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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagagtctttgtgatttatgtgataatctcaaatacttgaatccgtttatcatatcacttttcaataacttttgtgttcatctagGCCCCTTGATGACCCTGAGATGATACGGTTCGGGGCGCATATTGTTCTTGTGCTGAGGCACCTTTTCAGTGATGGGATGGATGATGAGTTAGATGAAAAA

Basic information

species Zea mays
transcript GRMZM2G348675_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G348675_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os11g42420.1 (Oryza sativa), 3'ss of exon 13
gtagagtctttgtgattt-atgtgataatctcaaatacttgaatccgtttatcatatcacttttcaataacttttgtgttcatctagGCCCCTTGATGACCCTGAGATGATACGGTTCGGGGCGCATATTGTTCTTGTGCTGAGGCACCTTTTCAGTGATGGGATGGATGATGAGTTAGATGAAAAA
|||     ||| |||||  | | |||  | || ||       || | ||   ||| |   |    | |||||| | || |||| |||||||| |||||||||||| |||||||| ||||| || |||||||||||||| |||||  |||||||||| || |  ||||| |||||||| || ||||| 
gtatgtattttatgattccaagagatggtttccaa-------atacattccacatttttttcacgactaacttctctggtcatttagGCCCCGTGATGACCCTGATATGATACGCTTCGGAGCACATATTGTTCTTGTTCTGAGATACCTTTTCAGCGACGAAATGGAAGATGAGTTTGAGGAAAAG
















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|211285653|gb|FL023028.1|FL023028
EST:     CTATGGTCATGGTTATCACCTGCTGAAGAGAACCATAATAATACTGCAAG                         GCCCCCTTGATGACCCTGAGATGATACGGTTCGGGGCACATATTGTTCTTG
genomic: CTATGGTCATGGTTATCACCTGCTGAAGAGAACCATAATAATACTGCAAGgtagagtctt ... gttcatctagGCCCC-TTGATGACCCTGAGATGATACGGTTCGGGGCGCATATTGTTCTTG
EST: gi|6526616|gb|AW215913.1|AW215913
EST:     CTATGGTCATGGTTATCACCTGCTGAAGAGAACCATAATAATACTGCAAG                         GCCCCTTGATGACCCTGAGATGATACGGTTCGGGGCACATATTGTTCTTGT
genomic: CTATGGTCATGGTTATCACCTGCTGAAGAGAACCATAATAATACTGCAAGgtagagtctt ... gttcatctagGCCCCTTGATGACCCTGAGATGATACGGTTCGGGGCGCATATTGTTCTTGT
EST: gi|31441055|gb|CD510486.1|CD510486
EST:     CTATGGTCATGGTTATCACCTGCTGAAGAGAACCATAATAATACTGCAAG                         GCCCCTTGATGACCCTGAGATGATACGGTTCGGGGCGCATATTGTTCTTGT
genomic: CTATGGTCATGGTTATCACCTGCTGAAGAGAACCATAATAATACTGCAAGgtagagtctt ... gttcatctagGCCCCTTGATGACCCTGAGATGATACGGTTCGGGGCGCATATTGTTCTTGT

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: 181

ATGAATCTCATGAGTGGAAATATATCTCATCTTCTTGACCTTCTATGGTCATGGTTATCACCTGCTGAAGAGAACCATAATAATACTGCAAGgtagagtctt ... gttcatctagGCCCCTTGATGACCCTGAGATGATACGGTTCGGGGCGCATATTGTTCTTGTGCTGAGGCACCTTTTCAGTGATGGGATGGATGATGAGTTAGATGAAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 44

ATGAATCTCATGAGTGGAAATATATCTCATCTTCTTGACCTTCTATGGTCATGGTTATCACCTGCTGAAGAGAACCATAATAATACTGCAAGgtagagtctt ... gttcatctagGCCCCTTGATGACCCTGAGATGATACGGTTCGGGGCGCATATTGTTCTTGTGCTGAGGCACCTTTTCAGTGATGGGATGGATGATGAGTTAGATGAAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

ATGAATCTCATGAGTGGAAATATATCTCATCTTCTTGACCTTCTATGGTCATGGTTATCACCTGCTGAAGAGAACCATAATAATACTGCAAGgtagagtctt ... gttcatctagGCCCCTTGATGACCCTGAGATGATACGGTTCGGGGCGCATATTGTTCTTGTGCTGAGGCACCTTTTCAGTGATGGGATGGATGATGAGTTAGATGAAAAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 53

ATGAATCTCATGAGTGGAAATATATCTCATCTTCTTGACCTTCTATGGTCATGGTTATCACCTGCTGAAGAGAACCATAATAATACTGCAAGgtagagtctt ... gttcatctagGCCCCTTGATGACCCTGAGATGATACGGTTCGGGGCGCATATTGTTCTTGTGCTGAGGCACCTTTTCAGTGATGGGATGGATGATGAGTTAGATGAAAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatacttgaatccgtttatcatatcacttttcaataacttttgtgttcatctagGCCCCTTGATGACCCTGAGATGATACGGTTCGGGGCGCATATTGTTCTTGTGCTGAGGCACCTTTTCAGTGATGGGATGGATGATGAGTTAGATGAAAAA
                                caataac  putative branch site (score: 53)
                                              ttcatct  putative PPT
                            ttttcaataactttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagagtctttgtgatttatgtgataatctcaaatacttgaatccgtttatcatatcacttttcaataacttttgtgttcatctagGCCCCTTGATGACCCTGAGATGATACGGTTCGGGGCGCATATTGTTCTTGTGCTGAGGCACCTTTTCAGTGATGGGATGGATGATGAGTTAGATGAAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA