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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatctcctgatatttctctgttatatatttttgacaatatgatatctgagctcttcttttgctactattgataccattctataaacttgtaatgctgtttcaatgtaatttatgctgcaactgcagGGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTTTTCTTGACACAACTTGGGATTGACAAGGATCGTCTCCGTTTCCGTCAAC

Basic information

species Zea mays
transcript GRMZM2G171688_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171688_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g32650.1 (Oryza sativa), 3'ss of exon 4
gtattatctcctgatatttctctgttatatatttt-tgacaatatgatatctgagctcttcttttgctactattgataccattctataaacttgtaatgctgtttcaatgtaatttatgctgcaactg-cagGGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTTTTCTTGACACAACTTGGGATTGACAAGGATCGTCTCCGTTTCCGTCAAC
||| ||| |   ||||  |||  | ||||||  || | || ||||   || | | ||||| |||| |||||  | ||||  || | |            |||| |||        | || |||||| | ||||| ||||| ||||||||||||||||||||||| |||||||||||||| || |||||||| || ||||| |||||||| |||||||| || ||||| || |
gtactatatttcgatagctcttcgctatataccttattactatatttgatttaaactcttgtttt-ctactcctaatactcttttgt------------ctgtctca--------tctgttgcaaccggcagGGGACTGTTAACAATGAGACCCTTGGCTACTTTATTGGAAGGGTCTATCTCTTCTTGACGCAGCTTGGAATTGACAAAGATCGTCTACGGTTCCGACAGC

upper sequence: GRMZM2G171688_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv01s0150g00150.t01 (Vitis vinifera), 3'ss of exon 4
gtattatctcctgatatttctctgttatatatttttgacaatatgatatctgagctcttcttttgctactattgataccattctataaacttgtaatgctgtttcaatgtaatt-tatgctgcaactgcagGGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTTTTCTTGACACAACTTGGGATTGACAAGGATCGTCTCCGTTTCCGTCAAC
                      || |    ||| |    |   |||  | |      || ||||| |  | |  | ||||     |  || | |     |||   ||| | ||  |    |||   |  |||||| ||| ||||||||||| |||| |||||||||||| || || ||||| ||| | ||||  ||||| || ||||||||  |  | |||||| | || |
--------------------gttggttcgaattctatctagattgaccttta----tttgttttgtt--tgtacaaaccaactgctccacctttgcatatgtgataatatgatggttcaatgctgat-tagGGAATTGTCAACAATGAGACACTTGCCTACTTCATTGGGAGAGTATACCTATTCCTAACACGTCTTGGCATAGACAAGGACAGGTTACGTTTCAGACAGC
















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|31356439|gb|CD440796.1|CD440796
EST:     TTGTAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTGTATCTGAG                         GGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTT
genomic: TGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTATATCTGAGgtattatctc ... gcaactgcagGGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTT
EST: gi|60350427|gb|DN217400.1|DN217400
EST:     CTTAAACTCGGAAATTCTATATCTGAG                         GGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTT
genomic: CTTAAACTCGGAAATTCTATATCTGAGgtattatctc ... gcaactgcagGGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTT
EST: gi|20301525|gb|BQ164468.1|BQ164468
EST:     TGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTGTATCTGAG                         GGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGTATTTGTCTACCTT
genomic: TGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTATATCTGAGgtattatctc ... gcaactgcagGGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTT
EST: gi|26558249|gb|CA830484.1|CA830484
EST:     TGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTGTATCTGAG                         GGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTT
genomic: TGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTATATCTGAGgtattatctc ... gcaactgcagGGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTT
EST: gi|5555434|gb|AI881385.1|AI881385
EST:     TGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTGTATCTGAG                         GGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTT
genomic: TGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTATATCTGAGgtattatctc ... gcaactgcagGGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTT
EST: gi|13126604|gb|BG317174.1|BG317174
EST:     TGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTATATCTGAG                         GGAACTGTGAACAATGAGACCCTTG
genomic: TGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTATATCTGAGgtattatctc ... gcaactgcagGGAACTGTGAACAATGAGACCCTTG
EST: gi|60342069|gb|DN209042.1|DN209042
EST:     TGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTATATCTGAG                         GGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTT
genomic: TGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTATATCTGAGgtattatctc ... gcaactgcagGGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTT
EST: gi|21987499|gb|BQ779027.1|BQ779027
EST:     TGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTGTATCTGAG                         GGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTT
genomic: TGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTATATCTGAGgtattatctc ... gcaactgcagGGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTT
EST: gi|31354132|gb|CD438489.1|CD438489
EST:     TGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTGTATCTGAG                         GGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTT
genomic: TGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTATATCTGAGgtattatctc ... gcaactgcagGGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTT
EST: gi|211446354|gb|FL194328.1|FL194328
EST:     TGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTGTATCTGAG                         GGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTT
genomic: TGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTATATCTGAGgtattatctc ... gcaactgcagGGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTT

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), 45 (downstream exon)
Score: 289

TGGTGATGTTTCTGATCTAGAGTTCTGGATGTTTCCGAGAGAGGATCAAATGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTATATCTGAGgtattatctc ... gcaactgcagGGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTTTTCTTGACACAACTTGGGATTGACAAGGATCGTCTCCGTTTCCGTCAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 179

TGGTGATGTTTCTGATCTAGAGTTCTGGATGTTTCCGAGAGAGGATCAAATGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTATATCTGAGgtattatctc ... gcaactgcagGGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTTTTCTTGACACAACTTGGGATTGACAAGGATCGTCTCCGTTTCCGTCAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 172

TGGTGATGTTTCTGATCTAGAGTTCTGGATGTTTCCGAGAGAGGATCAAATGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTATATCTGAGgtattatctc ... gcaactgcagGGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTTTTCTTGACACAACTTGGGATTGACAAGGATCGTCTCCGTTTCCGTCAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 197

TGGTGATGTTTCTGATCTAGAGTTCTGGATGTTTCCGAGAGAGGATCAAATGGCAGGAAGGTCAGCCACAAGACTTAAACTCGGAAATTCTATATCTGAGgtattatctc ... gcaactgcagGGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTTTTCTTGACACAACTTGGGATTGACAAGGATCGTCTCCGTTTCCGTCAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccattctataaacttgtaatgctgtttcaatgtaatttatgctgcaactgcagGGAACTGTGAACAATGAGACCCTTGGCTACTTCATTGGAAGGGTCTACCTTTTCTTGACACAACTTGGGATTGACAAGGATCGTCTCCGTTTCCGTCAAC
                          tttcaatgtaatttat  TA-rich tract