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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttcagattcttatgtgttactctgtatcgttttttctttacctattttttactatctgattgaatgtaactaacaccgtagtcatgtcatccttgtgtag

Basic information

species Zea mays
transcript GRMZM2G109785_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109785_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g05650.1 (Oryza sativa), 5'ss of exon 5
TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtt-------tcagattcttat----gtgtt---actctgtatcgttttttcttt---acctattttttactatctgattgaatgta----actaacaccgtagtcatgtc-atccttgtgtag
 |||||||| ||||||||||||||||  || |||| ||| ||||||||  | || ||||||||||| ||||| |||||||||||||       ||| || ||| |    |||||   |   | || ||||  |  |||   | |  || ||   | | ||| | || |||    |||||| |  | |||  ||  ||     |||||
GGGGCGCAAAGTTGAGGACCCTGACACATTGGAAAAGATACGGCTAACAGTTATTAACAACCTTCTGCAGTATCATCCTgtatgttccgagcgtcacatccttttacttgtgtttagaacttctaccgttagtaattttggatccgttcttgtttttatgaatcaaagtatcaaactaactcatttgtctggttgatatgcatgtag

upper sequence: GRMZM2G109785_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv13s0147g00220.t01 (Vitis vinifera), 5'ss of exon 5
---TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttcagattcttatgtgttactctgtatcgttttttctttacctatt-ttttactatctgattgaatgtaactaacaccgtagtcatgtcatccttgtgtag--------------------------------------------------
   ||| ||||| ||||| || |||||||||||||| || ||||| || || ||||||||||||||| |  |||| ||||| |||||| |  || |   |        ||  |   ||||| | ||||  | |  | |||||    |||  |||| ||  | |  |    |||  |  |     | |                                                    
TGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTACAATCATCAACAACCTTTTGAAGTATCATCCAgtatgtatttgagttgaacactaatttcactgatgttttatttttatttttagtcttactggtggatgaaatggaagaatcttcaccctcactttctttacatctctttcactgttgcatttcttttttaagtatccctttttggcatcctttctag

upper sequence: GRMZM2G109785_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S99_201V6.1 (Physcomitrella patens), 5'ss of exon 5
------TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttcagattcttatgtgttactctgtatcgttttttctttacctattttttactatctgattgaatgt---aactaacac-cgtagtcatgtcatccttgtgtag
             || || ||||| |||||  || | |||   ||||| || |||||||| |||||||| || ||||||||||||||| |   |   |    |     ||| |||    |||||     | |    | | |  | | |||||| |  |   | || |    || ||  |||  |  | |      
GGATAACAACAAAAAAGTGGAGGATCCTGAGCTGCTGGAAGCCATTCGCCTTACCATCATAAACAACCTGCTTCAGTACCATCCTgtacgaacc---tgtcgaaaccctaccctga--tgttttccgagtcctctctctctcttttgtgattgcacatttcagctgaggtacggagatatgagacgcatt-----

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|7227556|gb|AW566197.1|AW566197
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTTGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|7227473|gb|AW566114.1|AW566114
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGT

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: 48 (upstream exon), 49 (downstream exon)
Score: 350

TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 545

TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 768

TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 561

TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG