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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactttgttggcaattttaggctagctgtagagttgtagtccactattattcacgatattaaatagttcttatattcctagTGGGCTAACGTGACAAGATGGGAAATGCGGACTAAACCATTCATCCGAACTCTTGAATTTTTATGGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGG

Basic information

species Zea mays
transcript GRMZM2G107089_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107089_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g07060.1 (Oryza sativa), 3'ss of exon 2
gtaactttgttggcaattttaggctagctgtagagttgtagtccactattattcacgatattaaatagttcttatattcctagTGGGCTAACGTGACAAGATGGGAAATGCGGACTAAACCATTCATCCGAACTCTTGAATTTTTATGGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGG
|||||| | |  |||  |||     | |        || |||||| ||| ||| ||  || | | |  ||||| |   ||||||||||||| || ||||||||||||||| ||||||| ||||||||| |||||||||||||| ||||||||||||| |||||||| |||||||||||||| |
gtaactctatctgcatatttgaatcaaca-------tg-agtccaatatcatttactgtactgattt-ttcttgttaccctagTGGGCTAATGTCACAAGATGGGAAATGAGGACTAAGCCATTCATCAGAACTCTTGAATTTCTATGGCAAGAAGGTCATACAGCTCATGCCACCCTTGAAG

upper sequence: GRMZM2G107089_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G29890.1 (Glycine max), 3'ss of exon 4
gtaactttgttggcaattttaggctagctgtagagttgtagtccactattattcacgatatta-aatagttctta--tattcctagTGGGCTAACGTGACAAGATGGGAAATGCGGACTAAACCATTCATCCGAACTCTTGAATTTTTATGGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGG
||||   |||||  | |||      |  ||| |||    |     || |  |  | |||   | |||  |||| |  |  |   ||||||| ||||||||||||||||| ||||| |||||||||||  |  |||||||||||||| | ||||||||||| ||||| || ||||| || |  || |
gtaatgctgttgagagttt------atttgt-gagcaagaacttgctttgttgaatgatgggacaatttttctaacttgctttcagTGGGCAAACGTGACAAGATGGGAGATGCGCACTAAACCATTTGTGAGAACTCTTGAATTTCTTTGGCAAGAAGGACATACTGCTCATGCAACTCCAGAAG

upper sequence: GRMZM2G107089_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G24670.1 (Glycine max), 3'ss of exon 4
gtaactttgttggcaattttaggctagctgtagagttgtagtccactattattcacgatattaaatagttcttatattcctagTGGGCTAACGTGACAAGATGGGAAATGCGGACTAAACCATTCATCCGAACTCTTGAATTTTTATGGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGG
||||   |||||  | |||    ||        | ||| | |      | | | |||  |  |  | |      |  |   ||||||| ||||||||||||||||| ||||| || ||||||||  |  |||||||||||||| | ||||||||||| ||||| || ||||| || |  ||||
gtaatgctgttgtgagtttatttctgagcaagaacttgcattgt----tgaatgacgggacaattttgccaacttgctttcagTGGGCAAACGTGACAAGATGGGAGATGCGCACCAAACCATTTGTGAGAACTCTTGAATTTCTTTGGCAAGAAGGACATACTGCTCATGCAACTCCAGAGG

upper sequence: GRMZM2G107089_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT5G52520.1 (Arabidopsis thaliana), 3'ss of exon 4
---------gtaactttgttggcaattttaggctagctgtagagt-tgtagtccactattattcacgatattaaatagttcttatattc---ctagTGGGCTAACGTGACAAGATGGGAAATGCGGACTAAACCATTCATCCGAACTCTTGAATTTTTATGGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGG
         |  | |   |||   ||  |    |   || | | | ||   |  |  | | |||  | |  |   |   |  | | | |    |||||||| || || || ||||||||||||||||| |||||||| ||  | |||||||||||| |||||||||| || ||||| || |||||||| | |||||
gtctggacagacattcaattgtttatcattctttgtatgaaaaatctggtatttatgactgttcctggttatgtttttcttctttctgcgatttagTGGGCCAATGTCACTAGATGGGAAATGCGGACGAAACCATTTATTAGGACTCTTGAATTTCTATGGCAAGAGGGTCATACTGCTCATGCCACTCCTGAGG

upper sequence: GRMZM2G107089_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv16s0050g00960.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------gtaactttgttggcaattt---taggctagctgtagagttgtagtccactat-tattcacgatat-taaatagttcttatattcctagTGGGCTAACGTGACAAGATGGGAAATGCGGACTAAACCATTCATCCGAACTCTTGAATTTTTATGGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGG
                                            ||   ||  || |||  ||    |   |  ||   |   | |  |  | ||  | |||||  | | |   || ||  | | || | ||||||| || || || |||||||| |||||||| ||||||||  |  | |||||||||||| | |||||||| ||||| || || |||||||||| ||| |
gtgcattgctttttcttttttcttttctttttccttacagacaggtgcattgatttgcatgttactcaaattgtctcctgttatatgatttattacctgttcaccttttgtttgtaattgatttctttc-agTGGGCAAATGTTACGAGATGGGAGATGCGGACAAAACCATTTGTGAGGACTCTTGAATTTCTCTGGCAAGAGGGCCACACTGCTCATGCCACCCCTGAAG

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|76018748|gb|DT945918.1|DT945918
EST:     TCACCAAATGGATTCAGAGCTATCGTGATCTTCCTCTCATGATAAACCAG                         TGGGCTAACGTGACAAGATGGGAAATGCGGACTAAACCATTCATCCGAACT
genomic: TCACCAAATGGATTCAGAGCTATCGTGATCTTCCTCTCATGATAAACCAGgtaactttgt ... atattcctagTGGGCTAACGTGACAAGATGGGAAATGCGGACTAAACCATTCATCCGAACT
EST: gi|6194519|gb|AW146623.1|AW146623
EST:     TCACCAAATGGATTCAGAGCTATCGTGATCTTCCTCTCATGATAAACCAG                         TGGGCTAACGTGACAAGATGGGAAATGCGGACTAAACCATTCATCCGAACT
genomic: TCACCAAATGGATTCAGAGCTATCGTGATCTTCCTCTCATGATAAACCAGgtaactttgt ... atattcctagTGGGCTAACGTGACAAGATGGGAAATGCGGACTAAACCATTCATCCGAACT

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), 49 (downstream exon)
Score: 85

GTAAGACCAACAAGTGAGACCATTGTAAACCACATGTTCACCAAATGGATTCAGAGCTATCGTGATCTTCCTCTCATGATAAACCAGgtaactttgt ... atattcctagTGGGCTAACGTGACAAGATGGGAAATGCGGACTAAACCATTCATCCGAACTCTTGAATTTTTATGGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

GTAAGACCAACAAGTGAGACCATTGTAAACCACATGTTCACCAAATGGATTCAGAGCTATCGTGATCTTCCTCTCATGATAAACCAGgtaactttgt ... atattcctagTGGGCTAACGTGACAAGATGGGAAATGCGGACTAAACCATTCATCCGAACTCTTGAATTTTTATGGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 58

GTAAGACCAACAAGTGAGACCATTGTAAACCACATGTTCACCAAATGGATTCAGAGCTATCGTGATCTTCCTCTCATGATAAACCAGgtaactttgt ... atattcctagTGGGCTAACGTGACAAGATGGGAAATGCGGACTAAACCATTCATCCGAACTCTTGAATTTTTATGGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 230

GTAAGACCAACAAGTGAGACCATTGTAAACCACATGTTCACCAAATGGATTCAGAGCTATCGTGATCTTCCTCTCATGATAAACCAGgtaactttgt ... atattcctagTGGGCTAACGTGACAAGATGGGAAATGCGGACTAAACCATTCATCCGAACTCTTGAATTTTTATGGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtagagttgtagtccactattattcacgatattaaatagttcttatattcctagTGGGCTAACGTGACAAGATGGGAAATGCGGACTAAACCATTCATCCGAACTCTTGAATTTTTATGGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGG
                                        ttcttat  CT-rich tract
                             atattaaatagttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactttgttggcaattttaggctagctgtagagttgtagtccactattattcacgatattaaatagttcttatattcctagTGGGCTAACGTGACAAGATGGGAAATGCGGACTAAACCATTCATCCGAACTCTTGAATTTTTATGGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG