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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttggttacacgatttaggagtcttcttaaagaactgttgctatgtaagtacagcaagattgctcgacttgtgttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA

Basic information

species Zea mays
transcript GRMZM2G021846_T01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G021846_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 18
gtatttggttacacgatttaggagtcttcttaaagaactgttgctatgtaagta----cagcaagattgctcgacttgtgttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA
||| |  |    | | ||| |     |||||| | |||| |||| | |||  ||     |      |||||  ||   |||| |||| |||||||||||||||||||||||||||| || ||||| ||||||||||||||||| |||||||||||||||||| | |||||||||||||||||
gtaatcag--gaaagttttggagtatttcttacataactcttgcaaggtagttatttatatgggcgttgcttaacaattgttgtttgcagATACAATGGCGTGCTCTTGATGAGATAAACTCTGGGGTGTGTGATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGA

upper sequence: GRMZM2G021846_T01 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 19
-----------------gtatttggttacacg-atttagga-gtcttcttaaagaactgttgctatgtaagtacagcaagattgctcgacttgtgttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA
                 || | |||||      ||| | |   | |  || |  |    | | |    || |  |   |  |||    |||     ||| | ||||||||||||||||| ||||||||||| ||| | || ||||||||||| ||||| || | ||| || ||||||| |||||| ||||| | |||
gttagtgtcataattaagtttatggttgtgtacattcatgctatttatttcacaagaaataggttgacaaatgtacacattttgacttactatctatatgt-tagATACAATGGCGTGCACTTGATGAGATAAATGCAGGGGTGTGTGATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGA

upper sequence: GRMZM2G021846_T01 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 24
-----------------gtatttggttac--acgatttaggagtcttcttaaagaactgttgctatgtaagtacagcaagattgctcgacttgtgttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA
                 || | |||||    ||  |   |   | |  || | ||    | | |    || |  |   |  |||    |||     ||  | ||||||||||||||||| ||||||||||| ||  | || ||||||||||                                              
gttagtgtcatacttaagtttatggttgtgtacagtcatgctatttatttcacgagaaataggttgacaaatgtacacattttgacttactatctataagt-tagATACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATG----------------------------------------------

upper sequence: GRMZM2G021846_T01 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 29
gtatttggttacacgatttaggagtcttcttaaagaactgttgctatgtaagtacagcaagattgctcg-acttgtgttatttgta-----gATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA
      | |    | ||     ||||     ||| |    |||  |      ||||  |  | |||||   |   |  ||| | ||     |||||||||||| || ||||||||||| ||| | || ||||||||||||| ||| |||||||| || ||||| | |||||| ||||| |  ||
------gttagtgccatccttaagtcag--gaaatatggattgacaaaagtatacattattagtgctcctgcacttactatctatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAGACATATGAAGAAATCAAGAAGAACATGCCAGAGGAGTACGA

upper sequence: GRMZM2G021846_T01 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 20
--------gtatttggttacacgatttagg--agtcttcttaaagaactgttgctatgtaagtacagcaagattgc---tcgacttg-tgt---tatttgt-agATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA-
         || |||  |  |   ||  |   |||| | |||   |  |      |  || ||    |||  || |   | |||||  | |   ||| ||| |||||||||||||||| ||||||||||| ||  | || ||||||||||| ||||| |||| ||| || ||||||| |||||| ||||| | ||| 
ttagtgtcatacttgaatttaaagttgtgtgcagtcatgttatttatttcacaagaaataggt-tgacaaatttacacgttgacttactatctatatatgtcagaTACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGACATATGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAG

upper sequence: GRMZM2G021846_T01 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 18
-gtatttggttacacgatttaggagtcttcttaaagaactgttgc-tatgtaagtacagcaagattgctcgacttgtgttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA
  || |    | |   ||| ||||    | |  |   |||   |  || || | ||  ||       ||     | | |   |  |||||||||||||| || ||||||||||| ||| |||| ||||||||||||||||| |||||||| || ||||| | |||||| ||||| | |||
gttagtgtcatccttaattcaggaaa--tatggattgactaaagtatacgttattagtgctcctgcacttactatctatatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGA

upper sequence: GRMZM2G021846_T01 (Zea mays), 3'ss of exon 18
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 18
gtatttggttac--acgatttaggagtcttcttaaa---gaactgt-tgctatgtaagtacagcaagattg-ctcgacttgtgttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA
||   || ||||  ||  |      ||||||| |     ||  ||| |  ||| |   | |    | || |  |   | | | ||  |  ||| | ||||||||||| || || ||||||||| ||||||| |||||||||||||| ||||||||| ||||||| | |||||| || ||||  ||
gttggtgtttacctactgtccgaatgtcttctgactcttgaggtgtataatattttgttgcgaggaaatcgatttctcatattttcatcttagGTGCAATGGCGTGCCCTGGACGAGATCAATGCTGGAGTTTGTGATGGGATGACATATGAAGAGGTAAAGAAGAACATGCCAGAAGAATACGA

upper sequence: GRMZM2G021846_T01 (Zea mays), 3'ss of exon 18
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 18
--------gtatttgg-----ttacacgatttaggagtcttcttaaagaactgttgctatgtaagtacagcaagattgctcgacttgtgttattt--gtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA
        | |||| |     ||    |  | |  |       ||   |  |||    |  | |||| || || |||     |||| | |  |||  |||||||||||||||||| ||||||||||| ||| |||||||||||||||| ||||| ||||||||||||||||| | |||||| |||||||  ||
tagcttttgaatttagaaaaatttggtggataaccaacaaatctaggaatttgtgtggaaatgagtatag-aaaattctataacttttttacttttggtagATACAATGGCGTGCACTTGATGAGATAAATGCTGGAGTGTGTGATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGA

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|8103262|gb|AW927912.1|AW927912
EST:     CCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAG                         ATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATG
genomic: CCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAGgtatttggtt ... ttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATG
EST: gi|32925226|gb|CF030038.1|CF030038
EST:     CCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAG                         ATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATG
genomic: CCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAGgtatttggtt ... ttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATG
EST: gi|32926593|gb|CF031405.1|CF031405
EST:     CCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAG                         ATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATG
genomic: CCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAGgtatttggtt ... ttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATG
EST: gi|32838571|gb|CD978249.1|CD978249
EST:     CCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAG                         ATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATG
genomic: CCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAGgtatttggtt ... ttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATG
EST: gi|32941577|gb|CF046396.1|CF046396
EST:     CCCTTCACAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAG                         ATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATG
genomic: CCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAGgtatttggtt ... ttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATG
EST: gi|32941092|gb|CF045911.1|CF045911
EST:     CCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAG                         ATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATG
genomic: CCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAGgtatttggtt ... ttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATG
EST: gi|149062837|gb|EE157555.2|EE157555
EST:     CCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAG                         ATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATG
genomic: CCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAGgtatttggtt ... ttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATG

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: 48 (upstream exon), 47 (downstream exon)
Score: 52

ATATGGACCAGTACCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAGgtatttggtt ... ttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 200

ATATGGACCAGTACCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAGgtatttggtt ... ttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 51

ATATGGACCAGTACCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAGgtatttggtt ... ttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 159

ATATGGACCAGTACCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAGgtatttggtt ... ttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagaactgttgctatgtaagtacagcaagattgctcgacttgtgttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA
                                             ttatttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttggttacacgatttaggagtcttcttaaagaactgttgctatgtaagtacagcaagattgctcgacttgtgttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA