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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcatttcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA

Basic information

species Zea mays
transcript GRMZM5G804382_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
gtacaaaacagccagatg--cgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcatttcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
    ||| |    |||||   | | ||| ||||| |||| || |            | | || ||  | |||| |||  || ||   |     ||  ||||| ||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||| || || |||||||| |
--gtaaagcgattagatgattgtactgcttattgatgttattttt-----------ccttttttttttattttgaat--aactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
gtacaaaacagccagatg--cgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcatttcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
    ||| |    | |||   | | ||| ||||| |||| || |          | ||| ||  |  | |||| |||  || ||   |     ||  ||||| ||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||| || || |||||||| |
--gtaaagcgattatatgattgtactgcttattgatgttatttt----------tccttttttattttattttgaat--aactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 26
gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgctt--attgttactgttttcaatttaattacctgtgttcatttcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
                      |||   |   ||| | ||  | |||    ||  ||   ||    ||||    |  | |  |   |||  | | |   |  |||| | || ||||||||  | |||||||||||  |  ||||||| || |||||||||||||| || ||||||||||| || |||||| | |||||||| ||||
----------------------gtgtggaaatttgctctta-attggaactattttttggtttcagctgtggaaatctcagattattgttattactgtatacgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGGTGGAAGCAGTCTATTGCTTTGTCAAAGAAGGATA

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 26
----------------gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcattt-cttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
                 |       |    ||     ||     || |   |     |  |  || ||   |||   |   ||  ||    || |||  ||      ||   | ||||||| | |||||||||||| | |||||||||||| |  |||||||||||||||||||||| || || || |||||||||||||||||| | ||||||||||| |
gtgaatcttacttatcttttgtcttattttgacaattagcaaaaatcgagatcagaatg-ttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 24
gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgtttt-caatt--taattacctgtgttcatttct-tgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
         |   ||| | | ||     |    | |||||  |        | || ||   |||  ||||  |||||  | |||  || |    || | | || |||| | |||||||||||  | |||||||||||| |  ||||||| |||||||| ||||| ||||| || |||||||| ||||||||| | ||||| ||||| |
--tttttgtaattagaagtgaagacataaaacattttgttaaacc------aagcatagccttaaagtttgacaattagtgattggctttaacaatgtgtatgtgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTTGCTGCTTACATTTATAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 26
------gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcatttcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
      |||   || ||  |  |  | | | | | |||||         || |  | |   || |    | || |||    |   ||| |  |||  ||||     |||| | |||||||||||  | |||||||||||| |  | ||||| || ||||||||||| ||||| || |||||||| ||||||||| | ||||| ||||| |
atttttgtaattaaaagtgaagtcagaaat-cattttgttaaaccaagcatagccttaaagtt-tgacgattggttttggct---ttaacaatgtgtattt-----gcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTCGCTGCTTATATTTACAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 26
gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaat----ggtgtgatgcttattg-----ttactgttttcaattta--attacctgtgttcat---ttcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
||  |   | |  |  |      |   | |     ||     |||    | |  |    |||| |     |||   | ||  | |||  |||   ||  ||||    | | ||||||| | |||||||||||| | |||||||||||| |  | |||||||||||||||||||| || || || |||||||||||||||||| | ||||||||||| |
gtgaatctcggttatcttttgtcttattttgacaattagcaaaatctgagatcaggaagttatggaaaatttaaaatgtttgaattattattgattggcttcaacaatacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTAGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 26
gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcatttcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
                || | |       |  |  |||     ||  | |  |  |  ||||     | |   |||  |||||   | ||  | | |   |||| | || ||||||||  | |||||||||||  |  ||||||| || |||||||||||||| || ||||||||||| || |||||| | |||||||| ||||
---------------gtgtggaaatttgctcttaattggaactatttttttgttttagttgtggaaatctcagatt--attac---tattactgtatgatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGGTGGAAGCAGTCTATTGCTTTGTCAAAGAAGGATA

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 25
gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcatttcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
                |  || |     ||| ||  |||||  |   | |     |||   |||  |    |   |  ||||  | |  | || |     |||| | || ||||||||  | |||||||||||  |  ||||||| || |||||||||||||| || || |||||||| ||||||||  | |||||||| ||||
---------------gttggctgcattcattcttcatgttg--actatttttcagtta--attataggaaaccgatagattat-tattattatctggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAGCAGTCCATTGCCTTGTCAAAGAAGGATA

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 26
gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcatt--tcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
                      ||     ||    |   | ||  |     |   ||||  || |  ||    | | | ||| |  | |    |  |    |  || | ||||| || ||  |  |||| |||||  |  | ||||| || || || ||||| ||||| || ||||||||||| |||||| | |||||||||||||
----------------------gtaagagtttaaatctatctatcgagtacacatttatatttccccttaaatactaatttatcgttatgggatggtgcgaaatagATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTATAAGAAAGCTGGTAGATGGAAGCAATCGATTGCTTTGTCAAAGAAAGATA

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 26
gtacaaaacagccaga-tgcgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcatttcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
||| |   ||   | | | | |  |   |||| || |   | |||   ||  |     || |     |   | |  | |  | ||||||   ||     || ||| | ||||| || ||| |  |||| |||||  |  | ||||| || || |||||||| || ||||| ||||||||||| |||||  ||||||||||||| |
gtaaagttcaaatatactacccctttaatatt-ttctctctttaaaaatggaaaaagaatggccttagagatgatataatcttcctgtga--atggtgcgaacagATCGAGAAACACGAACTTGTTGAAATGAGACGTGTGGCTGCTTATATCTACAAGAAAGCGGGCAGATGGAAGCAATCAATTGCATTATCAAAGAAAGACA

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 26
gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcatttcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
          |  |||      |    |||| |||||  |||  ||||  | | | ||     |   | | ||    |  ||    ||    |     |  ||| | ||||| |||||  | || ||||||||| | |||||||| || ||||| ||||| || || || ||||| |||||||||||  | ||||||||||| |
----------gtgagagagattgaatttatt-ttgttaatgt--tggtaggcttcataagcagaacatgtacataagatctagtgatgcgtgt-----ggacagGTTGAGAAACATGAGCTTCTGGAGATGAGGCGTATTGCTGCTTATATTTATAAGAAAGCAGGTAGATGGAAACAATCCATTGCATTGTCAAAGAAAGACA

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcattt---cttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
              |  |   | |  || | | ||   ||||  |  | || || || |    |||| ||   |||| || | |  ||||  | |    |||||||| | ||||| || ||  | |||||||||||  |  ||||||| || ||||||||||| || ||||| ||||||||||| |||||  | || |||||||| |
------------gtggagtataatttctttaggtgcaattgtttttctttg-tggttctatgcactggtt--gatttcataagccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA

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|32846997|gb|CD986678.1|CD986678
EST:     AATCAGTTGACATGCATGACAACTTTGACCAAATAGGTCTTGCCCAGAAG                         CTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTAC
genomic: AATCAGTTGACATGCATGACAACTTTGACCAAATAGGTCTTGCCCAGAAGgtacaaaaca ... tcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTAC
EST: gi|32929767|gb|CF034579.1|CF034579
EST:     AATCAGTTGACATGCATGACACCTTTGACCAAATAGGTCTTGCCCAGAAG                         CTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTAC
genomic: AATCAGTTGACATGCATGACAACTTTGACCAAATAGGTCTTGCCCAGAAGgtacaaaaca ... tcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTAC
EST: gi|32848265|gb|CD987946.1|CD987946
EST:     AATCAGTTGACATGCATGACAACTTTGACCAAATAGGTCTTGCCCAGAAG                         CTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTAC
genomic: AATCAGTTGACATGCATGACAACTTTGACCAAATAGGTCTTGCCCAGAAGgtacaaaaca ... tcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTAC
EST: gi|89761296|gb|DY689368.1|DY689368
EST:     AATCAGTTGACATGCATGACAACTTTGACCAAATAGGTCTTGCCCAGAAG                         CTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTAC
genomic: AATCAGTTGACATGCATGACAACTTTGACCAAATAGGTCTTGCCCAGAAGgtacaaaaca ... tcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTAC
EST: gi|71765800|gb|DR963737.1|DR963737
EST:     AATCAGTTGACATGCATGACAACTTTGACCAAATAGGTCTTGCCCAGAAG                         CTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTAC
genomic: AATCAGTTGACATGCATGACAACTTTGACCAAATAGGTCTTGCCCAGAAGgtacaaaaca ... tcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTAC

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: 229

AGCCTTGAATGAGCTTTATGTTGAAGAGGAAGACTATGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAAATAGGTCTTGCCCAGAAGgtacaaaaca ... tcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 123

AGCCTTGAATGAGCTTTATGTTGAAGAGGAAGACTATGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAAATAGGTCTTGCCCAGAAGgtacaaaaca ... tcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 178

AGCCTTGAATGAGCTTTATGTTGAAGAGGAAGACTATGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAAATAGGTCTTGCCCAGAAGgtacaaaaca ... tcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

AGCCTTGAATGAGCTTTATGTTGAAGAGGAAGACTATGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAAATAGGTCTTGCCCAGAAGgtacaaaaca ... tcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgcttattgttactgttttcaatttaattacctgtgttcatttcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
                        atttaat  putative branch site (score: 173)
                                       ttcatttctt  putative PPT
      ttattgttactgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcatttcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA