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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcggcggtccttggcagctcagctctatctccaactttttttcctttcctgacgcgaaactgggctgacttccctgggcgcgtccgtgcagGTCGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTATGGCACGCCTCCCTGTGGCACATGCACGAGTCGCACCACCGGTCGTGCGAGGGCCCAT

Basic information

species Zea mays
transcript GRMZM2G163683_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G163683_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g48880.1 (Oryza sativa), 3'ss of exon 2
gtacgcggcggtc-cttggcagctcagctctatctccaactttttttcctttcctgacgcgaaactgggctgactt----ccctgggcgcgtccgtgcagGTCGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTATGGCACGCCTCCCTGTGGCACATGCACGAGTCGCACCACCGGTCGTGCGAGGGCCCAT
||| ||||| ||  |   |||      || | |   |     |     | ||       | ||| |  ||| | ||    | || |  | |    ||||||| ||||||||||||||||||| ||||||||||||  |||| |||||||||||||||||||||||||||||||||||||||||  || |||||||||| |
gtaagcggccgtgacaccgcaaaatccctgtttgctcgctgataacgtccttgggatgtcaaaattttgcttaattttgacgctcgctggggggttgcagGTTGGGATGGAGTTCTGGGCGCAGTGGGCGCACCGCTCGCTGTGGCACGCCTCCCTGTGGCACATGCACGAGTCGCACCACCGTGCGCGCGAGGGCCCGT

upper sequence: GRMZM2G163683_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G24530.1 (Glycine max), 3'ss of exon 2
----------gtacgcggcggtccttggcagctcagctctatctccaactttttttcctttcctgac--------------gcgaaactgggctg----acttccctgggcgcgtccg---tgcagGTCGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTATGGCACGCCTCCCTGTGGCACATGCACGAGTCGCACCACCGGTCGTGCGAGGGCCCAT
           | |       |  ||   |   ||  ||  | |  || |  ||||   |||   |               | |||  | || ||    | |    ||||   ||| |   | ||||| || |||||||| |||||  | ||||| ||| |||| |||||||| || ||||||||||||||||| |||                            
gtgagtaatcatccttttaattgattatgattccaattcagttttgaattgctttttaattcagaattgggtgagttctttgtgaattttgggtggtagattcaattgggtatgtctgattttcagGTGGGTATGGAGTTTTGGGCTAGATGGGCTCACAGGGCTCTATGGCATGCTTCCCTGTGGCACATGCATGAG----------------------------

upper sequence: GRMZM2G163683_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv02s0025g00240.t01 (Vitis vinifera), 3'ss of exon 2
gtacgc-ggcggtccttggcagctcagctctatctccaactttttttcctttcctgacgcgaaactgggctgacttccctgggcgc-gtccgtg--cagGTCGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTATGGCACGCCTCCCTGTGGCACATGCACGAGTCGCACCACCGGTCGTGCGAGGGCCCAT
||| |   ||   |  |   ||||    | |||    ||||  |      | | ||| |  ||  ||      ||    |||| || ||   |   ||||| ||||||||||| |||||||||||||| |||   ||||| ||||| || || |||||||| |||||||||                            
gtaagttagctaacgctataagctttcatgtatt---aactgctgaaaaatccttgaag-aaagatgatgaatctcaagtgggtgctgttgattatcagGTGGGGATGGAGTTTTGGGCGCGGTGGGCTCACAAAGCGCTCTGGCATGCTTCACTGTGGCATATGCACGAG----------------------------

upper sequence: GRMZM2G163683_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 2
gtacgcggcggtc-cttggcagctcagctctatctccaactttttttcct-ttcctgacgc-gaaactgggctgacttccctgggc--------gcgtccgtg-----cagGTCGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTATGGCACGCCTCCCTGTGGCACATGCACGAGTCGCACCACCGGTCGTGCGAGGGCCCAT
||| | | |  |  |    ||  |    ||  | || |  |     || | ||   || || |    || |  || | |  ||           |  |   |      ||||| || ||||||||||||||| | ||||| |||   || || |||||||||||| | |||||||||||||||                            
gtaagtgcctttttcccttcattttccttcggtttctagttccaaatcatgtttgcgaagctgggtttgaggcgattgcgttgaatcgaaataggtattttttattctcagGTAGGCATGGAGTTCTGGGCGAGATGGGCTCACAAAGCTCTCTGGCACGCCTCCTTATGGCACATGCACGAG----------------------------

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|78111406|gb|DV529803.1|DV529803
EST:     GTGCCGGAGACGACGCTAGACGATGAGGTCAGTGCCGCGGCGGCGCGGCGCGTCGCAGAGATGAAGGCGCGGAAGCGGTCCGAGCGGCGCACCTACCTGGTGGCCGCCGTGATGTCCAGGCTCGGG
genomic: GTGCCGGAGACGACGCTAGACGATGAGGTCAGTGCCGCGGCGGCGCGGCGCGTCGCAGAGATGAAGGCGCGGAAGCGGTCCGAGCGGCGCACCTACCTGGTGGCCGCCGTGATGTCCAGGCTCGGG
EST: gi|148979517|gb|EE026701.2|EE026701
EST:     GTGCCGGAGACGACGCTAGACGATGAGGTCAGTGCCGCGGCGGCGCGGCGCGTCGCAGAGATGAAGGCGCGGAAGCGGTCCGAGCGGCGCACCTACCTGGTGGCCGCCGTGATGTCCAGGCTCGGG
genomic: GTGCCGGAGACGACGCTAGACGATGAGGTCAGTGCCGCGGCGGCGCGGCGCGTCGCAGAGATGAAGGCGCGGAAGCGGTCCGAGCGGCGCACCTACCTGGTGGCCGCCGTGATGTCCAGGCTCGGG
EST: gi|91877187|gb|EB407144.1|EB407144
EST:     GTGCCGGAGACGACGCTAGACGATGAGGTCAGTGCCGCGGCGGCGCGGCGCGTCGCAGAGATGAAGGCGCGGAAGCGGTCCGAGCGGCGCACCTACCTGGTGGCCGCCGTGATGTCCAGGCTCGGG
genomic: GTGCCGGAGACGACGCTAGACGATGAGGTCAGTGCCGCGGCGGCGCGGCGCGTCGCAGAGATGAAGGCGCGGAAGCGGTCCGAGCGGCGCACCTACCTGGTGGCCGCCGTGATGTCCAGGCTCGGG
EST: gi|71441112|gb|DR822162.1|DR822162
EST:     GTGCCGGAGACGACGCTAGACGATGAGGTCAGTGCCGCGGCGGCGCGGCGCGTCGCAGAGATGAAGGCGCGGAAGCGGTCCGAGCGGCGCACCTACCTGGTGGCCGCCGTGATGTCCAGGCTCGGG
genomic: GTGCCGGAGACGACGCTAGACGATGAGGTCAGTGCCGCGGCGGCGCGGCGCGTCGCAGAGATGAAGGCGCGGAAGCGGTCCGAGCGGCGCACCTACCTGGTGGCCGCCGTGATGTCCAGGCTCGGG

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), 37 (downstream exon)
Score: 7

GGCGGCGCGGTCCCGGTGAGCGAGATGTTCGGCACGTTTGCGCTCTCCGTCGGCGCGGCGgtacgcggcg ... gtccgtgcagGTCGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTATGGCACGCCTCCCTGTGGCACATGCACGAGTCGCACCACCGGTCGTGCGAGGGCCCAT


Block sizes: 42 (upstream exon), 19 (downstream exon)
Score: 5

GGCGGCGCGGTCCCGGTGAGCGAGATGTTCGGCACGTTTGCGCTCTCCGTCGGCGCGGCGgtacgcggcg ... gtccgtgcagGTCGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTATGGCACGCCTCCCTGTGGCACATGCACGAGTCGCACCACCGGTCGTGCGAGGGCCCAT


Block sizes: 44 (upstream exon), 17 (downstream exon)
Score: 2

GGCGGCGCGGTCCCGGTGAGCGAGATGTTCGGCACGTTTGCGCTCTCCGTCGGCGCGGCGgtacgcggcg ... gtccgtgcagGTCGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTATGGCACGCCTCCCTGTGGCACATGCACGAGTCGCACCACCGGTCGTGCGAGGGCCCAT


Block sizes: 48 (upstream exon), 18 (downstream exon)
Score: 2

GGCGGCGCGGTCCCGGTGAGCGAGATGTTCGGCACGTTTGCGCTCTCCGTCGGCGCGGCGgtacgcggcg ... gtccgtgcagGTCGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTATGGCACGCCTCCCTGTGGCACATGCACGAGTCGCACCACCGGTCGTGCGAGGGCCCAT