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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttctgtcctctcccttcgcctttctcttcccgccatctctgccgtcccctaactttctttccgcgtcttgcagGAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTAGCCGGAGGTGCGGTGCCTTACGGGGCTAATCCGCGGCGCGGGATTTGGTCGATCAG

Basic information

species Zea mays
transcript GRMZM2G121456_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121456_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g19510.1 (Oryza sativa), 3'ss of exon 1
----gtttctgtcctctcccttcg-cctttctct-tcccgccatctctgccgtcccctaacttt--ctttccgcgtcttgcagGAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTAGCCGGAGGTGCGGTGCCTTACGGG-GCTAATCCGCGGCGCGGGATTTGGTCGATCAG
      | |  || || |||| |  |||  ||||   | | | |  || |  || |   ||  |  ||  |   ||||||||||||| ||||||||||||| |||||  | |||||||  ||||  | ||    |||    ||  ||| ||| | || |||||||||||||||||||
gttcactcccctcttccccctccctcctcactctactctgtcgtggctccactcgctctaccctaactgactcggtcttgcagGAGCCGGAGGTGCGCTCGGGCCGTGGCGACCGCCGCCGCCGCCGCTG----GCCACGGGGCCGCTCATCAGAGGAGCGGGATTTGGTCGATCAG
















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|149081623|gb|EE170768.2|EE170768
EST:     CGCCCGAACCCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAG                         GAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTAGCCGGAGGTGCGGT
genomic: CGCCCGAACCCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAGgtttctgtcc ... cgtcttgcagGAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTAGCCGGAGGTGCGGT
EST: gi|101401421|gb|EB822388.1|EB822388
EST:     CGCCCGAACCCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAG                         GAGCAAGAGGTGCGCTCGTGCCGTAACTACCGCC
genomic: CGCCCGAACCCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAGgtttctgtcc ... cgtcttgcagGAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCC
EST: gi|76281085|gb|DV020653.1|DV020653
EST:     CGCCCGAACCCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAG                         GAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTAGCCGGAGGTGCGGT
genomic: CGCCCGAACCCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAGgtttctgtcc ... cgtcttgcagGAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTAGCCGGAGGTGCGGT
EST: gi|32913968|gb|CF018780.1|CF018780
EST:     CGCCCGAACCCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAG                         GAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTAGCCGGAGGTGCGGT
genomic: CGCCCGAACCCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAGgtttctgtcc ... cgtcttgcagGAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTAGCCGGAGGTGCGGT
EST: gi|86472628|gb|DY238998.1|DY238998
EST:     CGCCCGAACCCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAG                         GAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTACCCGGAGGTGCGGT
genomic: CGCCCGAACCCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAGgtttctgtcc ... cgtcttgcagGAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTAGCCGGAGGTGCGGT
EST: gi|211481381|gb|FL023993.1|FL023993
EST:     CGCCCGAACTCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAG                         GAGCAGGAGGTGCGCTCGTGCCGTAACTACNGCCGTAGCCGGAGGTGCGGT
genomic: CGCCCGAACCCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAGgtttctgtcc ... cgtcttgcagGAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTAGCCGGAGGTGCGGT
EST: gi|61119391|gb|DN560352.1|DN560352
EST:     CGCCCGAACCCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAG                         GAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTAGCCGGAGGTGCGGT
genomic: CGCCCGAACCCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAGgtttctgtcc ... cgtcttgcagGAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTAGCCGGAGGTGCGGT

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: 142

CATCCATGGCGACCACCACCTCTTCCTCCTCGCTGACCACTCCTCTCCTCCGCCCGAACCCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAGgtttctgtcc ... cgtcttgcagGAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTAGCCGGAGGTGCGGTGCCTTACGGGGCTAATCCGCGGCGCGGGATTTGGTCGATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

CATCCATGGCGACCACCACCTCTTCCTCCTCGCTGACCACTCCTCTCCTCCGCCCGAACCCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAGgtttctgtcc ... cgtcttgcagGAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTAGCCGGAGGTGCGGTGCCTTACGGGGCTAATCCGCGGCGCGGGATTTGGTCGATCAG


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

CATCCATGGCGACCACCACCTCTTCCTCCTCGCTGACCACTCCTCTCCTCCGCCCGAACCCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAGgtttctgtcc ... cgtcttgcagGAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTAGCCGGAGGTGCGGTGCCTTACGGGGCTAATCCGCGGCGCGGGATTTGGTCGATCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 90

CATCCATGGCGACCACCACCTCTTCCTCCTCGCTGACCACTCCTCTCCTCCGCCCGAACCCCAATACCAACCCTGCTCCCAGATCTCTCCAACTCCTCAGgtttctgtcc ... cgtcttgcagGAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTAGCCGGAGGTGCGGTGCCTTACGGGGCTAATCCGCGGCGCGGGATTTGGTCGATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttctcttcccgccatctctgccgtcccctaactttctttccgcgtcttgcagGAGCAGGAGGTGCGCTCGTGCCGTAACTACCGCCGTAGCCGGAGGTGCGGTGCCTTACGGGGCTAATCCGCGGCGCGGGATTTGGTCGATCAG
                            ccctaac  putative branch site (score: 90)
                                  ctttctttccgcgtct  CT-rich tract
                               taacttt  TA-rich tract