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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaaatacatagttgatgttacctgttatggatgctctgtcatctattattctgtttttttttcttatgcatttgttgtattttctatgcagTGACAACAGCTTAATTCGTGTTGATCGTCTAGAATACCACATCAGGGAAGAGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGTCCTCTAAAG

Basic information

species Zea mays
transcript GRMZM2G048012_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048012_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 15
---------------------------------------------------------------------gtagaaatacatagttgatgttacctgttatgga----tgctctgtcatctattattctgtttttttttcttatgcatttg--ttgt-attttct---atgcagTGACAACAGCTTAATTCGTGTTGATCGTCTAGAATACCACATCAGGGAAGAGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGTCCTCTAAAG
                                                                        ||  | ||||    ||| |      ||||        || | |  | |  |   |    || || |  ||   |||||  |||  |||||||   |||||||||||| ||||||||||| ||||| ||||| ||||| || ||||| ||||||||||| ||||||||  | ||  |||||||||| |||  ||||||||||
gtagggatacttgaattgtttgttgttcttttgatgtaaattgaattgtttgttctttaggtcttaaggaatgagtttcataaagtatgctttggtctatgcgaaatcactttttttttttgtggacatcattattctgctactgatttgacttgccattttcttacatgcagTGACAATAGCTTAATTCGGGTTGACCGTCTTGAATATCATATCAGAGAAGAGCTTAATAAAACAGCTTCCCGTGCCATGGTTGTGTTGAATCCTCTAAAG
















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|67016826|gb|CO445575.1|CO445575
EST:     TCATCAACCGCAATAAATTCCTTTATCCGTGGAATCGGGATAACAAGAAG                         TGACAACAGCTTAATTCGTGTTGATCGTCTAGAATACCACATCAGGGAAGA
genomic: TCATCAACCGCAATAAATTCCTTTATCCGTGGAATCGGGATAACAAGAAGgtagaaatac ... ttctatgcagTGACAACAGCTTAATTCGTGTTGATCGTCTAGAATACCACATCAGGGAAGA
EST: gi|67014180|gb|CO442929.1|CO442929
EST:     TCATCAACCGCAATAAATTCCTTTATCCGTGGAATCGGGATAACAAGAAG                         TGACAACAGCTTAATTCGTGTTGATCGTCTAGAATACCACATCAGGGAAGA
genomic: TCATCAACCGCAATAAATTCCTTTATCCGTGGAATCGGGATAACAAGAAGgtagaaatac ... ttctatgcagTGACAACAGCTTAATTCGTGTTGATCGTCTAGAATACCACATCAGGGAAGA
EST: gi|71304661|gb|DR788447.1|DR788447
EST:     TCATCAACCGCAATAAATTCCTTTATCCGTGGAATCGGGATAACAAGAAG                         TGACAACAGCTTAATTCGTGTTGATCGTCTAGAATACCACATCAGGGAAGA
genomic: TCATCAACCGCAATAAATTCCTTTATCCGTGGAATCGGGATAACAAGAAGgtagaaatac ... ttctatgcagTGACAACAGCTTAATTCGTGTTGATCGTCTAGAATACCACATCAGGGAAGA

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: 230

GGGATGATCCCCGCTTGTTGACACTGGCTGGACTCCGGCGGCGGGGAGTATCATCAACCGCAATAAATTCCTTTATCCGTGGAATCGGGATAACAAGAAGgtagaaatac ... ttctatgcagTGACAACAGCTTAATTCGTGTTGATCGTCTAGAATACCACATCAGGGAAGAGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGTCCTCTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

GGGATGATCCCCGCTTGTTGACACTGGCTGGACTCCGGCGGCGGGGAGTATCATCAACCGCAATAAATTCCTTTATCCGTGGAATCGGGATAACAAGAAGgtagaaatac ... ttctatgcagTGACAACAGCTTAATTCGTGTTGATCGTCTAGAATACCACATCAGGGAAGAGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGTCCTCTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

GGGATGATCCCCGCTTGTTGACACTGGCTGGACTCCGGCGGCGGGGAGTATCATCAACCGCAATAAATTCCTTTATCCGTGGAATCGGGATAACAAGAAGgtagaaatac ... ttctatgcagTGACAACAGCTTAATTCGTGTTGATCGTCTAGAATACCACATCAGGGAAGAGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGTCCTCTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

GGGATGATCCCCGCTTGTTGACACTGGCTGGACTCCGGCGGCGGGGAGTATCATCAACCGCAATAAATTCCTTTATCCGTGGAATCGGGATAACAAGAAGgtagaaatac ... ttctatgcagTGACAACAGCTTAATTCGTGTTGATCGTCTAGAATACCACATCAGGGAAGAGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGTCCTCTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcatctattattctgtttttttttcttatgcatttgttgtattttctatgcagTGACAACAGCTTAATTCGTGTTGATCGTCTAGAATACCACATCAGGGAAGAGCTTAACAAAACAGCCCCTCGAACCATGGTTGTTTTGCGTCCTCTAAAG
                                         tattttct  CT-rich tract
       tattattctgtttttt  TA-rich tract