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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgctgcagaccaaaaaaaaaatggtttgctgtgctaaatgttccaacgcatttgagcaaaaacgcacaatgcttcccattcgttagtaagaggtttgtctcccggttaggcttaaacttttttttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG

Basic information

species Zea mays
transcript GRMZM2G044629_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044629_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 6
gtaagtgctgcagaccaaaaaaaaaatggttt--gctgtgctaaatgttccaacgca-tttgagcaaaaacgc--acaatgcttcccattcgttagtaagaggtttgtctcccggttaggcttaaactttt-----ttttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG
           ||| |||  |     |  |||    |||| ||| | |||||| | | ||| | |||||   |  |||      |||||||  ||||||      ||| |    | |||| || |||   |     ||||||||||||||||||||||||||||||||||| |||||||| |||||||| ||||| ||||||||||||||||||||||| | |
--------gtaagatcaagtacttttttttttcatttgtgttaactattccaatggaatttcaacaaaagatccaacaggatcccccattcactagtaa------tgtttaataggtaggtttgaacagctgaacattttcttggcagGTGACATTTTTCCAACAAGGCACCCTTCCATGTGTTTCTGCTGATGGCAGATTTATTATGGAGACACCATACAAG

upper sequence: GRMZM2G044629_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 6
gtaagtgctgcagaccaaaaaaaaaatggtttgctgtgctaaatgttccaacgcatttgagcaaaaacgcacaatgcttcccattcgttagtaagag--gtttgtctcccggtta---ggcttaaacttttttttcttg-gcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG
                                                            | || |   |  |||  ||  |||    || ||  |   ||||  ||   | |||     | |  |||    | | |     |||| || |||||||| ||||| ||| | || || |||||    ||||||||||||||||||||||| ||||| |||
------------------------------------------------------------gtaagatgtctaaatctttttcatgtactattagtactcgttttactattgtttacttaccatggactcacctctttgatatagGTTACCTTTTTCCAGCAAGGAACAATCCCTTGTGTTTCCAAGGATGGTAGATTTATTATGGAGACTCCATACAGG
















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|149081508|gb|EE170644.2|EE170644
EST:     CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAA                         GTGACATTTTTCCAACAAGGCACACTTCCCTGCGTTTCTGC
genomic: CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAAgtaagtgctg ... ttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGC
EST: gi|149015643|gb|EE045441.2|EE045441
EST:     CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAA                         GTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
genomic: CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAAgtaagtgctg ... ttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
EST: gi|40337292|gb|CK371362.1|CK371362
EST:     CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAA                         GTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGT
genomic: CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAAgtaagtgctg ... ttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
EST: gi|149014175|gb|EE043721.2|EE043721
EST:     CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAA                         GTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
genomic: CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAAgtaagtgctg ... ttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
EST: gi|148958334|gb|EC904558.2|EC904558
EST:     CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAA                         GTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
genomic: CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAAgtaagtgctg ... ttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
EST: gi|32941368|gb|CF046187.1|CF046187
EST:     CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAA                         GTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
genomic: CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAAgtaagtgctg ... ttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
EST: gi|71429565|gb|DR810615.1|DR810615
EST:     CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAA                         GTGACATTTTTC-AACAAGGCACACT
genomic: CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAAgtaagtgctg ... ttcttggcagGTGACATTTTTCCAACAAGGCACACT
EST: gi|148982619|gb|EE028417.2|EE028417
EST:     CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAA                         GTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
genomic: CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAAgtaagtgctg ... ttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
EST: gi|148956834|gb|EC902742.2|EC902742
EST:     CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAA                         GTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
genomic: CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAAgtaagtgctg ... ttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
EST: gi|149014877|gb|EE044588.2|EE044588
EST:     CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAA                         GTGACATTTTTCCAACA-GGCACACTTCCATGCGTTTCTGCCGATGGTAGA
genomic: CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAAgtaagtgctg ... ttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
EST: gi|148943648|gb|EC888712.2|EC888712
EST:     CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAA                         GTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
genomic: CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAAgtaagtgctg ... ttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
EST: gi|71757247|gb|DR955184.1|DR955184
EST:     CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAA                         GTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
genomic: CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAAgtaagtgctg ... ttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
EST: gi|31354041|gb|CD438398.1|CD438398
EST:     CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAA                         GTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA
genomic: CCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAAgtaagtgctg ... ttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGA

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), 43 (downstream exon)
Score: 112

TGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTACAGATGCTGCCACCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAAgtaagtgctg ... ttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 160

TGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTACAGATGCTGCCACCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAAgtaagtgctg ... ttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 263

TGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTACAGATGCTGCCACCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAAgtaagtgctg ... ttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 235

TGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTACAGATGCTGCCACCGCCAAATTCTTTGAAACCCGTAGATATTTTGGCTTAGACCCTGACCAAgtaagtgctg ... ttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgttagtaagaggtttgtctcccggttaggcttaaacttttttttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG
                                      cttttttttcttggc  CT-rich tract
                                 ttaaacttttttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgctgcagaccaaaaaaaaaatggtttgctgtgctaaatgttccaacgcatttgagcaaaaacgcacaatgcttcccattcgttagtaagaggtttgtctcccggttaggcttaaacttttttttcttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTTTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA