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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgatatttacattccttttctgttagaaaataagactacataaccccctgaactattaatatttgggtctactttaacccagaacctacataac...

Basic information

species Zea mays
transcript GRMZM2G152686_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 3
TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgatatttacattccttttctgttagaaaataagactacataaccccctgaactattaatat--ttgggtctactttaacccaga--acctacataac
|| ||||| || || |||||||||||||| || |||||||||||||||||||| ||||||||||||||||| |||||||| ||||||||||| |||||||||||| |||||| ||| | | || || || | | | | | |||| ||| | ||| ||| | | | || ||
TTCACAATTAAGAGAGGAGTTGGGACTGAGACATGTGTTAGCGTTAACTATGATGACTTTGTTAATGATGTAGAAGTGGGTGACATGCTCCTCGTAGATGgtatgtggatattccttcccctctaatcttt-aacttacttttgtctcctttgcatagacacacatatgattgtattcactgtaagcaaaacaactcactc---

upper sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G37210.1 (Glycine max), 5'ss of exon 3
TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat-atttacattccttttctgttagaaaataagactacataaccccctgaactattaatatttgggtctactttaacccagaacctacataac-----
||||| ||| ||||| ||||| |||| |||||||| || ||||||||||| || || |||||||| || ||||| |||||||| ||||| ||||||||| | | || | |||| |||| | | | | || ||| ||| | || | | | || | ||
TTTACCATCCGGAGGGGTGTTGGAACTGCAGATTGTGTTAGTGTGAACTATGACGATTTCGTCAATGATGTGGATGTGGGGGACATGCTTCTTGTTGATGgtatggcaaccaactaattggtaaaagtgtttgaaatataaaaaatgtgttttgctcgtggattgata-----agccacca-agcatgggactaatttattatttt

upper sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G30430.1 (Glycine max), 5'ss of exon 3
TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgatatttacattccttttc-tgttagaaaataagactacataaccccctgaactattaatatttgggtctactttaacccagaacctacataac
||||| ||| ||||| ||||| |||| |||||||| || ||||||||||| || || |||||||| || ||||| |||||||| ||||| ||||||||| | ||| | |||| |||| | || | | || || ||| || | | | | | |
TTTACCATCCGGAGGGGTGTTGGAACTGCAGATTGTGTTAGTGTGAACTATGACGATTTCGTCAATGATGTGGATGTGGGAGACATGCTTCTTGTTGATGgtatggcaaccaactgattggtaaaaatgtttgaaatataaacaatttgttatgctcgtgggttgataagccaccaaacatgggactaatttattctttt-

upper sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 5'ss of exon 3
TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgatatttacattccttttctgttagaaaataagactacataaccccct---gaactattaatatttgggtctactttaacccagaacctacataac
|||||||| | || ||||| | || | ||||| || ||||||||||| || || |||||||| || |||| ||| |||||||| ||||| ||||||||| || || ||| | | | || || | | | | | | |||| || | | |||| | ||
TTTACAATTGAGAGAGGAGTCAGCACACCAAGTTGTGTCAGTGTTAACTATGATGATTTCGTTAATGACGTGGAAGCGGGTGACATGCTTCTTGTTGATGgtatgtacatcttattatttggtgtacaa-gggttttacatctgctttagtcttttccaatatattgatggc-gcttttactatgttgtag------------

upper sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 5'ss of exon 3
TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgatatttacattccttttctgttagaaaataagactacataaccccctgaactattaatatt---tgggtctactttaacccagaacctacat-aac--
|| ||||| |||| || |||||||| | |||||||| ||||||||||| || ||||| |||||||| ||| ||||||||||||| || || ||||||| ||| | ||| |||||||| | | || || | || ||| || | || | || | | | | | ||| || |||
TTCACAATTCAAAGAGGCGTTGGGACAGCAGATTGTGTTAGTGTTAACTATGATGATTTTGTCAATGATGTAGAAATGGGCGACATGCTTCTCGTGGATGgta---tgaaac---catgttttttctgtcatacaaataggttttgtagtaacctctttcctttactttccatcagtttgttcacccacttatcctcaattaactt

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|148961971|gb|EE012768.2|EE012768
EST:     TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATG                         GAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT
genomic: TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT
EST: gi|148957677|gb|EC903791.2|EC903791
EST:     TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATG                         GAGGAATGATGTC
genomic: TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTC
EST: gi|148934386|gb|EC878416.2|EC878416
EST:     TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCCTGTAAATG                         GAGGAATGATGTCATTCTTGGTCAAATCAAAAAC
genomic: TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGGTCAAATCAAAAAC
EST: gi|5296084|gb|AI782959.1|AI782959
EST:     TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATG                         GAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT
genomic: TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT
EST: gi|71426208|gb|DR807258.1|DR807258
EST:     TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATG                         GAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT
genomic: TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT
EST: gi|67041095|gb|CO467350.1|CO467350
EST:     TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATG                         GAGGAATGATGTCATTCTTGGGTCAA-TCAAAAACTGAAGATTCTGTGAAA
genomic: TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGG-TCAAATCAAAAACTGAAGATTCTGTGAAA
EST: gi|211141481|gb|FL154590.1|FL154590
EST:     TGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATG                         GAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT
genomic: TGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT
EST: gi|67025561|gb|CO454310.1|CO454310
EST:     TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATG                         GAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT
genomic: TGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAAT

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: 196

TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAATGTGAAGTTATTGACGGTGGTGAATTGAAATCTAGGCGCCATCTGAATGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 154

TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAATGTGAAGTTATTGACGGTGGTGAATTGAAATCTAGGCGCCATCTGAATGT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 98

TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAATGTGAAGTTATTGACGGTGGTGAATTGAAATCTAGGCGCCATCTGAATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 434

TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgat ... caatttttagGAGGAATGATGTCATTCTTGGTCAAATCAAAAACTGAAGATTCTGTGAAATGTGAAGTTATTGACGGTGGTGAATTGAAATCTAGGCGCCATCTGAATGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTACAATCAAAAGGGGAGTTGGGACTGATACGTGTGTTAGCGTTAACTATGACGACTTTGTTAATGATGTTGAAGTGGGCGACATGCTCCTTGTAGATGgtatgctgatatttacattccttttctgttagaaaataagactacataaccccctgaactattaatatttgggtctactttaacccagaacctacataac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaataa