Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAATTCTTGAGAAGATTGCCCCCACATGGATGAATGTGTCAATTCAAATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaattactttatcctgtatgcaaaccgtgcaagttcttatgttcacttattacattattacaattccagccttctttgacctttag

Basic information

species Zea mays
transcript GRMZM2G035595_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035595_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g16600.1 (Oryza sativa), 5'ss of exon 4
ACAATTCTTGAGAAGATTGCCCCCACATGGATGAATGTGTCAATTCAAATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaattactttatcctgtatgcaaaccgtgcaagttctta--tgttcacttattacattattacaattccagccttctttgacctttag
| |   ||||||||||||||||| |||||||||||||| || |||||||||||||| ||| | ||||||||||||| |||||||||||| |||||||||| ||||||||  |    | |||    |   ||||  | |||   ||||   || |||   |   |   |       ||  ||||| | |||
ATACAACTTGAGAAGATTGCCCCTACATGGATGAATGTATCGATTCAAATGAAAGAAGATCAGGAGACAGATAAAGCTTTTGGATGGGTCTTGGAAATgtgagaattacgcttgtgtatattttcataatgcatttacttgcttgttacattgttatgattccaggttcttgtttttacttgacttctag

upper sequence: GRMZM2G035595_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA15G37490.3 (Glycine max), 5'ss of exon 5
ACAATTC--TTGAGAAGATTGCCCCCACATGGATGAATGTGTCAATTCAAATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaattactttatcctgtatgcaaaccgt--------gcaagttctta----tgttcacttattacattattacaattccagccttctt-tgacctttag
   |||   | |  |||||||||||||||||||||||| | ||  |  | |||||||||||   |||||| ||||||| ||||||||||||| | |||||||| |  ||||   |      ||  | |   |           || | ||     || | | ||  ||||||||   |||       ||||| ||      ||
--GATTTGATCGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATGAAAGAGGACCCAGAGACTGATAAAGCTTTTGGATGGGTGCTAGAAATgtatgtcttaccaaacaactgatagatatttttgttctagaagaggtattggaactgataatttgatacattatgctaatggtttttttcttgtggaaccaag

upper sequence: GRMZM2G035595_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA13G26610.1 (Glycine max), 5'ss of exon 5
ACAATTC--TTGAGAAGATTGCCCCCACATGGATGAATGTGTCAATTCAAATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaattac----------------tttatcctgtatgcaaaccgtgcaagttcttatgttcacttattacattattacaattccagccttctttgacctttag
   |||   |||  |||||||||||||||||||||||| | ||  |  | ||||||||||||  |||||| ||||||| ||||||||||||| | |||||||| |  ||||                | | |    | |  ||   ||    |  || ||  |    |  |  ||  | |  |||       |  | || |     
--GATTTGATTGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATGAAAGAGGATCCAGAGACTGATAAAGCTTTTGGATGGGTGCTAGAAATgtatgtcttaccaaaaaatctgatagatatttttgttttagaagaggtattggaactgatagttttctgctttatgttaatgattttttttcttgtggagccaag-

upper sequence: GRMZM2G035595_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA02G44810.1 (Glycine max), 5'ss of exon 6
ACAATTCTTGAGAAGATTGCCCCCACATGGATGAATGTGTCAATTCAAATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaattacttta-----tcctgtatgcaaaccgtgcaagttc---ttatgttcacttattacattattacaattccagccttctttgacctttag--------------------------------------------------------------
 |  |  | ||| | || ||  |||||||| | ||||| ||| |   ||||||||| ||| ||||||| ||||||| ||||||||||||| | ||||||| || |||||  ||     ||  | || ||      | | | |    || |  | | |||| |  |  | |   |     | || | | |  |||                                                                
TCTTTGATGGAGGAAATAGCTTCCACATGGGTAAATGTTTCATTGAGAATGAAAGATGATCAAGAGACTGATAAAGCTTTTGGATGGGTGCTTGAAATgtgagtattaccatagaaattcacgaattcacgattcggaggcttcattttttattatttatcatttactgatgttcttttcattttataatttttcctggaccgtggtctgtattaataggtctaaccttctgctgctttgattctctgttgagtaaag

upper sequence: GRMZM2G035595_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv06s0009g03360.t01 (Vitis vinifera), 5'ss of exon 4
ACAATTCTTGAGAAGATTGCCCCCACATGGATGAATGTGTCAATTCAAATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaag----------aattactttatcctgtatgcaaaccgtgcaagttctta-----tgttcacttattacattattacaattccagccttctttgacctttag------------
 |    || ||| | ||||| || |||||||||||| | ||  |   ||||||||| |||  |||||||||||||| ||||||||||||| | ||||||| ||          || || || ||| | | | ||     ||  ||||  |      |||||  |  ||   | ||   ||||      |  ||  |  |||              
TCCCAACTGGAGGAAATTGCACCTACATGGATGAATATTTCTTTGAGAATGAAAGATGATCCAGAGACAGATAAAGCTTTTGGATGGGTGCTAGAAATgtgagtagtaccttaaaatatttcatcttctgt-caggttctgtcagttgatggtgactgttctttggttttctgatatgaattttgatgtgtttccattttttctttgaaacaaag

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|5928606|gb|AW056003.1|AW056003
EST:     ATGAAAGAGGATAAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAAT                         GTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
genomic: ATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaatta ... tgacctttagGTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
EST: gi|211142481|gb|FL118078.1|FL118078
EST:     ATGAAGAAACAGATAAAGTTTTTGGATGGGTGTTGGAAAT                         GTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
genomic: ATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaatta ... tgacctttagGTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
EST: gi|71441274|gb|DR822324.1|DR822324
EST:     ATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAAT                         GTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
genomic: ATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaatta ... tgacctttagGTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
EST: gi|4776320|gb|AI665323.1|AI665323
EST:     ATGAAAGAGGATAAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAAT                         GTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
genomic: ATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaatta ... tgacctttagGTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
EST: gi|211025730|gb|FL435838.1|FL435838
EST:     CAGATAAAGTTTTTGGATGGGTGTTGGAAAT                         GTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
genomic: CAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaatta ... tgacctttagGTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
EST: gi|78027261|gb|DV495648.1|DV495648
EST:     ATGAAAGAGGATAAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAAT                         GTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
genomic: ATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaatta ... tgacctttagGTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
EST: gi|71759438|gb|DR957375.1|DR957375
EST:     ATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAAT                         GTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
genomic: ATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaatta ... tgacctttagGTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
EST: gi|86472181|gb|DY238551.1|DY238551
EST:     ATGAAAGAGGAGGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAAT                         GTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCAT-TCCCTTC
genomic: ATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaatta ... tgacctttagGTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATAT-CCTTC
EST: gi|149009585|gb|EE154018.2|EE154018
EST:     ATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAAT                         GTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
genomic: ATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaatta ... tgacctttagGTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
EST: gi|5928615|gb|AW056012.1|AW056012
EST:     ATGAAAGAGGATAAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAAT                         GTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
genomic: ATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaatta ... tgacctttagGTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
EST: gi|5816276|gb|AI987192.1|AI987192
EST:     ATGAAAGAGGATAAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAAT                         GTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
genomic: ATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaatta ... tgacctttagGTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
EST: gi|84970100|gb|DV171467.2|DV171467
EST:     ATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAAT                         GTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
genomic: ATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaatta ... tgacctttagGTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
EST: gi|211142480|gb|FL118077.1|FL118077
EST:     ATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAAT                         GTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG
genomic: ATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaatta ... tgacctttagGTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCG

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 3 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 19

ACAATTCTTGAGAAGATTGCCCCCACATGGATGAATGTGTCAATTCAAATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaatta ... tgacctttagGTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 34

ACAATTCTTGAGAAGATTGCCCCCACATGGATGAATGTGTCAATTCAAATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaatta ... tgacctttagGTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 616

ACAATTCTTGAGAAGATTGCCCCCACATGGATGAATGTGTCAATTCAAATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaatta ... tgacctttagGTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAATTCTTGAGAAGATTGCCCCCACATGGATGAATGTGTCAATTCAAATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAATgtaagaattactttatcctgtatgcaaaccgtgcaagttcttatgttcacttattacattattacaattccagccttctttgacctttag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA