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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcttctgtctctgctggcggcagctacctggctcagatcgatcgatcggtcggtcgatctaatacgcatgtgtctctgtacttggattgaaacggaacagAACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGACGACGAGACGGCGGTCGGGGTGGGGACCGTCGGCTCCTCGGAGGCCATCA

Basic information

species Zea mays
transcript GRMZM2G101069_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101069_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g37460.1 (Oryza sativa), 3'ss of exon 1
gtacgcttctgtctctgctggcggcagctacctggctcagatcgatcgatcggtcggtcgatctaatacgcatgtgtctctgtacttggattgaaacggaacagAACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGACGACGAGACGGCGGTCGGGGTGGGGACCGTCGGCTCCTCGGAGGCCATCA
                   |    || | |||  |   | | | | | | |  |   ||     ||  |     |||||    ||  ||||   |   |||||||||||||||||||||||||||||||| ||||||||||| |||||||| |||||||||||||||||||||||||| || || || || |||||||||||||
-------------------gtaaacaaccaccacgacaacaacaaac-acctctgcatctgcacaacgcat-catgtcta---acacggatccgat--gaacagAACCGGTGCGTGAACATGATCGCGCATCTGTTCAACGCGCCGATCGGGGACGACGAGACGGCGGTCGGGGTGGGCACGGTGGGGTCGTCGGAGGCCATCA

upper sequence: GRMZM2G101069_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g00920.t01 (Vitis vinifera), 3'ss of exon 2
--gtacgcttctgtctctgctggcggcagctacctggctcagatcgatcgatcggtcggtcgatctaatacgcatgtgtctctgtacttggattgaaacggaacagAACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGACGACGAGACGGCGGTCGGGGTGGGGACCGTCGGCTCCTCGGAGGCCATCA
   | |  |    |  || || || | |  ||    |   | | |  |  ||  || | | ||| |  ||    ||  |   |  |   | |||  ||     ||||||||||||||||||||||| || ||||| ||||| || ||  | || ||  | || || ||  | || |||||||| || ||||| |||||||| ||||
attttcaatctcattccttcttgcagaa--tattccgaatatacctttacatttgtggtttgat-tgttagaagtgaattaattaa---gaatttgaattcttcagAACCGGTGCGTGAACATGATAGCCCACCTCTTCAATGCTCCAGTGGGTGAGAATGAAACAGCAATTGGTGTGGGGACTGTGGGCTCATCGGAGGCGATCA
















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|74232649|gb|DT640563.1|DT640563
EST:     ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGAC
genomic: ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtacgcttct ... aacggaacagAACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGAC
EST: gi|71433668|gb|DR814718.1|DR814718
EST:     ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGAC
genomic: ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtacgcttct ... aacggaacagAACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGAC
EST: gi|74242398|gb|DT650312.1|DT650312
EST:     ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGAC
genomic: ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtacgcttct ... aacggaacagAACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGAC
EST: gi|71314902|gb|DR794072.1|DR794072
EST:     ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGAC
genomic: ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtacgcttct ... aacggaacagAACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGAC
EST: gi|78084684|gb|DV513077.1|DV513077
EST:     ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGAC
genomic: ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtacgcttct ... aacggaacagAACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGAC
EST: gi|71765903|gb|DR963840.1|DR963840
EST:     ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAG                         AACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGAC
genomic: ACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtacgcttct ... aacggaacagAACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGAC

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 2 RNA-Seq libraries.


Block sizes: 24 (upstream exon), 26 (downstream exon)
Score: 1

GACCACTTGGATGGAGCCCGAGTGCGACAAGCTCATCCAGTCCTCCATCAACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtacgcttct ... aacggaacagAACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGACGACGAGACGGCGGTCGGGGTGGGGACCGTCGGCTCCTCGGAGGCCATCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 35

GACCACTTGGATGGAGCCCGAGTGCGACAAGCTCATCCAGTCCTCCATCAACAAGAACTACGTCGACATGGATGAGTACCCCGTCACCACCGAGCTCCAGgtacgcttct ... aacggaacagAACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGACGACGAGACGGCGGTCGGGGTGGGGACCGTCGGCTCCTCGGAGGCCATCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcggtcggtcgatctaatacgcatgtgtctctgtacttggattgaaacggaacagAACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGACGACGAGACGGCGGTCGGGGTGGGGACCGTCGGCTCCTCGGAGGCCATCA
           atctaat  putative branch site (score: 35)
           atctaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcttctgtctctgctggcggcagctacctggctcagatcgatcgatcggtcggtcgatctaatacgcatgtgtctctgtacttggattgaaacggaacagAACCGGTGCGTGAACATGATCGCGCACCTGTTCAACGCCCCGATCGGCGACGACGAGACGGCGGTCGGGGTGGGGACCGTCGGCTCCTCGGAGGCCATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC