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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgttgtcaatgaatcacattttattatttgaaacaattatctgttaactccatgtttgtttcagGGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACTTCACATGGCAGCATTGAACGGTCACTTAGATTGCATGCAGTTGTTGATT

Basic information

species Zea mays
transcript AC194389.3_FGT001
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC194389.3_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g37730.3 (Oryza sativa), 3'ss of exon 4
gtatgtgttgtcaatgaatcac--attttat--tatttgaaacaattatctgttaactccatgt--------------ttgtttcagGGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACTTCACATGGCAGCATTGAACGGTCACTTAGATTGCATGCAGTTGTTGATT
|||||| || ||||   |  |    ||||||  | | |||| ||  || | |||||   | |||              || ||| || || ||| |||| || |||||||||||||| ||||| ||||||||||||||||| |||||||| ||||| ||||| || ||||||||||| |||||||||
gtatgtattttcaaacgagtattggttttatcctgtctgaagcagctaacagttaatgtcttgtcacatttcttatttttcttttagTGCTCGTTTGAGATATATCAACAAACCTGCTGATGGCGGTGTTACAGCACTTCATATGGCAGCTTTGAATGGTCATTTTGATTGCATGCAATTGTTGATT

upper sequence: AC194389.3_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g37730.2 (Oryza sativa), 3'ss of exon 4
gtatgtgttgtcaatgaatcac--attttat--tatttgaaacaattatctgttaactccatgt--------------ttgtttcagGGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACTTCACATGGCAGCATTGAACGGTCACTTAGATTGCATGCAGTTGTTGATT-----------------------------------------------
|||||| || ||||   |  |    ||||||  | | |||| ||  || | |||||   | |||              || ||| || || ||| |||| || |||||||||||||| ||||| ||||||||||||||||| |||||||| ||||| ||||| || ||||||||||| |||||||||                                               
gtatgtattttcaaacgagtattggttttatcctgtctgaagcagctaacagttaatgtcttgtcacatttcttatttttcttttagtgctcgtttgagatatatcaacaaacctgctgatggcggtgttacagCACTTCATATGGCAGCTTTGAATGGTCATTTTGATTGCATGCAATTGTTGATTGACTTGGGTGCTAATGTGTCAGCTGTCACATTCCCGTATGGCACTAC
















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|50326933|gb|CO522059.1|CO522059
EST:     AACAGTGGGAGCAGTCCTAATTCATCGTCGGGGCAGAAGTTTAATGAATC                         GGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACT
genomic: AACAGTGGGAGCAGTCCTAATTCATCGTCGGGGCAGAAGTTTAATGAATCgtatgtgttg ... tttgtttcagGGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACT
EST: gi|149014811|gb|EE044512.2|EE044512
EST:     AACAGTGGGAGCAGTCCTAATTCATCGTCGGGGCAGAAGTTTAATGAATC                         GGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACT
genomic: AACAGTGGGAGCAGTCCTAATTCATCGTCGGGGCAGAAGTTTAATGAATCgtatgtgttg ... tttgtttcagGGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACT
EST: gi|148961455|gb|EE012203.2|EE012203
EST:     AACAGTGGGAGCAGTCCTAATTCATCGTCGGGGCAGAAGTTTAATGAATC                         GGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACT
genomic: AACAGTGGGAGCAGTCCTAATTCATCGTCGGGGCAGAAGTTTAATGAATCgtatgtgttg ... tttgtttcagGGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACT
EST: gi|211432410|gb|FL439403.1|FL439403
EST:     AACAGTGGGAGCAGTCCTAATTCATCGTCGGGGCAGAAGTTTAATGAATC                         GGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACT
genomic: AACAGTGGGAGCAGTCCTAATTCATCGTCGGGGCAGAAGTTTAATGAATCgtatgtgttg ... tttgtttcagGGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACT
EST: gi|148942318|gb|EC887337.2|EC887337
EST:     AACAGTGGGAGCAGTCCTAATTCATCGTCGGGGCAGAAGTTTAATGAATC                         GGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACT
genomic: AACAGTGGGAGCAGTCCTAATTCATCGTCGGGGCAGAAGTTTAATGAATCgtatgtgttg ... tttgtttcagGGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACT

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), 49 (downstream exon)
Score: 46

CCTTGGAGGATATTGCTTCTTCTGTGGTGGATGGTGGTGATTGCCAGACAAACAGTGGGAGCAGTCCTAATTCATCGTCGGGGCAGAAGTTTAATGAATCgtatgtgttg ... tttgtttcagGGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACTTCACATGGCAGCATTGAACGGTCACTTAGATTGCATGCAGTTGTTGATT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 47

CCTTGGAGGATATTGCTTCTTCTGTGGTGGATGGTGGTGATTGCCAGACAAACAGTGGGAGCAGTCCTAATTCATCGTCGGGGCAGAAGTTTAATGAATCgtatgtgttg ... tttgtttcagGGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACTTCACATGGCAGCATTGAACGGTCACTTAGATTGCATGCAGTTGTTGATT


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 32

CCTTGGAGGATATTGCTTCTTCTGTGGTGGATGGTGGTGATTGCCAGACAAACAGTGGGAGCAGTCCTAATTCATCGTCGGGGCAGAAGTTTAATGAATCgtatgtgttg ... tttgtttcagGGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACTTCACATGGCAGCATTGAACGGTCACTTAGATTGCATGCAGTTGTTGATT


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 23

CCTTGGAGGATATTGCTTCTTCTGTGGTGGATGGTGGTGATTGCCAGACAAACAGTGGGAGCAGTCCTAATTCATCGTCGGGGCAGAAGTTTAATGAATCgtatgtgttg ... tttgtttcagGGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACTTCACATGGCAGCATTGAACGGTCACTTAGATTGCATGCAGTTGTTGATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatcacattttattatttgaaacaattatctgttaactccatgtttgtttcagGGCCCGTGTGAGGTACATCAACAAACCTGCAGATGGTGGTGTTACAGCACTTCACATGGCAGCATTGAACGGTCACTTAGATTGCATGCAGTTGTTGATT
                                tgttaac  putative branch site (score: 23)
                                             tttgtttc  putative PPT
        attttattatttgaaa  TA-rich tract