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

gtgctgtaacatctgtagacagtaatatttgcattatcaatgttcgtaatacctttttgtccttataatgaaggttgtaaaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA

Basic information

species Zea mays
transcript GRMZM2G056569_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 3
------gtgctgtaacatctgtagacagtaatatttgcattatcaatgttcgtaatacctttttgtccttataatgaaggttgtaaaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA
       | |  ||  |||| |    | |      ||||| || | || |    |   | ||| || || ||   ||| ||||| || ||||||||| |||||||| || |||||||| || || ||||||||| ||||||||||||| |||||||| |||||||| || || |||||||| || || || || |
gtaaatatccattagtatcttttagaacttcagaatgcatgataactgataagcagttcctttggttctcat---gaatgttgtgaatcgtgcagATACACACATCTAAGATGACATTGGCAGATGATGTGAACCTGGAAGAGTTTGTCATGACCAAGGATGAGTTTTCCGGTGCTGATATCAAAGCAATATGTA

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 4
--------gtgctgtaacatct-gtagacagtaatatt--tgcattatcaatgttcgtaatacctttttgtccttataatg-------aaggttgtaaacc------gtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA
         |  ||| | | |  ||   ||||   | |  | || | | |    |    || | | ||   | | || ||        |||||  || ||        |  |||| ||||||||||  |||||||||||||| ||||| || || ||||| |||||||||||||| ||||||||||| || |||||||| || || || || |
gtaggcacattttgtgaaagcaagttttcagtttcactgcttcactgttatatcttaatatgcttattctacttaattatatgactaaaaggtcttatacttctgaaatttagATACACACATCAAGGATGACATTAGCTGATGATGTCAATTTAGAAGAATTTGTTATGACCAAGGATGAGTTCTCTGGAGCTGATATAAAAGCAATATGTA

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 4
-------------gtgctgtaacatc-tgtagacagtaat-atttgcat-tatcaatgttcgtaat--acctttttgtccttataatgaaggttgtaaacc------gtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA
             || |||| | | | |||     ||  | | |  ||| | | ||| ||| || |  || |  || |   |      |||||  || ||        |  |||| || || ||||  |||||||||||||| ||||| ||||| ||||| ||||||||||| || ||||||||||| || |||||||| || || || || |
gtcggaatgactagttctgtgaaaacatgtttttggttttcactgacatatcttaatattcctattctacttagttatatctcactaaaaggtcttatacttttgatatttagATACATACTTCAAGGATGACATTAGCTGATGATGTCAACTTAGAAGAATTTGTTATGACTAAGGATGAGTTCTCTGGAGCTGATATAAAAGCAATATGTA

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 4
---------gtgctgtaacatctgtagacagtaatatttgcattatca-atgttcgtaatacctttttgtccttata-atgaaggttgtaaaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA
           | |||    ||||  ||   ||     |   ||| ||    | | |  | |  |  | | |||||| ||     |  |      |  |||| |||||||| |  |||||||||||||| ||||| ||||||||||| ||||||||||| |||||||| ||||| || |||||||| ||||| || || |
acccaacataagatgttgtttctgctgattctatgtgatatcttaacatgcatactttgttcaatcatatgcttatacattctcatactttggaattaagATACACACATCGAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTTGTTATGACTAAAGATGAATTCTCTGGAGCTGATATAAAGGCAATATGTA

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 4
----------gtgctgtaacatctgtagacagtaatatttgcattatcaatgttcgtaatacctttttgtccttata-atgaaggttgtaaaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA
            | |||    ||||  ||   ||     |   ||| ||   | | |  | |  |  | | |||| |  |     |  |      |  |||| ||||| ||||  |||||||||||||| ||||| ||||||||||| ||||||||||| ||||| || ||||| || |||||||| ||||| || || |
aacccaagatacgatgttgtttctgctgattctatgtgatatcttaacatgatactttgttcaatcatatgcttaaatgttctcatactttggaattaagATACACACGTCAAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTTGTTATGACTAAAGACGAATTCTCCGGAGCTGATATAAAGGCAATATGTA

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgctgtaac-----atctgtagacagtaatatttgcattatcaatgttc--gtaatacctttttgtccttataatgaaggttgtaaaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA
|| |   |||     |||  ||     |  |  ||   || | ||| |||  | || | ||  | |   ||  | || | |   | |       |||| ||||||||||| ||||| || ||||| ||||||||||| ||||||||||| ||||| ||||| |||||||| || |||||||| ||||| || ||||
gttccacaactggtgatccttaagttttctttctttttttgtgaattttctagaaagatctgatcggtttttaattgcatgccattatt-----agATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgctgtaacatctgtagacagtaatatt-tgcattatcaatgttcgtaatacctttttgtcctt----ataatgaaggttgtaaaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA
     |||| || |      | | | ||     || |   |  |     | || || |||| | |     |  ||     |||  |      |||| |||||||| || |||||  |  | || ||||| ||| | ||||||||||| ||||| ||||| |||||||| || |||||||| ||||| || ||||
-----gtaatatataattctactgagatggcaaatcaatgacttgttcgaaactttcttgttcattgaggttgtgggttctgtttataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCA

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------gtgctgtaacatctgtagaca----gtaatatttgcattatcaatgttcg--taatacctttttgtccttataatgaaggttgtaaaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA
                                      || ||   ||    |||     || | |  || || | |||   | |  | ||  || ||  |    | |||     || |  |   ||||||| || |||||||  |||||||| ||||| ||||| ||||||||||| ||||||||||| || |||||||| || || |||||||| ||||| || ||||
gtacatgtgtgtttaagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagca-aatctcatttatttaaattgcagATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCA

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 3
-gtgctgtaac---atctgtagacagt--aatattt-gcattatcaatgttcgtaatacctttttgtccttataatgaaggttgtaaa----ccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA
  | |  || |   || |||    |||   | |||  |  || |  ||   || ||| | |||     ||| |  ||     | | ||    |  |||||||||| || || | ||||||  | ||||| ||||| ||| | || |||||||| ||||||||||||||||| || || ||||| ||||| || ||||| |
tcttcattagctttatgtgtgagaagttggagattgagttttcttgataaacgaaattcttttgatcgcttgttttggtttcttttaatgatctctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTTGTGATGACCAAAGATGAGTTTTCTGGTGCTGACATTAAAGCTATCTGTA

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 4
gtgctgtaacatctgtagacagtaatatttgcattatcaatgttcgtaatacctttttgtccttataatgaaggttgtaaaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA
                             ||   | |   | ||| |  | |   |||||  ||    | |    | |    | ||||||| || ||||| | ||||||| |  |||||||||||||||| ||||||||||| ||||| || || || || || || ||||| || ||||| || ||||
----------------------------gtgacgtgttttttttctttgtgcgcgtttgtttttcc--taaccactttggttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGACGAATTTTCTGGAGCTGACATCAAGGCAATGTGCA

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 4
gtgctgtaacatctgtagacagtaatatttgcattatcaatgttcgtaatacctttttgtccttataatgaaggttgtaaaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA
                            |  | |  |   | ||  |  | |   |||||  ||   |  |    | |    | ||||||| || ||||| | ||||||| |  |||||||||||||||| ||||||||||| ||||| || ||||| ||||| || ||||| || ||||| || ||||
---------------------------gtgacgtcgtgcttattttttgtgcgcgtttgtttttccca--accactttggttcttgcagATCCATACATCGAGAATGACACTCTCTGACGATGTGAACTTTGAAGAGTTTGTGATGACGAAGGATGAATTCTCTGGAGCTGACATCAAGGCAATGTGCA

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|6194887|gb|AW146991.1|AW146991
EST:     ATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAG                         ATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
genomic: ATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaac ... aaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
EST: gi|113702544|gb|EE680048.1|EE680048
EST:     AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAG                         ATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
genomic: AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaac ... aaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
EST: gi|211247442|gb|FL282636.1|FL282636
EST:     AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAG                         ATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
genomic: AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaac ... aaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
EST: gi|88753157|gb|DY537298.1|DY537298
EST:     AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAG                         ATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
genomic: AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaac ... aaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
EST: gi|166701423|gb|EG166079.1|EG166079
EST:     AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAG                         ATTCACACATCAAAAAATGACATTAGC
genomic: AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaac ... aaccgtgcagATTCACACATCAAAAA-TGACATTAGC
EST: gi|62550417|gb|DN830837.1|DN830837
EST:     AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAG                         ATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
genomic: AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaac ... aaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
EST: gi|166633409|gb|EG174486.1|EG174486
EST:     GATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCAATCTTCCAG                         ATTCACACATCAAAAATGACATTAG
genomic: GATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCA-TCTTCCAGgtgctgtaac ... aaccgtgcagATTCACACATCAAAAATGACATTAG
EST: gi|116828199|gb|EC855484.1|EC855484
EST:     AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAG                         ATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
genomic: AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaac ... aaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
EST: gi|91054539|gb|EB164957.1|EB164957
EST:     AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAG                         ATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
genomic: AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaac ... aaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
EST: gi|14203652|gb|BG837329.1|BG837329
EST:     AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAG                         ATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
genomic: AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaac ... aaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
EST: gi|32937106|gb|CF041925.1|CF041925
EST:     AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAG                         ATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
genomic: AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaac ... aaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
EST: gi|211285728|gb|FL480875.1|FL480875
EST:     AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAG                         ATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT
genomic: AGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaac ... aaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTT

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), 49 (downstream exon)
Score: 330

CATTGAAAGTCTTGATCCTGCTTTGCTTCGGCCAGGCCGTATAGACCGGAAGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaac ... aaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 302

CATTGAAAGTCTTGATCCTGCTTTGCTTCGGCCAGGCCGTATAGACCGGAAGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaac ... aaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 290

CATTGAAAGTCTTGATCCTGCTTTGCTTCGGCCAGGCCGTATAGACCGGAAGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaac ... aaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

CATTGAAAGTCTTGATCCTGCTTTGCTTCGGCCAGGCCGTATAGACCGGAAGATTGAATTCCCTCTCCCAGATATTAAAACTAGAAGACGCATCTTCCAGgtgctgtaac ... aaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcaatgttcgtaatacctttttgtccttataatgaaggttgtaaaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA
                            ttataatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctgtaacatctgtagacagtaatatttgcattatcaatgttcgtaatacctttttgtccttataatgaaggttgtaaaccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT