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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacatcctctggcctgcatttgatgcataggatccatatgtgccttatgaaatgtcctgcttctctttcttttctggcaccttaattgtttctctgaatattctttttctatactgtagGGTTGTCTATACGGCCAGGCCACACGCACCAAGAACAGAAAAGGTTGTAGGCATAGGGTTTCAACCTGGGTTTGATCCTTACAAG

Basic information

species Zea mays
transcript GRMZM2G048067_T03
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048067_T03 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 20
--------------------------gttacatcctctggcctgcatttgatgcataggatccatatgtgccttatgaaatgt-cctgcttctctttcttttctggcaccttaattgtttctctgaa---tattctttttctatactgtagGGTTGTCTATACGGCCAGGCCACACGCACCAAGAACAGAAAAGGTTGTAGGCATAGGGTTTCAACCTGGGTTTGATCCTTACAAG
                             ||||  ||        |  |   || |    | |||      |  |  | |      ||| |   | | |   |   ||| || ||  |   ||  ||    | | |||  |  | ||||||| | || ||||| || || ||||| || |||||| ||||||||||||| || ||||| ||||| |||||||||||||| ||||||
gtaagtagatgtttgatgagatatcaaccacatgttccattgcagagatttcgcttcatgtgcatcctccgcccacaacacacatatgcatgcttatttgcgcgcacacatttatgctacttcctaagttcaatttttcccattgctgtagGCTAGTATATACAGCAAGACCACATGCCCCAAGATCAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAG

upper sequence: GRMZM2G048067_T03 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 21
--------------------------gttacatcctctggcctgcatttgatgcataggatccatatgtgccttatgaaatgt-cctgcttctctttcttttctggcaccttaattgtttctctgaa---tattctttttctatactgtagGGTTGTCTATACGGCCAGGCCACACGCACCAAGAACAGAAAAGGTTGTAGGCATAGGGTTTCAACCTGGGTTTGATCCTTACAAG
                             ||||  ||        |  |   || |    | |||      |  |  | |      ||| |   | |     |   ||| || ||  |   ||  ||    | | |||  |  | ||||||| | || ||||| || || ||||| || |||||| ||||||||||||| || ||||| ||||| |||||||||||||| ||||||
gtaagtagatgtttgatgagatatcaaccacatgttccattgcagagatttcgcttcatgtgcatcctctgcccacaacacacatatgcatgcttattcgcgcgcacacatttatgctacttcctaagttcaatttttcccattgctgtagGCTAGTATATACAGCAAGACCACATGCCCCAAGATCAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAG
















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: 49 (upstream exon), 49 (downstream exon)
Score: 103

TCTGCATCTCAGGTCTGCTCTGGACATTTTGCTGCTGGTTTTGCTGCTGGTTCTGTCAGGATATATGACATACGCTCTCCTGATAGgttacatcct ... tatactgtagGGTTGTCTATACGGCCAGGCCACACGCACCAAGAACAGAAAAGGTTGTAGGCATAGGGTTTCAACCTGGGTTTGATCCTTACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

TCTGCATCTCAGGTCTGCTCTGGACATTTTGCTGCTGGTTTTGCTGCTGGTTCTGTCAGGATATATGACATACGCTCTCCTGATAGgttacatcct ... tatactgtagGGTTGTCTATACGGCCAGGCCACACGCACCAAGAACAGAAAAGGTTGTAGGCATAGGGTTTCAACCTGGGTTTGATCCTTACAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 59

TCTGCATCTCAGGTCTGCTCTGGACATTTTGCTGCTGGTTTTGCTGCTGGTTCTGTCAGGATATATGACATACGCTCTCCTGATAGgttacatcct ... tatactgtagGGTTGTCTATACGGCCAGGCCACACGCACCAAGAACAGAAAAGGTTGTAGGCATAGGGTTTCAACCTGGGTTTGATCCTTACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

TCTGCATCTCAGGTCTGCTCTGGACATTTTGCTGCTGGTTTTGCTGCTGGTTCTGTCAGGATATATGACATACGCTCTCCTGATAGgttacatcct ... tatactgtagGGTTGTCTATACGGCCAGGCCACACGCACCAAGAACAGAAAAGGTTGTAGGCATAGGGTTTCAACCTGGGTTTGATCCTTACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcttttctggcaccttaattgtttctctgaatattctttttctatactgtagGGTTGTCTATACGGCCAGGCCACACGCACCAAGAACAGAAAAGGTTGTAGGCATAGGGTTTCAACCTGGGTTTGATCCTTACAAG
               ccttaat  putative branch site (score: 90)
                                    ttctttttctatact  putative PPT
                                aatattctttttctat  TA-rich tract