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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacctttgattcataagtgaagcacatatacaatatctacaagatcaataattatttatggttgatacgttgttgtacagATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAG

Basic information

species Zea mays
transcript GRMZM2G028535_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 10
--gtaacctttgattcataagtgaagcacatatacaa--tatctacaagatcaataattatttatggt--tgatacgttgttgtacagATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAG
    ||   ||  || |   |  ||| |  | ||  |  || ||||||   |||   ||||||||  |  | | |     ||||||||||||||||| |||| ||||||||||| |||||||| || ||||||||||| ||||||| ||||||||||||  ||||| | || |||
gtaaaatgatttttttagttggaaagaaactgtatcagttaactacaaag-caacg-ttatttatcatattaacataacattgtacagATTGCATCTTTAGCAATCCGAAGTGGAAATGGTCTTCTCTTGAAAGGAGGAAAAGAAGCTATGAGATCAAACACAATACTGCATAAG

upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv08s0007g01060.t01 (Vitis vinifera), 3'ss of exon 10
-------------------gtaacctttgattcataagtgaagcacatatacaatatctacaagatcaat-aattatttatggttgatacgttgttgtacagATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAG
                    |   || |  |   | ||  || |   | |  | ||| | |  |||  ||  |  ||| ||  ||  |   |  ||  | |||| || ||  |||| || || ||||| || ||| | || ||||||||||||||||||| ||  |||||||||||||| || ||||||
cattgaatagacagtggttttgtgctgttgtcagtcagctaatctactctgtagtattttcttgatttattgaccattaat--ttttttaatgattcaatagATAGCTTCATTAGCAATTCGGAGTGGGAACGGTTTACTGTTGAAAGGAGGGAAAGAAGCTAATAGATCAAATGCAATCTTGCACAAG
















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|32931318|gb|CF036130.1|CF036130
EST:     TGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAG                         ATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGG
genomic: TGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAGgtaacctttg ... tgttgtacagATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGG
EST: gi|33094388|gb|CF054382.1|CF054382
EST:     TGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAG                         ATTGCATCTCTAGCGATCCGAGGTGGTAATGGTCTCCTTTTGAAAGGAGGG
genomic: TGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAGgtaacctttg ... tgttgtacagATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGG
EST: gi|32931519|gb|CF036331.1|CF036331
EST:     TGGGTGTTCTTCTCATTATTTNTGAGTCTCGTCCTGATGCATTGGTCCAG                         ATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGG
genomic: TGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAGgtaacctttg ... tgttgtacagATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGG
EST: gi|24934245|gb|CA452463.1|CA452463
EST:     TGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAG                         ATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGG
genomic: TGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAGgtaacctttg ... tgttgtacagATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGG
EST: gi|211307860|gb|FL092738.1|FL092738
EST:     TGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAG                         ATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGG
genomic: TGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAGgtaacctttg ... tgttgtacagATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGG
EST: gi|211307861|gb|FL092739.1|FL092739
EST:     TGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAG                         ATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCCTTTGAAAGGAGGG
genomic: TGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAGgtaacctttg ... tgttgtacagATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGG
EST: gi|211307862|gb|FL092740.1|FL092740
EST:     TGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAG                         ATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGG
genomic: TGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAGgtaacctttg ... tgttgtacagATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGG
EST: gi|32932079|gb|CF036891.1|CF036891
EST:     TGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAG                         ATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGG
genomic: TGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAGgtaacctttg ... tgttgtacagATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGG

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: 46 (upstream exon), 48 (downstream exon)
Score: 114

GTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAGgtaacctttg ... tgttgtacagATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAG


Block sizes: 17 (upstream exon), 38 (downstream exon)
Score: 5

GTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAGgtaacctttg ... tgttgtacagATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAG


Block sizes: 43 (upstream exon), 36 (downstream exon)
Score: 6

GTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAGgtaacctttg ... tgttgtacagATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

GTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAGgtaacctttg ... tgttgtacagATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatacaatatctacaagatcaataattatttatggttgatacgttgttgtacagATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAG
                                  ggttgat  putative branch site (score: 262)
      aatatctacaagatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacctttgattcataagtgaagcacatatacaatatctacaagatcaataattatttatggttgatacgttgttgtacagATTGCATCTCTAGCGATCCGAAGTGGTAATGGTCTCCTTTTGAAAGGAGGGAAAGAAGTTATGAGATCAAATGCAATATTACACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA