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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcggttgggaatattagtatgatatgctttaccactcacgttatttcattgaatacttttgacatttgtgtttgcttcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC

Basic information

species Zea mays
transcript GRMZM2G045259_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g10150.2 (Oryza sativa), 3'ss of exon 8
gttcggttgggaatattagtatgatatgctttaccactcacgttatttcattgaatacttttgacatttgtgtttgcttc-ataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC
||| |  | | ||  ||| || |||     | |     ||| ||| || ||||| | |  |   | | | ||| |||| |  |||||||||| |||||||| |||||||| ||||||||||||||||||||||||||  | ||||||||||| ||||||||||| |||||||| |||||||| ||||||
gtttgaatagaaagtttattacgatgcctatcattttgcacattactttattga-tgcgctcttcctgtttgtctgctactgtaaacagGGGTACTGTTCGTTATGCTAGTGTGCATGCCCACTTGGGAAGAACTGGATGCAGGAGAGATGACCTTGAATCCCTTGCATACACACTTATTTTCCTTCTC

upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 8
gttcggttgggaatattagtatgatatgctttaccactcacgttatttcattgaatacttttgacatttgtgtttgcttcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC
  |   ||       ||| |||  |||    |       ||||       ||||||  |||||  |  | | |      ||    |||||| || ||||| ||||||||||||||||| ||  | || ||||| || ||||||||||||||  | ||||| || || ||||||||| | |||||||| 
-gtaaattatttgc-ttaatatc-tataaactgtagtaaacgtccaggttttgaatgattttgtaaactatatacttgcca----cagGGGCACAGTTCGTTATGCTAGCGTGCATGCTCATCTTGGTAGAACAGGTAGTAGGAGAGATGACTTAGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT

upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 8
---gttcggttgg-gaatattagtatgatatgctttaccactcacgttatttcattgaatacttttgacatttgtgtttgcttcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC
     |   |||   |||||   ||   | |  |  |     || |||||      || |  ||||   |  | | ||     ||    |||||| || ||||| ||||||||||||||||||||  | || ||||| || || |||||||||||  | ||||| || || ||||||||| | |||||||| 
gtaaattatttgctaaatatctataaactgtagtcaat-gtccaggttat------gagtgattttataaactatattcttgcca----cagGGGCACAGTTCGTTATGCTAGCGTGCATGCCCATCTTGGTAGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTT

upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 8
gttcggttgggaatattagtatgatatgctttaccactcacgttatttcattgaatacttttg---acatttgtgtttgctt-----cataa-----------acagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC
  |    |  |||  | |||||   |     | |   |  | | |||| | ||     |||||   |   || ||||| |||      | ||           |||||||||| || || |||||||| |||||||| ||| | ||||| ||||| || || ||||||||| | ||||| || || ||||| || ||||||||||||
-gtaaaatcagaacttgagtattcaactgccttcagttagcttcattttaatgtgggattttgtatatccttttgtttacttgctggtacaatatgttatgctacagGGGAACAGTACGTTATGCTAGTGTGCATGCTCACCTTGGAAGGACTGGAAGCAGAAGAGATGATTTGGAATCTCTTGCTTACACCCTCATTTTTCTTCTC

upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 8
-------------------gttcggttgggaatattagtatgatatgctt-taccac-tcacgttatttcatt-gaatacttttgacatttgtgtttgcttcataa-------------acagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC
                    ||   ||   ||||||  | |  | | ||| ||||   |  | |||||  ||| | ||| |     |   |   | ||  |||| |             | ||||||||||| || |||||||| ||||| || || ||||| |||||||| ||||||||||||||| | ||||| || || |||||||||||||| || |||
gtacaatcattgacaatttcttgttttataaatatttatgtactttccttctaccctgtttctttattatatttgcatattaaaacctcctacttctgactcattagaataatggtcttatagGGGAACTGTGCGATATGCTAGTGTGCACGCTCATTTGGGGAGAACTGGCAGTAGGAGAGATGATTTGGAATCTCTTGCTTACACTCTTATTTTCCTCCTC

upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 8
-------------------------gttcggttgggaatattagtatgatatgctttaccactca--------cgttatttcattga---atacttttgacatttgtgtttgcttcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC
                          |   ||||  | |  |  | ||   || |||  |  |           ||| |  |  |||   ||| |||     | |||  || |   | |  ||| ||||||||||||||||| || |||||||| || |||||||| |||||||||||||| || ||  | ||||| || || |||||| |  | || ||||| 
gtgaggttcttccccctgtcctgatctgtagttgccattcctgttttggc-tgttttggcggttgggagtgactgttttgcccctgagctatattttgattctgtgtaatttccgtacatgcagTGGAACTGTTCGCTATGCAAGTGTGCATGCACATTTGGGAAGGACTGGGAGTAGGAGGGACGACTTGGAATCACTGGCTTACACTTTGGTATTCCTTCTG

upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S208_44V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------gttcggttgggaatattagtatgatatgctttaccactcacgttatttcattga-atacttttgacatttgtgtttgcttcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC
                               |   ||||  | |  |  | ||         | |       ||| ||    |  ||| ||| |   | |||  ||     | |  ||| ||||||||||||||||| ||  ||||||| ||  ||||||| |||||||||||||  || ||  |   ||| || ||  | ||| |  | || ||| | 
gtgagactctctccccccccttgtcctaatctgtagttgccattcctgttttggcggttgggagcgactgttttacttttgagctatattttgggtttgtgtaattttcgtacatgcagTGGAACTGTTCGCTATGCGAGTTTGCATGCACATATGGGAAGGACTGGGAGTAGGAAGGACGACTTGAGATCACTGGCTCATACTTTAGTATTCCTTGTG

upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S496_15V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------gttcggttgggaatattagtatgatatgctttaccactcac-gttatttcattga---atacttttgacatttgtgtttgcttcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC
                               | || || |     |||  | |  |     ||   |   || ||| |    ||||   ||| |||     | |||  ||     | |  ||| ||||||||||||||||| || |||||||| ||  ||||||| |||||||||||||  || ||  | | ||| || || || ||| |  | || ||| | 
gtgaggctcttccccctcccccccttgtcctgatctgtagttgccattcctgttttggcggttgggagcgactgttttgcttttgagctatattttgattctgtgtaattttcgtacatgcagTGGAACTGTTCGCTATGCGAGTGTGCATGCACATATGGGAAGGACTGGGAGTAGGAAGGACGACTTGGGATCACTGGCTTATACTTTGGTATTCCTTATG

upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S613_17V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------gttcggttgggaatattagtatgatatgctttaccactcac-gttatttcattga---atacttttgacatttgtgtttgcttcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC
                           | || || |     |||  | |  |     ||   |   || ||| |    ||||   ||| |||     | |||  ||     | |  ||| ||||||||||||||||| || |||||||| ||  ||||||| |||||||||||||  || ||  | | ||| || || || ||| |  | || ||| | 
gtgaggctcttctccctctcttgtcctgatctgtagttgccattcctgttttggcggttgggagcgactgttttgcttttgagctatattttgattctgtgtaattttcgtacatgcagTGGAACTGTTCGCTATGCGAGTGTGCATGCACATATGGGAAGGACTGGGAGTAGGAAGGACGACTTGGGATCACTGGCTTATACTTTGGTATTCCTTATG

upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S471_4V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------gttcggttgggaatattagtatgatatgctttaccactcac-gttatttcattga---atacttttgacatttgtgtttgcttcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC
                                           | || || |     |||  | |  |     ||   |   || ||| |    ||||   ||| |||     | |||  ||     | |  ||| ||||||||||||||||| || |||||||| ||  ||||||| |||||||||||||  || ||  | | ||| || || || ||| |  | || ||| | 
gcccgatgtgttccggagaggctctcccccccccccttgtcctgatctgtagttgccattcctgttttggcggttgggagcgactgttttgcttttgagctatattttgattctgtgtaattttcgtacatgcagTGGAACTGTTCGCTATGCGAGTGTGCATGCACATATGGGAAGGACTGGGAGTAGGAAGGACGACTTGGGATCACTGGCTTATACTTTGGTATTCCTTATG

upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S176_7V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------gttcggttgggaatattagtatgatatgctttaccactcacgttatttcattga-atacttttgacatttgtgtttgcttcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC
                              |   ||||  | |  |  | ||         | |       ||| ||    |  ||| |||     | |||  ||     | |  ||| ||||||||||||||||| || |||||| | ||  ||||||| |||||||||||||  || ||  | | ||| || || || ||| | || || ||| | 
gtgaggggctcccccccccttgtcttgatctgtagttgccattcctgttttggcggttgggagcgactgttttacttttgagctatattttgattctgtgtaattatcgtacatgcagTGGAACTGTTCGCTATGCGAGTGTGCATACACATATGGGAAGGACTGGGAGTAGGAAGGACGACTTGGGATCACTGGCTTATACTTTGATATTCCTTATG

upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S251_2V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------------------------gttcggttgggaatattagtatgatatgctttaccactcacgttatttcattga-atacttttgacatttgtgtttgcttcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC
                                         |   ||||  | |  |  | ||         | |       ||  ||    |  ||| |||     | |||  ||     | |  ||| ||||||||||||||||| || |||||||| ||| ||||||| |||| ||||||||  || ||  | | |||  | || || ||| | || || ||| | 
gtgaggctctttccccccctcccctcccccttgtcttgatttgtagttgccattcctgttttggcggttgggagcgactgttttgcttttgagctatattttgattctgtgtaattttcgtacatgcagTGGAACTGTTCGCTATGCGAGTGTGCATGCACACATGGGAAGGACTGAGAGTAGGAAGGACGACTTGGGATCATTGGCTTATACTTTGATATTCCTTATG

upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S489_24V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------gttcggttgggaatattagtatgatatgctttaccactcac-gttatttcattga---atacttttgacatttgtgtttgcttcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC
                               | || || |     |||  | |  |     ||   |   || ||| |    ||||   ||| |||     | |||  ||     | |  ||| ||||||||||||||||| || |||||||| ||  | ||||| |||||||||||||  || ||  | | ||| || || || ||| |  | || ||| | 
gtgaggctcttccccctcccccccttgtcctgatctgtagttgccattcctgttttggcggttgggagcgactgttttgcttttgagctatattttgattctgtgtaattttcgtacatgcagTGGAACTGTTCGCTATGCGAGTGTGCATGCACATATAGGAAGGACTGGGAGTAGGAAGGACGACTTGGGATCACTGGCTTATACTTTGGTATTCCTTATG

upper sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S360_49V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------gttcggttgggaatattagtatgatatgctttaccactcac-gttatttcattga---atacttttgacatttgtgtttgcttcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC
                                         | || || |     |||  | |  |     ||   |   || ||| |    ||||   ||| |||     | |||  ||  |  | |  ||| ||||||||||||||||| || |||||||| ||  || |||| |||||||||||||  || ||  | | ||| || || || ||| |  | ||  || | 
gtgaggctcttctcccccccccccctccccccccttctcttgatctgtagttgccattcctgttttggcggttgggagcgactgttttgcttttgagctatattttgattctgtgtaatttttgtacatgcagTGGAACTGTTCGCTATGCGAGTGTGCATGCACATATGAGAAGGACTGGGAGTAGGAAGGACGACTTGGGATCACTGGCTTATACTTTGGTATTCATTATG

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|32929439|gb|CF034251.1|CF034251
EST:     GGTACGGGGCACCATGTTGAATATGATCAGAGACCTGATATTTTTAG                         GGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAG
genomic: GGTACGGGGCACCATGTTGAATATGATCAGAGACCTGATATTTTTAGgttcggttgg ... tcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAG
EST: gi|32928927|gb|CF033739.1|CF033739
EST:     ATGTTGAATATGATCAGAGACCTGATATTTTTAG                         GGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAG
genomic: ATGTTGAATATGATCAGAGACCTGATATTTTTAGgttcggttgg ... tcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAG

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: 129

CAACTAAATGGAAGGATGCTGGTACGGGGCACCATGTTGAATATGATCAGAGACCTGATATTTTTAGgttcggttgg ... tcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

CAACTAAATGGAAGGATGCTGGTACGGGGCACCATGTTGAATATGATCAGAGACCTGATATTTTTAGgttcggttgg ... tcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

CAACTAAATGGAAGGATGCTGGTACGGGGCACCATGTTGAATATGATCAGAGACCTGATATTTTTAGgttcggttgg ... tcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

CAACTAAATGGAAGGATGCTGGTACGGGGCACCATGTTGAATATGATCAGAGACCTGATATTTTTAGgttcggttgg ... tcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccactcacgttatttcattgaatacttttgacatttgtgtttgcttcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC
                                       tttgcttc  CT-rich tract
         ttatttcattgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcggttgggaatattagtatgatatgctttaccactcacgttatttcattgaatacttttgacatttgtgtttgcttcataaacagGGGAACTGTTCGCTATGCTAGCGTGCATGCCCACTTGGGAAGAACTGGGAGTAGGAGAGATGATCTTGAATCCCTCGCATACACTCTTATTTTTCTTCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG