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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgatctgagtctgattatcattccctactttttagcattttgttttccaccatgtgtcagctctcgtgcttataagttatcatgatatgatcaatgcagGCCATTATTACTGAAATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATACGGACAACAGATCCTAGATC

Basic information

species Zea mays
transcript GRMZM2G153977_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153977_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 7
------gtgatctgagtctgattatcattccctactttttagcattttgttttccaccatgtgtcagctctcgtgcttataagttatcatgatatgatcaatgcagGCCATTATTACTGAAATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATACGGACAACAGATCCTAGATC
         |       ||  |  | |||  || | |  |  | | ||  ||   |||| ||  ||      | | | |  |||||     | |  ||||  ||||||||| || ||||||||||| || |||||||||||| |||| ||||||||||| || |||||||| |||||||||||||| |||||||||||||||||||
gctttccacactcatccctactctttattgtcttcatactgtcttgtttgttcttaccaagttccaatgagtg-gttcacgagtta-----acacaatcatcgcagGCCATAATCACTGAAATCAATGAGAAGATCGGTGCTACTGGGGTAGTCAGCCAAGAATGCAAGACAGTTGTTTCTCAATATGGACAACAGATCCTAGATC
















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|60400185|gb|DN232992.1|DN232992
EST:     GTTGTGCAGCAATAGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACA                         GCCATTATTACTGAAATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAGC
genomic: GTTGTGCAGCAATAGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACAgtaagttttg ... atcaatgcagGCCATTATTACTGAAATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAGC
EST: gi|21331514|gb|BQ486895.1|BQ486895
EST:     GTTGTGCAGCAATAGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACA                         GCCATTATTACTGAAATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAGC
genomic: GTTGTGCAGCAATAGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACAgtaagttttg ... atcaatgcagGCCATTATTACTGAAATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAGC
EST: gi|31627888|gb|CD526338.1|CD526338
EST:     GTTGTGCAGCAATAGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACA                         GNCCATTATTACTGAAATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAG
genomic: GTTGTGCAGCAATAGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACAgtaagttttg ... atcaatgcagG-CCATTATTACTGAAATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAG
EST: gi|32807838|gb|CD960072.1|CD960072
EST:     GTTGTGCAGCAATAGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACA                         GCCATTATTACTGAAATCAACGAAAAGATTGGTGCTGCTGGTGTAGTCAGC
genomic: GTTGTGCAGCAATAGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACAgtaagttttg ... atcaatgcagGCCATTATTACTGAAATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAGC

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: 594

GGTTTTGTGCTGGTGGTTGTGCAGCAATAGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACAgtaagttttg ... atcaatgcagGCCATTATTACTGAAATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATACGGACAACAGATCCTAGATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1018

GGTTTTGTGCTGGTGGTTGTGCAGCAATAGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACAgtaagttttg ... atcaatgcagGCCATTATTACTGAAATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATACGGACAACAGATCCTAGATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1076

GGTTTTGTGCTGGTGGTTGTGCAGCAATAGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACAgtaagttttg ... atcaatgcagGCCATTATTACTGAAATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATACGGACAACAGATCCTAGATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1186

GGTTTTGTGCTGGTGGTTGTGCAGCAATAGCAGATTCTGGAACTTCCTTGCTTGCTGGCCCCACAgtaagttttg ... atcaatgcagGCCATTATTACTGAAATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATACGGACAACAGATCCTAGATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccaccatgtgtcagctctcgtgcttataagttatcatgatatgatcaatgcagGCCATTATTACTGAAATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATACGGACAACAGATCCTAGATC
                         ttataagttatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatctgagtctgattatcattccctactttttagcattttgttttccaccatgtgtcagctctcgtgcttataagttatcatgatatgatcaatgcagGCCATTATTACTGAAATCAACGAAAAGATCGGTGCTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATACGGACAACAGATCCTAGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
-tgatctg
- - - - - - - - - -cattccc
- - - - - - - - - - - - - - - - - - - - - - - - - -catgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgctta