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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAACAATTTTGAGTACTTAATGGAACTTAACACACTGGCTGGGCGCAGTTACAATGACATTACTCAGgtcagtatcctgtatacttaatatttctggccgaatctagcgacctgtagtcctgatattgtttctgcttgtgcag

Basic information

species Zea mays
transcript GRMZM2G044143_T01
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044143_T01 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os04g46894.1 (Oryza sativa), 5'ss of exon 20
ATCAACAATTTTGAGTACTTAATGGAACTTAACACACTGGCTGGGCGCAGTTACAATGACATTACTCAGgtcagtatcctgtatacttaatatttctggccgaatctagcgacctgtagtcctgatattgtttctgcttgtgcag
|| | ||||||||||||||| |||||||| |||||||||||||| || |||||||||||||| |||||||||||| | ||| |    || |  ||||     ||    |  || | |  | || | | | |   ||| |||||||
ATTAGCAATTTTGAGTACTTGATGGAACTGAACACACTGGCTGGACGAAGTTACAATGACATAACTCAGgtcagtttactgcacttgtatttcttctc-taaaacaaggtaacttatcattctaacaatttacatgcatgtgcag

upper sequence: GRMZM2G044143_T01 (Zea mays), 5'ss of exon 20
lower sequence: AT3G60920.1 (Arabidopsis thaliana), 5'ss of exon 21
ATCAACAATTTTGAGTACTTAATGGAACTTAACACACTGGCTGGGCGCAGTTACAATGACATTACTCAGgtcagtatcctg--------------tatacttaatatttctggccgaatctagcgacctgtagtcctgat--attgtttctgcttgtgcag
|||| ||||||||||||||||||| | || |||||| |||||||||| ||||| |||||||| |||||||| | | || ||              | | ||||  || | ||     || |        ||  || ||||  ||| ||  |   | |||||
ATCAGCAATTTTGAGTACTTAATGCAGCTCAACACATTGGCTGGGCGTAGTTATAATGACATCACTCAGgtaaatctcgtgctagttaaaatgttttttcttataatctttgatatcattttctctttggttatcttgatctatttttcatatctttgcag

upper sequence: GRMZM2G044143_T01 (Zea mays), 5'ss of exon 20
lower sequence: AT2G45540.2 (Arabidopsis thaliana), 5'ss of exon 22
ATCAACAATTTTGAGTACTTAATGGAACTTAACACACTGGCTGGGCGCAGTTACAATGACATTACTCAGgtcagtatcctgtatacttaatatttctggccgaatctagcga--cctgtagt--cctgatat-----tgtttctgcttgtgcag
|||| ||||||||| ||||||||| | ||||||||  ||||||| || |||||||||||||||||||||||   | |  ||     |||   ||||  |  |||  |  | |  ||  || |  | |||||      | | |     | |||||
ATCAGCAATTTTGAATACTTAATGCAGCTTAACACGTTGGCTGGCCGTAGTTACAATGACATTACTCAGgtagatcttgtgctcttttacgttttcctggtgaacttgtcaatgcccttacttgcttgatagatagatatgttattctttgcag

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: 48 (upstream exon), 49 (downstream exon)
Score: 51

ATCAACAATTTTGAGTACTTAATGGAACTTAACACACTGGCTGGGCGCAGTTACAATGACATTACTCAGgtcagtatcc ... gcttgtgcagTACCCTGTTTTTCCCTGGGTAGTAGCAGATTACAAATCCCGAGTGTTGAATCTGGATGACCCTTTGTCGTATCGAGATCTTTCAAAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 57

ATCAACAATTTTGAGTACTTAATGGAACTTAACACACTGGCTGGGCGCAGTTACAATGACATTACTCAGgtcagtatcc ... gcttgtgcagTACCCTGTTTTTCCCTGGGTAGTAGCAGATTACAAATCCCGAGTGTTGAATCTGGATGACCCTTTGTCGTATCGAGATCTTTCAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 82

ATCAACAATTTTGAGTACTTAATGGAACTTAACACACTGGCTGGGCGCAGTTACAATGACATTACTCAGgtcagtatcc ... gcttgtgcagTACCCTGTTTTTCCCTGGGTAGTAGCAGATTACAAATCCCGAGTGTTGAATCTGGATGACCCTTTGTCGTATCGAGATCTTTCAAAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 70

ATCAACAATTTTGAGTACTTAATGGAACTTAACACACTGGCTGGGCGCAGTTACAATGACATTACTCAGgtcagtatcc ... gcttgtgcagTACCCTGTTTTTCCCTGGGTAGTAGCAGATTACAAATCCCGAGTGTTGAATCTGGATGACCCTTTGTCGTATCGAGATCTTTCAAAG