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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctagattttccatcagactatcggttgttgttgcaagtgcttgttcctttctcatgtttttgtttcaatgtttgtttattacttttacacagGACTCACAGATTTCAGCTATTGCGAATGGTTCCCTTCTCAGTGAGACACTCTTTTCTACTGCAAATGAAAGCATAGGAGTAGTAAGTGGTTATCCTGGAT

Basic information

species Zea mays
transcript GRMZM2G158162_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 7
gtaagctagattttcca--------tcagactatcggttgttgttgcaagtgcttgttcctttctcatgtttttgtt------tcaatgtttgtttattacttttacacagGACTCACAGATTTCAGCTATTGCGAATGGTTCCCTTCTCAGTGAGACACTCTTTTCTACTGCAAATGAAAGCATAGGAGTAGTAAGTGGTTATCCTGGAT
||||| ||||||||||         ||  ||||     | ||  ||||| |||||||| |  | || | |||   ||      ||||||||| | | |||||| |  ||||||||||||||||||||||||||| || |||||| ||||  | || ||| | ||||||| | ||||||| |   ||| | |||||||||||||| | ||||
gtaagttagattttcctaacattcttcctactaatttattttcctgcaaatgcttgtttcactttcctttttcccttcctttatcaatgtttttatgttacttctgtacagGACTCACAGATTTCAGCTATTGCCAACGGTTCCATTCTTGGGGATACATTATTTTCTAGTACAAATGAGAATTTAGCAATAGTAAGTGGTTATTCAGGAT
















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|5268958|gb|AI770922.1|AI770922
EST:     GGAAACTTGTTATGGGCTTTCGGAAGGCCACAAATACTGGCAGTCTGCCA                         GACTCACAGATTTCAGCTATTGCGAATGGTTCCCTTCTCAGTGAGACACTC
genomic: GGAAACTTGTTATGGGCTTTCGGAAGGCCACAAATACTGTCAGTCTGCCAgtaagctaga ... ttttacacagGACTCACAGATTTCAGCTATTGCGAATGGTTCCCTTCTCAGTGAGACACTC
EST: gi|67034443|gb|CO462993.1|CO462993
EST:     GGAAACTTGTTATGGGCTTTCGGAAGGCCACAAATACTGTCAGTCTGCCA                         GACTCACAGATTTCAGCTATTGCGAATGGTTCCCTTCTCAGTGAGACACTC
genomic: GGAAACTTGTTATGGGCTTTCGGAAGGCCACAAATACTGTCAGTCTGCCAgtaagctaga ... ttttacacagGACTCACAGATTTCAGCTATTGCGAATGGTTCCCTTCTCAGTGAGACACTC
EST: gi|67040653|gb|CO466908.1|CO466908
EST:     -AAACTTGTTATGGGCTTTCG-AANGGC-ACAAATACTGTCAGTCTGCCA                         GACTCACAGATTTCAGCTATTGCGAATGGGTCCCTTCTCAGTGAGAC
genomic: GAAACTTGTTATGGGCTTTCGGAA-GGCCACAAATACTGTCAGTCTGCCAgtaagctaga ... ttttacacagGACTCACAGATTTCAGCTATTGCGAATGGTTCCCTTCTCAGTGAGAC
EST: gi|13150757|gb|BG321079.1|BG321079
EST:     GGAAACTTGTTATGGGCTTTCGGAAGGCCACAAATACTGTCAGTCTGCCA                         GACTCACAGATTTCAGCTATTGCGAATGGTTCCCTTCTCAGTGAGACACTC
genomic: GGAAACTTGTTATGGGCTTTCGGAAGGCCACAAATACTGTCAGTCTGCCAgtaagctaga ... ttttacacagGACTCACAGATTTCAGCTATTGCGAATGGTTCCCTTCTCAGTGAGACACTC
EST: gi|6564045|gb|AW231667.1|AW231667
EST:     GGAAACTTGTTATGGGCTTTCGGAAGGCCACAAATACTGTCAGTCTGCCA                         GACTCACAGATTTCAGCTATTGCAAATGGTTCCCTTCTCAGTGAGACACTC
genomic: GGAAACTTGTTATGGGCTTTCGGAAGGCCACAAATACTGTCAGTCTGCCAgtaagctaga ... ttttacacagGACTCACAGATTTCAGCTATTGCGAATGGTTCCCTTCTCAGTGAGACACTC

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), 48 (downstream exon)
Score: 268

TGACCTTTAGTCGTATAGATCCTGGAGGGAAACTTGTTATGGGCTTTCGGAAGGCCACAAATACTGTCAGTCTGCCAgtaagctaga ... ttttacacagGACTCACAGATTTCAGCTATTGCGAATGGTTCCCTTCTCAGTGAGACACTCTTTTCTACTGCAAATGAAAGCATAGGAGTAGTAAGTGGTTATCCTGGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 160

TGACCTTTAGTCGTATAGATCCTGGAGGGAAACTTGTTATGGGCTTTCGGAAGGCCACAAATACTGTCAGTCTGCCAgtaagctaga ... ttttacacagGACTCACAGATTTCAGCTATTGCGAATGGTTCCCTTCTCAGTGAGACACTCTTTTCTACTGCAAATGAAAGCATAGGAGTAGTAAGTGGTTATCCTGGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 224

TGACCTTTAGTCGTATAGATCCTGGAGGGAAACTTGTTATGGGCTTTCGGAAGGCCACAAATACTGTCAGTCTGCCAgtaagctaga ... ttttacacagGACTCACAGATTTCAGCTATTGCGAATGGTTCCCTTCTCAGTGAGACACTCTTTTCTACTGCAAATGAAAGCATAGGAGTAGTAAGTGGTTATCCTGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 453

TGACCTTTAGTCGTATAGATCCTGGAGGGAAACTTGTTATGGGCTTTCGGAAGGCCACAAATACTGTCAGTCTGCCAgtaagctaga ... ttttacacagGACTCACAGATTTCAGCTATTGCGAATGGTTCCCTTCTCAGTGAGACACTCTTTTCTACTGCAAATGAAAGCATAGGAGTAGTAAGTGGTTATCCTGGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttgttcctttctcatgtttttgtttcaatgtttgtttattacttttacacagGACTCACAGATTTCAGCTATTGCGAATGGTTCCCTTCTCAGTGAGACACTCTTTTCTACTGCAAATGAAAGCATAGGAGTAGTAAGTGGTTATCCTGGAT
                                         ttactttt  CT-rich tract
                             aatgtttgtttattac  TA-rich tract