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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagccattttgatattgttgagcaaaattatgtttgttgaacagtcaagacttgattttcttatgatgtagaatcttttgctgtagGATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTTTTTTCAAAG

Basic information

species Zea mays
transcript GRMZM2G062761_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 3
-gtagccattttgatattgttgagcaaaattatgtt--tgttgaacagtcaagacttgattttcttatgatgtagaatcttttgctgtagGATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTTTTTTCAAAG
  ||| |||||   || ||||||| | |  | | ||     ||||||| ||   ||||   |       || |   ||  || | | |||||||| ||||| |||||||||||||| || ||||| || |||||||||||||||||||||
gttaggcattt-attaatgttgagaagatatttcttaacaatgaacagccatatcttggcatctaatgaattttccatgcttcgttctagGATTATGTGGCAACTAGATGGTATCGTGCCCCAGAGTTGTGTGGCTCCTTTTTTTCAAAG

upper sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0011g04920.t01 (Vitis vinifera), 3'ss of exon 3
gtagccattttgatattgttgagcaaaattatgtttgttga-acagtcaagacttgattttcttatgatgtagaatcttttgctgtagGATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTTTTTTCAAAG
|||   || |  || || |  |   ||||||||    ||       |    ||  |||     | | |  ||    | |||  || ||||||||||||| |||||||||||||| ||||| ||| | ||||| | |||||| || || 
gta--tatatctattttttgcaatgaaattatgagctttagtgttattttaacaggatgagtctgtaacttatctacattt--tgaagGATTACGTGGCAACTAGATGGTATCGTGCTCCTGAACTCTGTGGTTGCTTTTTCTCCAAA
















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|74245616|gb|DT653530.1|DT653530
EST:     GCCTTGCCCGCGTTTCATTCAATGACACTCCATCAGCCATATTCTGGACG                         GATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCNNN
genomic: GCCTTGCCCGCGTTTCATTCAATGACACTCCATCAGCCATATTCTGGACGgtagccattt ... tttgctgtagGATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTT
EST: gi|5871276|gb|AW017747.1|AW017747
EST:     TCATTCAATGACACTCCATCAGCCATATTCTGGACG                         GATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCNNN
genomic: TCATTCAATGACACTCCATCAGCCATATTCTGGACGgtagccattt ... tttgctgtagGATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTT
EST: gi|76018133|gb|DT945303.1|DT945303
EST:     GCCTTGCCCGCGTTTCATTCAATGACACTCCATCAGCCATATTCTGGACG                         GATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTT
genomic: GCCTTGCCCGCGTTTCATTCAATGACACTCCATCAGCCATATTCTGGACGgtagccattt ... tttgctgtagGATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTT
EST: gi|76934717|gb|DV173988.1|DV173988
EST:     GCCTTGCCCGCGTTTCATTCAATGACACTCCATCAGCCATATTCTGGACG                         GATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCNNN
genomic: GCCTTGCCCGCGTTTCATTCAATGACACTCCATCAGCCATATTCTGGACGgtagccattt ... tttgctgtagGATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTT

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: 36

CAAGAATATTCTAGCCAATGCTGACTGCAAGCTGAAGATTTGTGATTTTGGCCTTGCCCGCGTTTCATTCAATGACACTCCATCAGCCATATTCTGGACGgtagccattt ... tttgctgtagGATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTTTTTTCAAAG


Block sizes: 43 (upstream exon), 35 (downstream exon)
Score: 14

CAAGAATATTCTAGCCAATGCTGACTGCAAGCTGAAGATTTGTGATTTTGGCCTTGCCCGCGTTTCATTCAATGACACTCCATCAGCCATATTCTGGACGgtagccattt ... tttgctgtagGATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTTTTTTCAAAG


Block sizes: 49 (upstream exon), 35 (downstream exon)
Score: 14

CAAGAATATTCTAGCCAATGCTGACTGCAAGCTGAAGATTTGTGATTTTGGCCTTGCCCGCGTTTCATTCAATGACACTCCATCAGCCATATTCTGGACGgtagccattt ... tttgctgtagGATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTTTTTTCAAAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 35

CAAGAATATTCTAGCCAATGCTGACTGCAAGCTGAAGATTTGTGATTTTGGCCTTGCCCGCGTTTCATTCAATGACACTCCATCAGCCATATTCTGGACGgtagccattt ... tttgctgtagGATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTTTTTTCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgttgaacagtcaagacttgattttcttatgatgtagaatcttttgctgtagGATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTTTTTTCAAAG
                  acttgat  putative branch site (score: 35)
                                          tcttttgct  putative PPT
                       attttcttat  TA-rich tract