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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactccctatccgcatcaccccccttcctctcttgctcaccactgcccctcccggcatcgtggcgaggctagctgccgcggtcggatttggtggctaactagggtttggtgcttgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGCGGCGGGTGGCCGACCACTACAGCGCGCGGTCCAACCAGACACTCGAGGA

Basic information

species Zea mays
transcript GRMZM2G042398_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042398_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g08200.2 (Oryza sativa), 3'ss of exon 1
gta-ctc-cctatccgcatcaccccccttcctctcttgctcaccact-gcccctcccggcatcg-tggcgaggctagctgccgcggtcggatttggtggctaactagggtttggtgcttgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGCGGCGGGTGGCCGACCACTACAGCGCGCGGTCCAACCAGACACTCGAGGA
||| ||| |   ||| |  ||||  || ||   ||      ||| ||    ||  ||   | || ||  | || | |  ||      ||| ||||| |  |   |     |||| |     || |  ||||||||||||||   |  ||| || |||||||| |||||||||||||||||||||||||| ||||||||||||||| |||| |||||||| ||||||||
gtaactcactcctcctctccaccaaccctctcgtcaaatcaacccctcaatccagccaaaaccgatgctgcgggtggtagctaactacggttttggcgtttttttt---cttgggg----ggtagGCGGCGGAGGGTATGG---GGGGCATGGGTACTCGGAGGAGCGGAGCAGCGCGCGGCGGGTGGCGGACCACTACAGCGCGAGGTCGAACCAGACGCTCGAGGA
















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|32919824|gb|CF024636.1|CF024636
EST:     CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAG                         GCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
genomic: CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
EST: gi|211188180|gb|FL095407.1|FL095407
EST:     CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAG                         GCGGARGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCA
genomic: CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCA
EST: gi|211188185|gb|FL095412.1|FL095412
EST:     CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAG                         GCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
genomic: CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
EST: gi|211031436|gb|FL127268.1|FL127268
EST:     CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAG                         GCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
genomic: CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
EST: gi|211188183|gb|FL095410.1|FL095410
EST:     CCGCGACGACCACTCCTTCGCCTCCGCGCCCAASCGCCAGTATGGCGCAG                         GCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
genomic: CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
EST: gi|211185780|gb|FL095396.1|FL095396
EST:     CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAG                         GCGGAGGGTATGGCCCGCAGCAGGGTTAC
genomic: CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTAC
EST: gi|211031437|gb|FL127269.1|FL127269
EST:     CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAG                         GCGGAGGGTATGGCCCGCAGCATGGTTACTCGGAAGAGCGGAGCAGCGCGC
genomic: CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
EST: gi|211188173|gb|FL095400.1|FL095400
EST:     CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAG                         GCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
genomic: CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
EST: gi|211185783|gb|FL095399.1|FL095399
EST:     CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAG                         GCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGARCAGCGCGC
genomic: CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
EST: gi|211185782|gb|FL095398.1|FL095398
EST:     CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAG                         GCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
genomic: CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
EST: gi|211188181|gb|FL095408.1|FL095408
EST:     CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAG                         GCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
genomic: CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
EST: gi|211188179|gb|FL095406.1|FL095406
EST:     CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAG                         GCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
genomic: CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
EST: gi|211188176|gb|FL095403.1|FL095403
EST:     CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAG                         GCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
genomic: CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
EST: gi|211185781|gb|FL095397.1|FL095397
EST:     CCGCGACGACCACTCCTTCGCCTCHGCGCCCAAGCGCCAGTATGGCGCAG                         GCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC
genomic: CCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGC

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: 113

TTGTGAATCGCCGGAAAAACATCTGTTGGCGGCGTCATGAATAAGCGGCCCCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGCGGCGGGTGGCCGACCACTACAGCGCGCGGTCCAACCAGACACTCGAGGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 86

TTGTGAATCGCCGGAAAAACATCTGTTGGCGGCGTCATGAATAAGCGGCCCCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGCGGCGGGTGGCCGACCACTACAGCGCGCGGTCCAACCAGACACTCGAGGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 135

TTGTGAATCGCCGGAAAAACATCTGTTGGCGGCGTCATGAATAAGCGGCCCCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGCGGCGGGTGGCCGACCACTACAGCGCGCGGTCCAACCAGACACTCGAGGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 89

TTGTGAATCGCCGGAAAAACATCTGTTGGCGGCGTCATGAATAAGCGGCCCCGCGACGACCACTCCTTCGCCTCCGCGCCCAAGCGCCAGTATGGCGCAGgtactcccta ... tgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGCGGCGGGTGGCCGACCACTACAGCGCGCGGTCCAACCAGACACTCGAGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagctgccgcggtcggatttggtggctaactagggtttggtgcttgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGCGGCGGGTGGCCGACCACTACAGCGCGCGGTCCAACCAGACACTCGAGGA
                        ggctaac  putative branch site (score: 89)