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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattatctttttttacctttttctgttcacatataatcttgaatctgttttttatgttgttgatagatggccatcttttctacagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGGAGCCCATTAAAACCTTAT

Basic information

species Zea mays
transcript GRMZM2G139038_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139038_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g41100.6 (Oryza sativa), 3'ss of exon 2
gtaattatc--tttttttacctttttctgttcac-atataatcttgaatctgttttttatgttgttgatagatggccatcttttcta---cagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGGAGCCCATTAAAACCTTAT
|||| | |   |||      || ||| ||||  | |  ||  ||  || || |  |      |||  |  |||   ||| ||   ||   |||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||||||||| |||||  |||||||||| 
gtaactgttgatttgacgctctatttttgtttgccaagtatcctcaaacctatcctgatgcctgtatactgatatgcattttccatataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAATATGTGATTTTGGACTATCTCGTCAATATGGAAGCCCGCTAAAACCTTAC
















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|67025976|gb|CO454725.1|CO454725
EST:     CAGCTGCTAGAGGGTGTAAAATATCTACATGACAATTGTGTACTCCATAG                         GGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAAT
genomic: CAGCTGCTAGAGGGTGTAAAATATCTACATGACAATTGGGTACTCCATAGgtaattatct ... ttttctacagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAAT
EST: gi|89760369|gb|DY688806.1|DY688806
EST:     CAGCTGCTAGAGGGTGTAAAATATCTACATGACAATTGGGTACTCCATAG                         GGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAAT
genomic: CAGCTGCTAGAGGGTGTAAAATATCTACATGACAATTGGGTACTCCATAGgtaattatct ... ttttctacagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAAT

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: 46 (upstream exon), 48 (downstream exon)
Score: 96

AGACCATGAAACAACCATATACACAAAGCGAGGTCAAATGTTTGATGCTTCAGCTGCTAGAGGGTGTAAAATATCTACATGACAATTGGGTACTCCATAGgtaattatct ... ttttctacagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGGAGCCCATTAAAACCTTAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 46

AGACCATGAAACAACCATATACACAAAGCGAGGTCAAATGTTTGATGCTTCAGCTGCTAGAGGGTGTAAAATATCTACATGACAATTGGGTACTCCATAGgtaattatct ... ttttctacagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGGAGCCCATTAAAACCTTAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 51

AGACCATGAAACAACCATATACACAAAGCGAGGTCAAATGTTTGATGCTTCAGCTGCTAGAGGGTGTAAAATATCTACATGACAATTGGGTACTCCATAGgtaattatct ... ttttctacagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGGAGCCCATTAAAACCTTAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 63

AGACCATGAAACAACCATATACACAAAGCGAGGTCAAATGTTTGATGCTTCAGCTGCTAGAGGGTGTAAAATATCTACATGACAATTGGGTACTCCATAGgtaattatct ... ttttctacagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGGAGCCCATTAAAACCTTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atataatcttgaatctgttttttatgttgttgatagatggccatcttttctacagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGGAGCCCATTAAAACCTTAT
                           tgttgat  putative branch site (score: 63)
                                        ccatcttttct  putative PPT
           aatctgttttttat  TA-rich tract