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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagatcggagcatctctgttgctgtctgctgccttctctacggggtactattatctttatctaacaagatggtgcctttatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAGCGTGGGGACTTCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAG

Basic information

species Zea mays
transcript GRMZM2G099598_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099598_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g04050.1 (Oryza sativa), 3'ss of exon 7
gtaaaagatcggagcatctctgttgctgtctgctgccttctctacggggtactattatctttatctaacaagatggtgcctttatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAGCGTGGGGACTTCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAG
|||||  || ||||||  |   || |||||   || |   ||   |    |  | | | | | |  | |||     |  |  | | |||||||||||||||||||||||| |||||||||||||| ||| | || |||||||| ||||| ||||| || ||||| ||||||||||| ||| |||||||||
gtaaat-attggagcactttgatttctgtcatatggcagatcgttgtctaagaaatctatctcttcatcaa-----tctccctgttgcagCTATCGTTCCAGGAATGGACTCAGCAGATGAGGGATATGTTAGATGCTAGGAAACGTGGAGACTTTGCGTTTCGTGATAAAGATTTTAAGACAGCCATAG

upper sequence: GRMZM2G099598_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA02G48030.1 (Glycine max), 3'ss of exon 5
gtaaaagatcggagcatctctgttgctgtctgctgccttctctacggggtactattatctttatctaacaagatggtgcctttatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAGCGTGGGGACTTCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAG
||||  ||| || |||| |  |||    | | ||   || |     || |  |||   | | |  |   ||  |||     ||    ||| | |||||||| || ||||| || |||||||| || |||||||| || ||||||||||| ||||  || || || || || || || ||| ||||||| |
gtaactgatgggtgcat-tgggtttaaatttacta--tttttggttggatgatat-gccataaggtttgaatttgga----ttggttcagTTGTCGTTCCAAGAGTGGACTCAACAGATGAGAGATATGCTGGAGGCAAGGAAGCGTGGAGACTATGCATTCCGTGACAAGGACTTTAAGACAGCCATTG

upper sequence: GRMZM2G099598_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv03s0038g03270.t01 (Vitis vinifera), 3'ss of exon 7
----gtaaaagatcggagcatctctgttgctgtctgctgccttctctacggggtactattatctttatctaacaagatggtgcctttatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAGCGTGGGGACTTCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAG
     | |    | |  | |  | | ||  || |  ||   | ||||       | |  |   |   | || |  | || ||  ||  |  ||| | || ||||| |||||||| || |||||||| || ||||| ||||| ||||||||||||||||| || || || || || ||||| ||  | ||||| |
gtaattgagttgttgatgaaggtttttttttggcatctctatactcttacatccaatggtgagtg-gtttatcttggtgttgtattggtt-cagTTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGGAAGCGTGGGGACTTTGCATTCCGTGACAAGGATTTTAAAACTGCCATTG

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|60397498|gb|DN230314.1|DN230314
EST:     ATCAAATTCTAGTGAACACGCATTACAGGGACGATGAAGGGAGCAACGAG                         CTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
genomic: ATCAAATTCTAGTGAACACGCATTACAGGGACGATGAAGGGAGCAACGAGgtaaaagatc ... tttatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
EST: gi|8383297|gb|BE056240.1|BE056240
EST:     ATCAGATTCTAGTGAACACGCATTACAGGGACGATGAAGGGAGCAACGAG                         CTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
genomic: ATCAAATTCTAGTGAACACGCATTACAGGGACGATGAAGGGAGCAACGAGgtaaaagatc ... tttatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
EST: gi|211493754|gb|FL287302.1|FL287302
EST:     ATCAAATTCTAGTGAACACGCATTACAGGGACGATGAAGGGAGCAACGAG                         CTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
genomic: ATCAAATTCTAGTGAACACGCATTACAGGGACGATGAAGGGAGCAACGAGgtaaaagatc ... tttatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
EST: gi|50335562|gb|CO530688.1|CO530688
EST:     AGGGACGATGAAGGGAGCAACGAG                         CTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
genomic: AGGGACGATGAAGGGAGCAACGAGgtaaaagatc ... tttatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
EST: gi|71762708|gb|DR960645.1|DR960645
EST:     ATCAAATTCTAGTGAACACGCATTACAGGGACGATGAAGGGAGCAACGAG                         CTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
genomic: ATCAAATTCTAGTGAACACGCATTACAGGGACGATGAAGGGAGCAACGAGgtaaaagatc ... tttatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
EST: gi|74234524|gb|DT642438.1|DT642438
EST:     ATCAAATTCTAGTGAACACGCATTACAGGGACGATGAAGGGAGCAACGAG                         CTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
genomic: ATCAAATTCTAGTGAACACGCATTACAGGGACGATGAAGGGAGCAACGAGgtaaaagatc ... tttatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
EST: gi|76016248|gb|DT943418.1|DT943418
EST:     ATCAAATTCTATTGAACACGCATTACAGGGACGATGAAGGGAGCAACGAG                         CTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
genomic: ATCAAATTCTAGTGAACACGCATTACAGGGACGATGAAGGGAGCAACGAGgtaaaagatc ... tttatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
EST: gi|149112519|gb|EE295384.2|EE295384
EST:     GGGAGCAACGAG                         CTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG
genomic: GGGAGCAACGAGgtaaaagatc ... tttatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGG

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), 49 (downstream exon)
Score: 77

TCTCTCTCCCATGGGTGAAGCCTGTTCTAGGACGGATCTGACAGCTATCCATCAAATTCTAGTGAACACGCATTACAGGGACGATGAAGGGAGCAACGAGgtaaaagatc ... tttatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAGCGTGGGGACTTCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 131

TCTCTCTCCCATGGGTGAAGCCTGTTCTAGGACGGATCTGACAGCTATCCATCAAATTCTAGTGAACACGCATTACAGGGACGATGAAGGGAGCAACGAGgtaaaagatc ... tttatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAGCGTGGGGACTTCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

TCTCTCTCCCATGGGTGAAGCCTGTTCTAGGACGGATCTGACAGCTATCCATCAAATTCTAGTGAACACGCATTACAGGGACGATGAAGGGAGCAACGAGgtaaaagatc ... tttatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAGCGTGGGGACTTCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 84

TCTCTCTCCCATGGGTGAAGCCTGTTCTAGGACGGATCTGACAGCTATCCATCAAATTCTAGTGAACACGCATTACAGGGACGATGAAGGGAGCAACGAGgtaaaagatc ... tttatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAGCGTGGGGACTTCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttctctacggggtactattatctttatctaacaagatggtgcctttatcgcagCTATCGTTCCAGGAATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAGCGTGGGGACTTCGCCTTTCGCGATAAAGATTTCAAGGCAGCCATAG
                           atctaac  putative branch site (score: 84)
                                           cctttatc  putative PPT
                 tattatctttatctaa  TA-rich tract