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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtttgttgccagaagattggagctttggctgtagatctctcttctccccgtttcctcgatagtttcgcgaccgaccaatttcttggtgatttttggctgttgcctgtgttacagTGCGGGAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGGCACGAGATTGCCGAG

Basic information

species Zea mays
transcript GRMZM2G052926_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052926_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g36120.2 (Oryza sativa), 3'ss of exon 1
---------------------------------gtaatgtttgttgccagaagattggagctttggctgtagatctc-tcttctccccgtttcctcgatagtttcgcgacc--gaccaatttcttggtgatttttggctgttg-cctgtgttacagTGCGG------GAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGGCACGAGATTGCCGAG
                                  | |  |   |  | |   |         || ||  || ||||  |||||||  | ||   | |  || ||| |      | ||     ||| ||    ||     || | |||||| |   ||||||      ||||||| | |||||||| ||||| ||||||||||| |||||||||||||| || || |||
gtgagcaccccgtacggacgtccctcttccttcctcacatccttctctatccg--caccctcttcgccttaaatcttatcttctcttctttggtttggaagcttctctcttttggccttaaccttagtacggttaacagGTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGGTGATCCACATCCGGAACGTCGGGCACGAAATCGCTGAG

upper sequence: GRMZM2G052926_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g36120.1 (Oryza sativa), 3'ss of exon 1
----------------------gtaatgtttgttgccagaagattggagctttggctgtagatctc-tcttctccccgtttcctcgatagtttcgcgacc--gaccaatttcttggtgatttttggctgttg-cctgtgttacagTGCGG------GAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGGCACGAGATTGCCGAG
                       | |  |   |  | |   |         || ||  || ||||  |||||||  | ||   | |  || ||| |      | ||     ||| ||    ||     || | |||||| |   ||||||      ||||||| | |||||||| ||||| ||||||||||| |||||||||||||| || || |||
gtacggacgtccctcttccttcctcacatccttctctatccg--caccctcttcgccttaaatcttatcttctcttctttggtttggaagcttctctcttttggccttaaccttagtacggttaacagGTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGGTGATCCACATCCGGAACGTCGGGCACGAAATCGCTGAG
















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|93284255|gb|EB676519.1|EB676519
EST:     TCTTAAACCCTCTCAACAAG                         TGCGGGAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGG
genomic: TCTTAAACCCTCTCAACAAGgtaatgtttg ... tgtgttacagTGCGGGAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGG
EST: gi|76013333|gb|DT940503.1|DT940503
EST:     GCCGACGGCAAAACCCTAGATCTCTCTCCCTCTTAAACCCTCTCAACAAG                         TGCGGGAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGG
genomic: GCCGACGGCAAAACCCTAGATCTCTCTCCCTCTTAAACCCTCTCAACAAGgtaatgtttg ... tgtgttacagTGCGGGAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGG
EST: gi|78087001|gb|DV515394.1|DV515394
EST:     CCGACGGCAAAACCCTAGATCTCTCTCCCTCTTAAACCCTCTCAACAAG                         TGCGGGAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGG
genomic: CCGACGGCAAAACCCTAGATCTCTCTCCCTCTTAAACCCTCTCAACAAGgtaatgtttg ... tgtgttacagTGCGGGAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGG
EST: gi|31250253|gb|CD219277.1|CD219277
EST:     GCCGACGGCAAAACCCTAGATCTCTCTCCCTCTTAAACCCTCTCAACAAG                         TGCGGGAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGG
genomic: GCCGACGGCAAAACCCTAGATCTCTCTCCCTCTTAAACCCTCTCAACAAGgtaatgtttg ... tgtgttacagTGCGGGAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGG
EST: gi|78080905|gb|DV509317.1|DV509317
EST:     GCCGACGGCAAAACCCTAGATCTCTCTCCCTCTTAAACCCTCTCAACAAG                         TGCGGGAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGG
genomic: GCCGACGGCAAAACCCTAGATCTCTCTCCCTCTTAAACCCTCTCAACAAGgtaatgtttg ... tgtgttacagTGCGGGAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGG

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: 167

ACACTACTGCCGTGCCCCCCTCCCTTCTCTCTCTCTTCGCCGCAGCGTCAGCCGACGGCAAAACCCTAGATCTCTCTCCCTCTTAAACCCTCTCAACAAGgtaatgtttg ... tgtgttacagTGCGGGAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGGCACGAGATTGCCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

ACACTACTGCCGTGCCCCCCTCCCTTCTCTCTCTCTTCGCCGCAGCGTCAGCCGACGGCAAAACCCTAGATCTCTCTCCCTCTTAAACCCTCTCAACAAGgtaatgtttg ... tgtgttacagTGCGGGAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGGCACGAGATTGCCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

ACACTACTGCCGTGCCCCCCTCCCTTCTCTCTCTCTTCGCCGCAGCGTCAGCCGACGGCAAAACCCTAGATCTCTCTCCCTCTTAAACCCTCTCAACAAGgtaatgtttg ... tgtgttacagTGCGGGAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGGCACGAGATTGCCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 78

ACACTACTGCCGTGCCCCCCTCCCTTCTCTCTCTCTTCGCCGCAGCGTCAGCCGACGGCAAAACCCTAGATCTCTCTCCCTCTTAAACCCTCTCAACAAGgtaatgtttg ... tgtgttacagTGCGGGAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGGCACGAGATTGCCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttcgcgaccgaccaatttcttggtgatttttggctgttgcctgtgttacagTGCGGGAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGGCACGAGATTGCCGAG
                 aatttctt  TA-rich tract