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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGGCGCAAGGTTGAGGATCCTGACATGTTAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCTgtatgtttcagattcttgtgtgtgttagttgttactctgcatctttattgctttacctatttttaactatttcattgaattcaactaacacatcagtcatgtcgtccttgtatag

Basic information

species Zea mays
transcript GRMZM2G066496_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066496_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g05650.1 (Oryza sativa), 5'ss of exon 5
CGGGCGCAAGGTTGAGGATCCTGACATGTTAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCTgtatgtt-------tcagattcttgtg--tgtgtt---agttgttactctgcatctttattgctttacctatttttaactatttcattgaattcaactaacacatcagtcatgtcg-tccttgtatag
 |||||||| |||||||| |||||||  || |||| ||||||||||||  | || |||||||| || |||||||||||||||||||       ||| || ||| |   ||||||   |  |  |||  |   |  || | | |       | |||   |   |||  | ||  ||||||| |||  |||  || | |     | |||
GGGGCGCAAAGTTGAGGACCCTGACACATTGGAAAAGATACGGCTAACAGTTATTAACAACCTTCTGCAGTATCATCCTgtatgttccgagcgtcacatccttttacttgtgtttagaacttctaccgttagtaattttggatccgttcttgtttttatgaatcaaagtatcaaactaactcatttgtctggttgatatgcatgtag

upper sequence: GRMZM2G066496_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA20G24450.1 (Glycine max), 5'ss of exon 5
------CGGGCGCAAGGTTGAGGATCCTGACATGTTAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCTgta----tgtttcaga------ttcttgtgtgtgttagtt---gttactctgcatctttattgctttacctatttttaactatttcat-tgaattcaactaacacatcagtcatgtcgtccttgtatag------------------------------------------------------------
       || ||||| ||||| |||||||| |||||||| ||||| ||||| ||||| || ||||| ||| |  | ||||||||||||    ||||||| |      ||| | ||  | |  | |   |||||| |  || |     |||   | | |  |||||  |||  | | ||  ||| |    | |  || |  |  | |   ||||                                                             
AGACACTGGACGCAAAGTTGAAGATCCTGATATGTTAGAGAGGATTCGGCTTACCATTATTAACAATCTGTTGAAATATCATCCTgtaagtttgtttcatagataatttcctctggatttctgatatggttactttatatataagaagctcc-cttgtaattaacatttttttataaacacaatttttcctt--gttaccttttgcaaatatactttagtttgctcttaattttaagttttttcttactcacaaatattatataatttgtgtag

upper sequence: GRMZM2G066496_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv13s0147g00220.t01 (Vitis vinifera), 5'ss of exon 5
---CGGGCGCAAGGTTGAGGATCCTGACATGTTAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCTgtatgtttcagattcttgtg-tgtgttagttgttactctgcatctttattgctttacctatttttaact--atttcattgaattcaactaacacatcagtcatgtcgtccttg-tatag----------------------------------------
    || ||||| ||||| ||||||||||||||||| || || || || || ||||||||||||||  |  |||||||||| |||||| |  || |       |   ||   || |  | |  || ||||||  |   | || |  |   |  | |  |   |  |  ||   ||| |   | |  ||    |   | | |                                        
TGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTACAATCATCAACAACCTTTTGAAGTATCATCCAgtatgtatttgagttgaacactaatttcactgatgtttt--atttttatttttagtcttactggtggatgaaatggaagaatcttcaccctcactttctttacatctctttcactgttgcatttcttttttaagtatccctttttggcatcctttctag

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|67022635|gb|CO451384.1|CO451384
EST:     TAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCT                         GAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCTgtatgtttca ... ccttgtatagGAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|32830465|gb|CD970143.1|CD970143
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTATCATCCT                         GAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCTgtatgtttca ... ccttgtatagGAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|32804124|gb|CD956360.1|CD956360
EST:     TAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCT                         GAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCTgtatgtttca ... ccttgtatagGAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|32801615|gb|CD953851.1|CD953851
EST:     TAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCT                         GAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCTT
genomic: TAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCTgtatgtttca ... ccttgtatagGAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|118406764|gb|EH038212.1|EH038212
EST:     TAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCT                         GAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCTgtatgtttca ... ccttgtatagGAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCT

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: 375

CGGGCGCAAGGTTGAGGATCCTGACATGTTAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCTgtatgtttca ... ccttgtatagGAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 496

CGGGCGCAAGGTTGAGGATCCTGACATGTTAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCTgtatgtttca ... ccttgtatagGAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 635

CGGGCGCAAGGTTGAGGATCCTGACATGTTAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCTgtatgtttca ... ccttgtatagGAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 364

CGGGCGCAAGGTTGAGGATCCTGACATGTTAGAAAGGATACGGCTAACCATCATCAACAACCTGCTCCAGTATCATCCTgtatgtttca ... ccttgtatagGAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAG