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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtataatctgtcagcttggtttaagttgaaattagtttttttttacttttaaattacagtagactggtgaacataagttttttcttgataattatgtttttaacattgcttgcattttatttttgatctttttgtcaactaaaaacatttgcattcaacctatccaccttccagTTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCAGACATGGGGCTTGGTGTTCCATTCAACATCGCATCATATTCTCTCCTGA

Basic information

species Zea mays
transcript GRMZM2G005990_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 8
gtcagtataatctgtcagcttggtttaagttgaaattagtttttttttacttttaaattacagtagactggtgaacataagttttttcttgataattatgtttttaacattgcttgcattttatttttgatctttttgtcaactaaaaacatttgcattcaacc-tatccaccttccagTTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCAGACATGGGGCTTGGTGTTCCATTCAACATCGCATCATATTCTCTCCTGA
                                                                                  | | |||   |   |   | | ||  ||| |    |  | || |   |   |||| |     | |     |||| | |||   | | |  ||||||||| ||||| || |  ||||||||||| ||||||||||||||||||||||| || ||||| |||||||||||||||||||| |||||||||||||| ||||
-------------------------------------------------------------------------------ttctctctctctctctctccatgtgtagaattacagtaaaatgatatacaaatattttcttgtagatagtttcttgcttacaataattttcttcttccagTTTTATGTTGAGAGCGGGGAGCTATCGTGCCAGATGTATCAACGCTCTGCTGATATGGGACTTGGTGTTCCATTCAACATTGCATCATATTCTCTTCTGA

upper sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 8
gtcagtataatctgtcagcttggtttaagttgaaattagtttttttttacttttaaattacagtagactggtgaacataagttttttcttgataattatgtttttaacattgcttgcattttatttttgatctttttgtcaactaaaaacatttgcattcaacctatccaccttccagTTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCAGACATGGGGCTTGGTGTTCCATTCAACATCGCATCATATTCTCTCCTGA
                                                                           |   || | | | | | |  || | |||  || |   ||  | |||| | |       |||||||||||         | | || |   | |   || |  |||||||||| |  |||||||||||||| || || |||||||| || ||||| |||||||| || ||||| ||||| || || ||||| ||| | |||||||
-------------------------------------------------------------------------gtccgcagctatatttgggt--ttctctttggaagagctctctctttttctctcatgaagttttgtcaact---------tccttttattgttttttccctgtagTTCTATGTAGCTAATGGGGAGCTATCATGTCAAATGTATCAGCGATCTGCCGACATGGGCCTGGGTGTCCCATTTAATATTGCATCTTATGCACTCCTGA

upper sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 7
gtcagtataatctgtcagcttggtttaagttgaaattagtttttttttacttttaaattacagtagactggtgaacataagttttttcttgataattatgtttttaacattgcttgcattttatttttgatctttttgtcaactaaaaacatttgcattcaacctatccaccttccagTTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCAGACATGGGGCTTGGTGTTCCATTCAACATCGCATCATATTCTCTCCTGA
                                                                        |  |  |  | | ||     |   | | | |||   |   ||  | |||| | |       ||||||  |||        ||  |||     | |    | | ||||||||||| | ||||||||||||||| || || |||||||| || ||||| |||||||| || ||||| ||||| || || ||||| ||| | |||||||
------------------------------------------------------------------------gtccgcagctatatt-----tgggtttctctttggaagaactctctttttctctcatgaaattttgttgact-----tccttttatt-gttttttttttcctgcagTTCTATGTAGCAAATGGGGAGCTATCATGTCAAATGTATCAGCGATCTGCCGACATGGGCCTGGGTGTCCCATTTAATATTGCATCTTATGCGCTCCTGA

upper sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 7
gtcagtataatctgtcagcttggtttaagttgaaattagtttttttttacttttaaattacagtagactggtgaacataagttttttcttgataattatgtttttaacattgcttgcattttatttttgatctttttgtcaactaaaaacatttgcattca-acctatccaccttccagTTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCAGACATGGGGCTTGGTGTTCCATTCAACATCGCATCATATTCTCTCCTGA
                                                                                 ||    | || ||||| |   |||| ||||  || | |  | ||   |      | || || |  ||   ||   |||      | || || || ||||| ||||| |  |||||||||||||| || || |||||||| |||||||| || ||||| |||||||| ||||| ||||| || || ||| || |  |||
-------------------------------------------------------------------------------gtttggaacatgctaattct--ctttatcatttttttcctcattttacgg------tagtaaaatgcaatgtttcttatttgcgtatttctacattgcagTTTTATGTAGCCAATGGGGAGCTATCCTGTCAAATGTATCAGCGCTCTGCTGATATGGGTCTTGGTGTGCCATTTAACATTGCTTCTTATGCTTTATTGA

upper sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ18561 (Selaginella moellendorffii), 3'ss of exon 9
gtcagtataatctgtcagcttggtttaagttgaaattagtttttttttacttttaaattacagtagactggtgaacataagttttttcttgataattatgtttttaacattgcttgcattttatttttgatctttttgtcaactaaaaacatttgcattcaacctatccaccttccagTTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCAGACATGGGGCTTGGTGTTCCATTCAACATCGCATCATATTCTCTCCTGA
                                                                                                                         ||  | |     | | |||   |       | || |      || |      |||||||||||||    ||||| ||||| ||||||||||||||||||||||||   |||||||| || ||||||||||||||||| || || ||  | ||  | |
------------------------------------------------------------------------------------------------------------------------gtaagtctagaactctcgtc--tttgttttctctgaagcgtgactgtgtg---tccagTTCTATGTTTCCAATGGCGAGCTCTCTTGCCAGATGTATCAACGCTCTTGTGACATGGGACTCGGTGTTCCATTCAACATTGCGTCCTACGCACTGTTAA

upper sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ36491 (Selaginella moellendorffii), 3'ss of exon 7
gtcagtataatctgtcagcttggtttaagttgaaattagtttttttttacttttaaattacagtagactggtgaacataagttttttcttgataattatgtttttaacattgcttgcattttatttttgatctttttgtcaactaaaaacatttgcattcaacctatccaccttccagTTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCAGACATGGGGCTTGGTGTTCCATTCAACATCGCATCATATTCTCTCCTGA
                                                                                                                         ||  | |     | | |||   |       | || |      || |      |||||||||||||    ||||| ||||| ||||||||||||||||||||||||   |||||||| || ||||||||||||||||| || || ||  | ||| | |
------------------------------------------------------------------------------------------------------------------------gtaagtctagaactctcgtc--tttgttttctctgaagcgtgactgtgtg---tccagTTCTATGTTTCCAATGGCGAGCTCTCTTGCCAGATGTATCAACGCTCTTGTGACATGGGACTCGGTGTTCCATTCAACATTGCGTCCTACGCACTCTTAA

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|29946486|gb|CB816173.1|CB816173
EST:     CTTCAGATCTCAAGAAGATGGCTCTTCCTCCTTGCCACATGTTTGCACAA                         TTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCA
genomic: CTTCAGATCTCAAGAAGATGGCTCTTCCTCCTTGCCACATGTTTGCACAAgtcagtataa ... caccttccagTTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCA
EST: gi|50331959|gb|CO527085.1|CO527085
EST:     CTTCAGATCTCAAGAAGATGGCTCTTCCTCCTTGCCACATGTTTGCACAA                         TTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCA
genomic: CTTCAGATCTCAAGAAGATGGCTCTTCCTCCTTGCCACATGTTTGCACAAgtcagtataa ... caccttccagTTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCA
EST: gi|6020322|gb|AW065250.1|AW065250
EST:     CTTCAGATCTCAAGAAGATGGCTCTTCCTCCTTGCCACATGTTTGCACAA                         TTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCA
genomic: CTTCAGATCTCAAGAAGATGGCTCTTCCTCCTTGCCACATGTTTGCACAAgtcagtataa ... caccttccagTTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCA
EST: gi|33466386|gb|CF243435.1|CF243435
EST:     CTTCAGATCTCAAGAAGATGGCTCTTCCTCCTTGCCACATGTTTGCACAA                         TTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCA
genomic: CTTCAGATCTCAAGAAGATGGCTCTTCCTCCTTGCCACATGTTTGCACAAgtcagtataa ... caccttccagTTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCA
EST: gi|211500703|gb|FL332819.1|FL332819
EST:     CTTCAGATCTCAAGAAGATGGCTCTTCCTCCTTGCCACATGTTTGCACAA                         TTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCA
genomic: CTTCAGATCTCAAGAAGATGGCTCTTCCTCCTTGCCACATGTTTGCACAAgtcagtataa ... caccttccagTTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCA

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: 212

GATCAAGAATGATCCTGACGACCGTCGAATAATTTTGTCGGCGTGGAATCCTTCAGATCTCAAGAAGATGGCTCTTCCTCCTTGCCACATGTTTGCACAAgtcagtataa ... caccttccagTTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCAGACATGGGGCTTGGTGTTCCATTCAACATCGCATCATATTCTCTCCTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 144

GATCAAGAATGATCCTGACGACCGTCGAATAATTTTGTCGGCGTGGAATCCTTCAGATCTCAAGAAGATGGCTCTTCCTCCTTGCCACATGTTTGCACAAgtcagtataa ... caccttccagTTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCAGACATGGGGCTTGGTGTTCCATTCAACATCGCATCATATTCTCTCCTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

GATCAAGAATGATCCTGACGACCGTCGAATAATTTTGTCGGCGTGGAATCCTTCAGATCTCAAGAAGATGGCTCTTCCTCCTTGCCACATGTTTGCACAAgtcagtataa ... caccttccagTTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCAGACATGGGGCTTGGTGTTCCATTCAACATCGCATCATATTCTCTCCTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

GATCAAGAATGATCCTGACGACCGTCGAATAATTTTGTCGGCGTGGAATCCTTCAGATCTCAAGAAGATGGCTCTTCCTCCTTGCCACATGTTTGCACAAgtcagtataa ... caccttccagTTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCAGACATGGGGCTTGGTGTTCCATTCAACATCGCATCATATTCTCTCCTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgatctttttgtcaactaaaaacatttgcattcaacctatccaccttccagTTCTATGTGGAAAATGGGGAGCTATCTTGCCAGATGTATCAACGCTCTGCAGACATGGGGCTTGGTGTTCCATTCAACATCGCATCATATTCTCTCCTGA
                 aactaaa  putative branch site (score: 184)
                                       cctatccaccttcc  putative PPT
                 aactaaaaacattt  TA-rich tract