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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaggctgtttatctcatacagtaaatctgttgtgccccgcacaacacaccttgttggaaattggccctcacatgactccaaatgatgttacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG

Basic information

species Zea mays
transcript GRMZM2G304362_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 3
------------------------------------acaag-gctgtttatctcatacagtaaatctgttgtgccccgcacaacacaccttgttggaa--attggc----------cctcacatgactccaaatgatgttaca-----tttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG
                                    | |   | | ||  ||| ||     |||| |  ||| ||   ||    |    |  || | |  ||||            | ||  | |  | |  ||| | | |       |||||||||||| ||||||||||||| |||||||||||||||||||| ||||| || || || ||||| ||||| ||||||||||||||||||||  |||| ||||
gtgagatatcaaattaaactttagggacttgcactgatagctgttcttgttctgatttgtaaaatttactgttccattcaatttattggtcattaggattattgatgtatgttatgcttcttacggtttctgatgttctgatccttattttcagAATGCTTCTCGCTTGGACAGCGAGATAATTTATGATAGGGACTTCGATTATGATTATTTTGGTTTCAAGACTCTGGAGAGGTCTTACCTCCTGAAACTTG

upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 2
acaaggctgtttatctcatacagtaaatctgttgtgccccgcacaacacaccttgttggaaattggccctcacatg-actccaaatgatgttacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG
    |  ||| |     ||    |   | |||  |                 ||| |   | |||    |||| |    |     |  ||||   ||| |||||| |||||| ||||||||||||||||| |||||||| || || ||||| || |||||||| |||||||| || |||||||| ||| |  ||||| || 
-tgtgtgtgtgtggtgtatttgttggttgtgtgattttgtttgactgttgttttggtatgatttgaaattcacgtttgttttgttttctgttttgttttagAATGTTGCTCGATTGGACAGTGAGATAATCTATGATAGAGACTTTGACTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCATACATCCTGAAGGTTC

upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 3
acaaggctgtttatctcatacagtaaatctgt-tgtgccccgcacaacacaccttgttggaaattggccctcacatgactccaaatgatgttacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG
  |    || || ||  || |   || | | | | || |               |||    || |   | |    |      |  |  ||||   ||  |||||||||||||  | |||||||||||||| ||||| || || || ||||| || || ||||| |||||||| || |||||||||||||| |||||| || 
ttatttatgctt-tcaaatgcttgaagtttttgtttggctgttgttttttcgtatgtgatgaaataatcttttattattattattttttgtttggttgtagAATGCTGCTCGTCTAGACAGTGAGATAATCTATGACAGAGACTTTGACTATGATTATTTTGGATTCAAAACCCTTGAGAGGTCTTACCTCTTGAAGGTTC

upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 3
acaaggctgtttatctcatacagtaaatctgttgtgccccgcacaac-acaccttgttggaaattggccctcacat-gactccaaatgatgttacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG
    |  ||  | |    ||     |  || ||  |    |     |      ||  |   |  ||    |||| | |        |  | ||   ||| ||||||||||||| ||||||||||||||||| ||||||||||| || ||||| || |||||||| ||||||||||| |||||||| ||||| |||||| || 
--gtgtgtgagtgtggtgtaattctatgcttttaagttttgtttggctgtgttttagtatgatgtgaaattcactttggtattgttttctattttgttttagAATGCTGCTCGATTGGACAGTGAGATAATCTATGATAGGGACTTTGACTATGATTACTTTGGTTTCAAAACTCTTGAGAGGTCATACCTCTTGAAGGTTC

upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 3
acaaggctgtttatctcatacagtaaatct-gttgtgccccgcacaacacacctt-gt-tggaaattggccctcacatgactccaaatgatgttacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG
       | |||||    |  | |   |   |||||     |         | || || ||  ||       ||   |      |  |  ||||    |  |||||||||||||  | ||||| |||||||| ||||| ||||| || ||||| || || ||||| |||||||| || |||||||||||||| |||||| || 
---gatttatttatggtttgaaattctttaagttgttgtttggctgttgttcttttgtgtgtgaagaaataatcttttattattattttgtgtttggctgtagAATGCTGCTCGTCTAGACAGCGAGATAATCTATGACAGGGACTTTGACTATGATTATTTTGGATTCAAAACCCTTGAGAGGTCTTACCTCTTGAAGGTTC

upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT2G21790.1 (Arabidopsis thaliana), 3'ss of exon 3
----acaaggct---gtttatctcatacagtaaatctgttgtgccccgcacaacacaccttgttggaaat---tggccctcacatgactccaaatgatgttacatt-------tcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG
    | ||  ||   ||| | ||| |  | | ||||||||       |    | | |  |   |  | ||   ||   || | |   | |  | |  |||   | |       |||||| |||||||| |||||||||||||| || |||||  | ||||| || || || |||||||| || |||||||| ||||| || ||||| |||||  |  
gtaaagaaatcttgtgttaagctcttg-attcaatctgtttcttggtgtgatatatatatatatatatatgtatgtatcttataaatcactgacttgtgtgttactggtttcttcagAACGCTGCTCGTTTGGACAGTGAGATCATCTATGACCGTGATTTTGAATATGATTACTTTGGATTTAAAACTCTTGAGAGATCGTACCTCTTGAAAGTCC

upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 3
acaaggctgtttatctcatacagtaaatctgttgtgccccgcacaacacaccttgttggaaattggccctcacatgactccaaatgatgttacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG
     | |||  || ||      |  |  ||                   |||||    ||||     |     |   |    ||    |     |||||||||||||||| ||||||||||| || ||||||||  |||| || || || || |||||||| |||||||| || |||||||| |||||  ||||| || 
ctggtggtgtgcatgtctggatcttgacttggaaatatagaattgctggtccttgacacaaatctcaacaattctatttgtttatttcttctttcttcagAATGCTGCTCGTTTGGACAGTGAAATCATTTATGACCGGGACTTTGATTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCCTACCTCCTGAAGATTC

upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S64_38V6.1 (Physcomitrella patens), 3'ss of exon 2
acaaggctgtttatctcatacagtaaatctgttgtgccccgcacaacaca--ccttgttggaaattggccct---cacatgactccaa----atgatgttacattt-------cagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG
  | | ||| | || | |       ||     | | |  |     | |||  ||  |||  |  ||         | | || |  |      |    | ||   ||        |||||||  | ||| ||||||| ||||| || ||||| ||||| || |||||||| |||||||||||||| ||  | ||||| ||||| ||  ||||  || 
gtacgactgatgatttgaatatcagaacgaactctccttcctgggatacaatccacgtttcatcttcatttcttgcgcgtgccctctgtcttacagcgctatgcttgtctttgtagAATGCCCCGCGCCTGGACAGCGAGATTATATATGACAGGGACTTTGACTACGATTACTTTGGCTTCAAGACATTAGAGAGATCTTATCTTCTGAAAGTTA

upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------acaaggctgt-ttatctc-atacagtaaatctgttgtgccccgcac------aacacaccttgttggaaattgg--ccctcacatgactccaaatgatgttacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG
                    ||| | | | | | |||  |      |||  ||| | | || |        ||    || ||       |  |   |      |||  | |  | |  ||   |   |||| || ||||   ||||||| ||||||||||||||| |||| ||||| ||||||||||| |||||||| || |||||||| || ||  |  |||   |  
gtagcgataacaattaatggcaaagttatgtcagctctgtgttcgcaattcgtttttctccacttgtttttaagtttccctgcccatggtctgaatctgtgtttgatccgacttcaatttggttactagAACGCGGCTCTTCTGGACAGCGAGATAATTTATGATCGGGACTTCGATTACGACTACTTCGGCTTCAAGACACTGGAGAGATCATATTTACTGAGAGTGA

upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ14283 (Selaginella moellendorffii), 3'ss of exon 3
acaaggctgtttatctcatacagtaaatctgttgtgccccgcacaacacaccttgttggaaattggccctcacatgactccaaatgatgttacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG
                             ||  ||   ||   ||      ||  ||     |  |  ||||      | |   |  | ||    | ||||| || ||     | || || || || || ||||| |||||||||||||| ||||||||||| ||||| || || || || || ||||| |||||  |  
----------------------------gtga-gtattcccgtcattggttctccttt----tctgttctcat-cagtttctctttctcttttcgtccagAACGCGGCGAAGCTTGATAGCGAAATCATCTATGACAGGGATTTCGACTATGACTACTTTGGATTCAAGACGCTCGAAAGATCATACCTCTTGAAAGTGA

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|93012077|gb|EB637597.1|EB637597
EST:     GGCTGATGGCCCCTCTTGTCGCTGAAGATGTTTATGAAATCATCATGAAG                         AATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTAC
genomic: GGCTGATGGCCCCTCTTGTCGCTGAAGATGTTTATGAAATCATCATGAAGgtgagattct ... tacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTAC
EST: gi|31355936|gb|CD440293.1|CD440293
EST:     GGCTGATGGCCCCTCTGGTCGCTGAAGATGTTTATGAAATCATCATGAAG                         AATGCTGCTCGCTTGGACAGTGAGATAATTTATGACAGGGATTTCAACTAC
genomic: GGCTGATGGCCCCTCTTGTCGCTGAAGATGTTTATGAAATCATCATGAAGgtgagattct ... tacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTAC
EST: gi|32796379|gb|CD948615.1|CD948615
EST:     GGCTGATGGCCCCTCTTGTCGCTGAAGATGTTTATGAAATCATCATGAAG                         AATGCTGCTCGCTTGGACAGTGAGATAATTTATGACAGGGATTTCGACTAC
genomic: GGCTGATGGCCCCTCTTGTCGCTGAAGATGTTTATGAAATCATCATGAAGgtgagattct ... tacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTAC
EST: gi|32803077|gb|CD955313.1|CD955313
EST:     GGCTGATGGCCCCTCTTGTCGCTGAAGATGTTTATGAAATCATCATGAAG                         AATGCTGCTCGCTTGGACAGTGAGATAATTTATGACAGGGATTTCGACTAC
genomic: GGCTGATGGCCCCTCTTGTCGCTGAAGATGTTTATGAAATCATCATGAAGgtgagattct ... tacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTAC
EST: gi|88756462|gb|DY540603.1|DY540603
EST:     GGCTGATGGCCCCTCTTGTCGCTGAAGATGTTTATGAAATCATCATGAAG                         AATGCTGCTCGCCTGGACAGTGAGATAATTTATGATAGGGATTTCGACTAC
genomic: GGCTGATGGCCCCTCTTGTCGCTGAAGATGTTTATGAAATCATCATGAAGgtgagattct ... tacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTAC
EST: gi|31355336|gb|CD439693.1|CD439693
EST:     GGCTGATGGCCCCTCTGGTCGCTGAAGATGTTTATGAAATCATCATGAAG                         AATGCTGCTCGCTTGGACAGTGAGATAATTTATGACAGGGATTTCGACTAC
genomic: GGCTGATGGCCCCTCTTGTCGCTGAAGATGTTTATGAAATCATCATGAAGgtgagattct ... tacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTAC

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: 201

GATTAAGGACATGTACATGCACTTCAACAAGAGATCCGGGCTGATGGCCCCTCTTGTCGCTGAAGATGTTTATGAAATCATCATGAAGgtgagattct ... tacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 44

GATTAAGGACATGTACATGCACTTCAACAAGAGATCCGGGCTGATGGCCCCTCTTGTCGCTGAAGATGTTTATGAAATCATCATGAAGgtgagattct ... tacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 31

GATTAAGGACATGTACATGCACTTCAACAAGAGATCCGGGCTGATGGCCCCTCTTGTCGCTGAAGATGTTTATGAAATCATCATGAAGgtgagattct ... tacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 43

GATTAAGGACATGTACATGCACTTCAACAAGAGATCCGGGCTGATGGCCCCTCTTGTCGCTGAAGATGTTTATGAAATCATCATGAAGgtgagattct ... tacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacaccttgttggaaattggccctcacatgactccaaatgatgttacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG
                     ccctcac  putative branch site (score: 43)
                                            ttacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaggctgtttatctcatacagtaaatctgttgtgccccgcacaacacaccttgttggaaattggccctcacatgactccaaatgatgttacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - ggctgtt
- - - - - - - - catacag
- - - - - - - - - - - - - - ctgttgt
- - - - - - - - - - - - - - - - - - ccccgca
- - - - - - - - - - - - - - - - - - - - - -caacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgatgt