Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagcttttagattttcagtcaatgttaagcactttttccatctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG

Basic information

species Zea mays
transcript GRMZM2G030169_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030169_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g36650.1 (Oryza sativa), 3'ss of exon 2
----gtaactgtagtcgcttggcatcatattctctaatga---ttcctctttttccatacagcttttagattttcagtcaatgttaagca----ctttttccatctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG
      ||  ||  |  |||||||||  ||| |  ||  |   |||  | |  |    |    | ||| | ||          | ||| |    || ||| ||| | | ||||||||| |||||||||||||| ||||| |||||||||||||| ||||| ||||| ||||| || || || || || ||||||||||||||||| || ||||
gtaataaaaagtgatgacttggcatcgcattgttgaacaaaatttctacctgatggtaattattgttacaattgagaagctcatcaagtattaactgttttcatttttcatagGCTGGGTTTGCTGGAGATGATGCTCCCCGTGCTGTTTTCCCGAGTATTGTTGGCCGTCCGCGACATACAGGCGTTATGGTTGGGATGGGACAAAAAGATG

upper sequence: GRMZM2G030169_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G39380.2 (Glycine max), 3'ss of exon 2
gtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagcttttagattttcagtcaatg-ttaagcactttttccatctct-tatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG
      ||     ||| |||   | |||| | ||| |     |   || ||  ||  |     |  | |   || | || |   || |    |||| | || |||| || |||||||| ||||| |||||  | ||||| || || ||||| ||||| || || ||||| |||||||| |||||||||||||| || |||||||
------gttagtactttgcagtttcttctgttatg-tgtaattgcatctat-tagtctcggtttcgttatcaaacgatttatttctataatgatctgtgtacagGCAGGATTTGCTGGTGATGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGCCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATG

upper sequence: GRMZM2G030169_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 2
gtaactgtagtcgcttggcatcatattctcta-atgattcctctttttccatacagcttttagattttcagtcaatgttaagcactttttccatctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG-
      ||     ||| |||   | || |     | ||| |   | ||   |   | |||   ||| |   ||||| |||   |  |  ||       || |||| || |||||||  || || |||||  | ||||| || || ||||| |||||||| || ||||| |||||||| |||||||||||||| || ||||||| 
------gttagtactttgcagtttcttgttagtgtaattgcatctatttagtcttggtttc--attattgctcaat-ttatttaaatgatcatctgtgtacagGCAGGATTTGCTGT-GACGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGTCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATGC

upper sequence: GRMZM2G030169_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 2
-----------gtaactgtagtcgcttggcatcatattctctaatgattcctctttttccataca-gctt--ttagattttcagtcaatgttaagcactttttccatctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG
            |   |  | | | |  |       |   ||| |||         |||  |    ||||  ||| || |    | ||| | |     ||| ||||    ||  |||| || ||||| || |||||||||||  | || || ||||| |||||  |||| || ||||| || || ||||| |||||||||||||| ||||||||||
gttagaacatgttttttccaattgatgagtgcttcttgtgctattgaagtagacagttcgctctgtgcttgcttaaatatgatattaatat-atattttttctccaatgtttgcagGCGGGTTTTGCAGGTGATGACGCTCCTAGGGCCGTGTTCCCCAGTATTATTGGGCGACCACGCCATACCGGTGTAATGGTTGGGATGGGTCAGAAGGATG

upper sequence: GRMZM2G030169_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G05570.1 (Glycine max), 3'ss of exon 2
---------------------------gtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagcttttagattttcagtcaatgttaagcactttttccatctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG
                           ||   | | ||  | | | |  | | | |  | |   | ||   ||   || ||  | ||| || |    |  || | |   | ||||  |     ||  ||||||| ||||| || ||||| |||||  | || || ||||| || ||  ||||  | ||||| || |||||||| |||||||||||||| ||||||||||
gttagaagatgttttgccaattgatgagtgtttcttgtgccattgaagaagactgttcactctgtgcttgcttagtattca-ttgttaaatatgatattgatat-atatatttttctcgatgtttgcagGCTGGTTTTGCAGGTGATGATGCTCCTAGGGCCGTGTTCCCCAGCATTATTGGGAGACCACGCCATACTGGTGTAATGGTTGGGATGGGTCAGAAGGATG

upper sequence: GRMZM2G030169_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 1
gtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagcttttagattttcagtcaatgttaagcactt--tttccatctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG
      ||     ||| ||  | |  | | |  || ||| | |  ||   | || ||  |||  ||    |||    | |    ||  |||  || |   | ||||||| |||||||| ||||| |||||  | ||||| || || ||||| ||||| || || || ||||||||||| |||||||||||||| || |||||||
------gttagtacttagcggctttgttttt--tgtttcatgtgctt--gtgcatctgctagccttgagttcataactgaatctttgattttaatatggaacagGCTGGATTTGCTGGTGATGATGCTCCCAGGGCTGTCTTTCCCAGTATTGTTGGCCGACCTCGACACACTGGTGTTATGGTTGGGATGGGTCAAAAGGATG

upper sequence: GRMZM2G030169_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaactgtagtcgcttggcatcatattctctaatgatt-cctctttttccatacagcttttagattttcagtcaatgttaagcactttttccatctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG
|| | |      | ||      ||| | | |  |  |  |||  |||    ||||  | | ||| |     |||           |||||  || | | | ||||||| |||||||| ||||| || ||  | || || ||||||||||| |||||||||||  | |||||||||||||||||||| ||||| ||||| ||||
gtgagttagactgtttatttagatactgtatggttctaaccttctttgttgtacatgtgtaagactactgatca--------tgatttttgtatat-taacagGCTGGTTTTGCTGGTGATGATGCCCCGAGAGCAGTGTTCCCAAGTATTGTTGGTCGTCCTAGGCACACTGGTGTCATGGTTGGTATGGGTCAGAAAGATG

upper sequence: GRMZM2G030169_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 3'ss of exon 3
gtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagctttt-agattttcagtcaatgttaagcactttttccatctcttata----gGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG
    |||| ||  |||    |    |  | |   ||||  |  | ||   | | |||  | | ||  ||| |     | |        |   ||   |||||    |||||| ||||| || ||||| |||||  | || || || || ||||| || ||||| ||| | |||||||||||||||||||||||||| || || ||||
--gtctgttgtttctt--tcttgcttgatatgcagatttgttgtgttgtttgctgctcctcaaatgctcaatttgaataagctttccatgttatgctttatatgcagGCTGGATTTGCGGGTGATGATGCTCCCAGGGCAGTGTTTCCTAGTATTGTGGGTCGGCCAAGGCACACTGGTGTCATGGTTGGGATGGGTCAAAAAGATG

upper sequence: GRMZM2G030169_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv12s0178g00200.t01 (Vitis vinifera), 3'ss of exon 1
gtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagcttt--tagattttcagtcaatgttaagcactttttccatctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG
   | |  | |   |  |  |  | |       ||| |   | ||        | ||||  ||| |||    |||    | | | ||  | | |     |  ||||||| |||||||| ||||| |||||  | ||||| ||||| ||||| ||||| || || || ||||| |||||||||||||||||||| || |||||||
---attaaactgattctgtttgctgtggcgaggtgaatttgcattcagtgattatctttgttagttttgttttcacacattaacgctgct-caaaaatgtgcagGCTGGATTTGCTGGTGATGATGCTCCGAGGGCTGTGTTCCCCAGTATTGTTGGCCGACCTCGACACACAGGTGTCATGGTTGGGATGGGCCAAAAGGATG

upper sequence: GRMZM2G030169_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 3
gtaactgtagtcgcttggcatcatattctctaatgattcctctttt--tccatacagcttttagatt--ttcagtcaatgttaagcactttttccatctctta----tagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG
              || ||||| |  | | |||||      | ||   |  | ||   |||  |||   | |  || |   |  |     |||   |   ||      ||||||| || |||||||| || ||||| || ||||||||||| || || ||||| || ||  | |||||||| || ||||| || |||||||||||||| |
----------ctcttttgcatctttatttataatgggcagacattggatgtagactaatttatgatcaatcctctcgaaactgtgtttaattttggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GRMZM2G030169_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaactgtagtcgct-tggcatcatattctctaatgattcctctttttccatacagcttttagattttcagtcaatgttaagcactttttccatctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG
  || |   |      |||| |   ||  |   |  ||||   |   | ||       | |  |     |  |  |||| |     |  |  ||       ||||||| || |||||||| || ||||| || ||||||||||| || || ||||| || ||  | |||||||| || ||||| || |||||||||||||| |
-caattcatgctataatggcgtt-catgataatactattcaagtgacttcagttgtgctgtccagaacgaaaccgtgtttaat-tgtggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

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|211318076|gb|FL324826.1|FL324826
EST:     CAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAG                         GCTGGCTTTGCTGGAGATGATGCTCCCCGTGCTGTTTTCCCAAGTATAGTT
genomic: CAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaactgtag ... tctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTT




















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: 47 (upstream exon), 49 (downstream exon)
Score: 186

ATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaactgtag ... tctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 91

ATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaactgtag ... tctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 75

ATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaactgtag ... tctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 128

ATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAGgtaactgtag ... tctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatacagcttttagattttcagtcaatgttaagcactttttccatctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG
                                  cactttttccatctct  CT-rich tract
         ttttagatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactgtagtcgcttggcatcatattctctaatgattcctctttttccatacagcttttagattttcagtcaatgttaagcactttttccatctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG