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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcatgataatctagattgatttgtctcagtattgggtactcagcaagagaacacttgcttgaatttgtcctcatctgatgtagccttgtaaacctgcagGTGCTATCTGTTGCAGTTTACAACCACTATAAACGGATATACCATCAATCTTTACAAAAGGG

Basic information

species Zea mays
transcript GRMZM2G101791_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101791_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g35630.1 (Oryza sativa), 3'ss of exon 1
ctcatgataatctagattgatttgtctcagtattgggtactcagcaagag-aacacttgcttgaatttg---tcctcatctgatgtagccttgtaaacctgcagGTGCTATCTGTTGCAGTTTACAACCACTATAAACGGATATACCATCAATCTTTACAAAAGGG
   | |  ||  |  | |  |||| || ||| |||   | | | ||| || ||| | |   |   ||||   | || ||||     |||||  |||| || |||||||||||||||||||| ||||| || |||||||| ||||||||| |||| |||||||| ||
-ataagtcaacttcaagtcttttg-cttagtgttg--cattaatcaacagtaacgcctctatacttttgatatgctgatctctcacagcctgttaaatctacagGTGCTATCTGTTGCAGTGTACAATCATTATAAACGAATATACCATAAATCATTACAAAAAGG
















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|22472601|gb|BU037081.1|BU037081
EST:     TTTGCAAGGGGCTCGACAAGTATGTGATTGGGCAGGACAGAGCCAAGAAG                         G-GCTATCTGTTGCAGTTTACAACCACTATAAACGGATATACCATCAATCT
genomic: TTTGCAAGGGGCTCGACAAGTATGTGATTGGGCAGGACAGAGCCAAGAAGgtgaaataaa ... aaacctgcagGTGCTATCTGTTGCAGTTTACAACCACTATAAACGGATATACCATCAATCT
EST: gi|148945417|gb|EC890645.2|EC890645
EST:     TTTGCAAGGGGCTCGACAAGTATGTGATTGGGCAGGACAGAGCCAAGAAG                         GTGCTATCTGTTGCAGTTTACAACCACTATAAACGGATATACCATCAATCT
genomic: TTTGCAAGGGGCTCGACAAGTATGTGATTGGGCAGGACAGAGCCAAGAAGgtgaaataaa ... aaacctgcagGTGCTATCTGTTGCAGTTTACAACCACTATAAACGGATATACCATCAATCT
EST: gi|26558610|gb|CA830845.1|CA830845
EST:     TTTGCAAGGGGCTCGACAAGTATGTGATTGGGCAGGACAGAGCCAAGAAG                         GTGCTATCTGTTGCAGTTTACAACCACTATAAACGGATATACCATCAATCT
genomic: TTTGCAAGGGGCTCGACAAGTATGTGATTGGGCAGGACAGAGCCAAGAAGgtgaaataaa ... aaacctgcagGTGCTATCTGTTGCAGTTTACAACCACTATAAACGGATATACCATCAATCT
EST: gi|87156336|gb|DY401125.1|DY401125
EST:     TTTGCAAGGGGCTCGACAAGTATGTGATTGGGCAGGACAGAGCCAAGAAG                         GTGCTATCTGTTGCAGTTTACAACCACTATAAACGGATATACCATCAATCT
genomic: TTTGCAAGGGGCTCGACAAGTATGTGATTGGGCAGGACAGAGCCAAGAAGgtgaaataaa ... aaacctgcagGTGCTATCTGTTGCAGTTTACAACCACTATAAACGGATATACCATCAATCT

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), 47 (downstream exon)
Score: 162

GGGCTGGGGTGGTTCCAATCTCGGCAGGGATTTACCCACGCCCAAGGAGATTTGCAAGGGGCTCGACAAGTATGTGATTGGGCAGGACAGAGCCAAGAAGgtgaaataaa ... aaacctgcagGTGCTATCTGTTGCAGTTTACAACCACTATAAACGGATATACCATCAATCTTTACAAAAGGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 100

GGGCTGGGGTGGTTCCAATCTCGGCAGGGATTTACCCACGCCCAAGGAGATTTGCAAGGGGCTCGACAAGTATGTGATTGGGCAGGACAGAGCCAAGAAGgtgaaataaa ... aaacctgcagGTGCTATCTGTTGCAGTTTACAACCACTATAAACGGATATACCATCAATCTTTACAAAAGGG


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 87

GGGCTGGGGTGGTTCCAATCTCGGCAGGGATTTACCCACGCCCAAGGAGATTTGCAAGGGGCTCGACAAGTATGTGATTGGGCAGGACAGAGCCAAGAAGgtgaaataaa ... aaacctgcagGTGCTATCTGTTGCAGTTTACAACCACTATAAACGGATATACCATCAATCTTTACAAAAGGG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 151

GGGCTGGGGTGGTTCCAATCTCGGCAGGGATTTACCCACGCCCAAGGAGATTTGCAAGGGGCTCGACAAGTATGTGATTGGGCAGGACAGAGCCAAGAAGgtgaaataaa ... aaacctgcagGTGCTATCTGTTGCAGTTTACAACCACTATAAACGGATATACCATCAATCTTTACAAAAGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagagaacacttgcttgaatttgtcctcatctgatgtagccttgtaaacctgcagGTGCTATCTGTTGCAGTTTACAACCACTATAAACGGATATACCATCAATCTTTACAAAAGGG
                            atctgat  putative branch site (score: 151)
              ttgaattt  TA-rich tract