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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaggatcaactagtgtcgagtcaaatgtgaaatcttttctcttcaccttcttattatttccttgctgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG

Basic information

species Zea mays
transcript GRMZM2G440916_T01
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G440916_T01 (Zea mays), 3'ss of exon 25
lower sequence: LOC_Os05g51790.2 (Oryza sativa), 3'ss of exon 25
gtatgaaggatcaactagtgtcgagtcaaatgtgaaatcttttctcttcaccttcttattatttccttgctgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG
|||||||  |  |||||   |    |  | | |  ||   | |  |||   |||  ||||||||  |||||  || |||||||||||| || || |||||| |||| ||||| |||||||||||||||||||||||||| |||||||| |||||||||||||||||||
gtatgaaaaa--aacta---ttagatgcattctagaaaaatatgccttatacttactattatttt-ttgctcctttatagGAGCGATCAGTTTCAACCATCCTGTACCTTGTATCACTTCAAGATCTTACCAACTGCCCCTTTCGGGTCGTTGATGAGATAAATCAAG

upper sequence: GRMZM2G440916_T01 (Zea mays), 3'ss of exon 25
lower sequence: GLYMA20G34020.1 (Glycine max), 3'ss of exon 26
gtatgaaggatcaactagtgtcgagtcaaatgtgaaatcttttctcttcaccttcttattatttccttgctgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG
|||| |   |  || | || ||   | | || ||   | | || || || | |  | |   ||    |    |||  ||||| || || || || || ||  | |||||||| || |||||||||||||| |||||||| ||| | || ||||||||||| || ||||
gtattacaaag-aatttgtttcttattacatttgttctatgttttcctcccttaatgaaccttggggtttgattttctagGAACGCTCAGTTTCAACTATTGTTTATCTTGTTTCCCTTCAAGATCTTACAAACTGCCCATTTAGAGTCGTTGATGAGATCAACCAAG

upper sequence: GRMZM2G440916_T01 (Zea mays), 3'ss of exon 25
lower sequence: Vv13s0064g00180.t01 (Vitis vinifera), 3'ss of exon 25
gtatgaaggatcaactagtgtcgagtcaaatgtgaaatcttttctcttcacctt--cttattatttcc---ttgctgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG
|||  | | || ||| |   |    | | ||   | ||||||| |    |  ||  |||| |   |     || |  |||  |||||||| || ||  | || ||  |||||||||| || || |||||||| || |||||||||||| |||| |||||||||||||||||||
gtaccatg-atgaaccaacttt---ttacattcaagatcttttatgactattttgtcttactgccttgaaatttccattttgtagGAGCGCTCAGTTGCAACTATTCTGTATCTTGTTTCTCTACAAGATCTCACAAACTGCCCTTTTAGGGTGGTTGATGAGATAAATCAAG

upper sequence: GRMZM2G440916_T01 (Zea mays), 3'ss of exon 25
lower sequence: EFJ13183 (Selaginella moellendorffii), 3'ss of exon 23
gtatgaaggatcaactagtgtcgagtcaaatgtgaaatcttttctct-tcacctt--cttattatttccttgctgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG
                             |  | |  ||  |  |   | |||||   || |   ||   |   ||||   |||| || || || || || ||  | || ||||| ||||| ||||| |||||| |||| || ||||| ||||| ||||||||||| ||||
---------------------------gtacataatttccgtgattagtaaccttggtttgtggattgagtctcgtttt-cagGAACGCTCGGTGTCAACTATTCTCTACCTTGTCTCACTCCAAGACCTTACCCACTGTCCGTTTCGTGTTGTGGATGAGATAAACCAAG

upper sequence: GRMZM2G440916_T01 (Zea mays), 3'ss of exon 25
lower sequence: EFJ24458 (Selaginella moellendorffii), 3'ss of exon 24
gtatgaaggatcaactagtgtcgagtcaaatgtgaaatcttttctct-tcacctt--cttattatttccttgctgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG
                             |  | |  ||  |  |   | |||||   || |   ||   |   ||||   |||| || || || || || ||  | || ||||| ||||| ||||| |||||| |||| || ||||| ||||| ||||||||||| ||||
---------------------------gtacataatttccgtgattagtaaccttggtttgtggattgagtctcgtttt-cagGAACGCTCGGTGTCAACTATACTCTACCTTGTCTCACTCCAAGACCTTACCCACTGTCCGTTTCGTGTTGTGGATGAGATAAACCAAG

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|32930688|gb|CF035500.1|CF035500
EST:     GCAAACTAGTCAGCTGCAGGTGCTAAGCTCTCATCACCAATCTGGAGGG                         GAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACC
genomic: GCAAACTAGTCAGCTGCAGGTGCTAAGCTCTCATCACCAATCTGGAGGGgtatgaagga ... tgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACC
EST: gi|211323885|gb|FK953781.1|FK953781
EST:     GGCAAACTAGTCAGCTGCAGGTGCTAAGCTCTCATCACCAATCTGGAGGG                         GAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACC
genomic: GGCAAACTAGTCAGCTGCAGGTGCTAAGCTCTCATCACCAATCTGGAGGGgtatgaagga ... tgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACC
EST: gi|33092036|gb|CF052030.1|CF052030
EST:     GCAAACTAGTCAGCTGCAGGTGCTAAGCTCTCATCACCAATCTGGAGGG                         GAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACC
genomic: GCAAACTAGTCAGCTGCAGGTGCTAAGCTCTCATCACCAATCTGGAGGGgtatgaagga ... tgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACC
EST: gi|211323884|gb|FK953780.1|FK953780
EST:     GCAAACTAGTCAGCTGCAGGTGCTAAGCTCTCATCACCAATCTGGAGGG                         GAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACC
genomic: GCAAACTAGTCAGCTGCAGGTGCTAAGCTCTCATCACCAATCTGGAGGGgtatgaagga ... tgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACC
EST: gi|78075393|gb|DV503827.1|DV503827
EST:     GGCAACCTAGTCAGCTGCAGGTGCTAAGCTCTCATCACCAATCTGGAGGG                         GAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACC
genomic: GGCAAACTAGTCAGCTGCAGGTGCTAAGCTCTCATCACCAATCTGGAGGGgtatgaagga ... tgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACC

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: 47 (upstream exon), 49 (downstream exon)
Score: 210

GCAAACTAGTCAGCTGCAGGTGCTAAGCTCTCATCACCAATCTGGAGGGgtatgaagga ... tgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 42

GCAAACTAGTCAGCTGCAGGTGCTAAGCTCTCATCACCAATCTGGAGGGgtatgaagga ... tgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 53

GCAAACTAGTCAGCTGCAGGTGCTAAGCTCTCATCACCAATCTGGAGGGgtatgaagga ... tgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 43

GCAAACTAGTCAGCTGCAGGTGCTAAGCTCTCATCACCAATCTGGAGGGgtatgaagga ... tgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaatgtgaaatcttttctcttcaccttcttattatttccttgctgtttcatagGAGCGATCTGTATCGACCATCTTGTATCTTGTGTCACTTCAAGATCTTACCAACTGCCCTTTTCGGGTTGTTGATGAGATAAATCAAG
            tcttttctcttcacct  CT-rich tract
                           ttcttattattt  TA-rich tract