTTGACCAAGAGTGCAAAGCCAGGCAAGGATGGGCCGTCTACCAGCAGTCCACATACTGCTGAGTTGTTCAGCCAGgttttttgca ... agtgtttcagGTCAATCATCTCAGAGAGGAGCTGCAAATGTTGTCTAAATCAAATCATGTTTCCATTGTCACTGTTGATGGTAGACCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaacaccaattgcatgtatcattagttcattactcatcagatcaagtgtttcagGTCAATCATCTCAGAGAGGAGCTGCAAATGTTGTCTAAATCAAATCATGTTTCCATTGTCACTGTTGATGGTAGACCTG
 ctttaac  putative branch site (score: 122)
                 tatcatta  TA-rich tract