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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatgaatctagaagttgttttgtttttattagtctgaacttggccatgtacatgattaataatgccattgaaaaacattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTTAGAGCAATCTCGAGACAATAACTCAAATGGCCCCTCAAACTTCACTCTT

Basic information

species Zea mays
transcript GRMZM2G075978_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 6
gtatgatgaatctagaag------ttgttttgtttttattagtctgaacttggccatgtacatgattaataatgccattgaaaaacattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTTAGAGCAATCTCGAGACAATAACTCAAATGGCCCCTCAAACTTCACTCTT
||||| || ||||| ||       |   |||||||  |||    ||| || | | |  | |||   | || | ||     | |  ||||||||||||| |||||||||||||| || || ||||||||||||||||||||||| || ||||| || |||||    ||||| ||||| |||||||| || || |||
gtatgttggatctaaaacatctgctcagtttgtttccattttgttgagctagactacttgcatagctgatgacgct-caaatattcattttgcagCCAAAAGGGTGCTGTTGGAGTCAAACAGCCTTACATTAGAGTTGTGGGGTTGGAGCAGTCCCGAGATGCCAACTCGAATGGTCCCTCAAATTTTACACTT
















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|87153503|gb|DY398292.1|DY398292
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211096879|gb|FL135596.1|FL135596
EST:     ACTANATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCANCCTTACATTAGAGTTGNGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211329963|gb|FL157736.1|FL157736
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211094408|gb|FL135586.1|FL135586
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|32866416|gb|CF006098.1|CF006098
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211094409|gb|FL135587.1|FL135587
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211094411|gb|FL135589.1|FL135589
EST:     CTATGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: CTA-GATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211329958|gb|FL157731.1|FL157731
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211094402|gb|FL135580.1|FL135580
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211094412|gb|FL135590.1|FL135590
EST:     ACTANATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAANCAGCCTTACATTAAAGTTG
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTG
EST: gi|211096881|gb|FL135598.1|FL135598
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211096877|gb|FL135594.1|FL135594
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|32945450|gb|CF050269.1|CF050269
EST:     TACCAAACATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: TACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|19058027|gb|BM736694.1|BM736694
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211542713|gb|FK958380.1|FK958380
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211329962|gb|FL157735.1|FL157735
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTANAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211094414|gb|FL135592.1|FL135592
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211094403|gb|FL135581.1|FL135581
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211096880|gb|FL135597.1|FL135597
EST:     ACTANATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCANAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTANAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211094410|gb|FL135588.1|FL135588
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAAGGGTGCTGTTGG
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAA-GGGTGCTGTTGG
EST: gi|211329960|gb|FL157733.1|FL157733
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211329959|gb|FL157732.1|FL157732
EST:     ACTANATTAACTGTTGTTGGCATCTACAGCGNGTACCAAGCATCCACAAC                         CCANAAGGGTGCTGNTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211096878|gb|FL135595.1|FL135595
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211094404|gb|FL135582.1|FL135582
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211091941|gb|FL135578.1|FL135578
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTANAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211091939|gb|FL135576.1|FL135576
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAAGGGTGGCTGTTGATGTTAAGCAGCCTTACATTAAGAGTTGTGGG
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAA-GGGTG-CTGTTGGTGTTAAGCAGCCTTACATTA-GAGTTGTGGG
EST: gi|211329965|gb|FL157738.1|FL157738
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211094407|gb|FL135585.1|FL135585
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGNGTGTACCAAGCATCCACAAC                         CCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTANAGTTGNGGGTTT
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTT
EST: gi|211094401|gb|FL135579.1|FL135579
EST:     ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAAC                         CCANAAAGGTGCTGTTGGTGTTAAGCAGCCTTACATTA
genomic: ACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTA

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), 48 (downstream exon)
Score: 161

ATGTGCTGCTTTCTGTAGATAGGCACCTAGTTCAGACTATTGTTCCAGGGACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTTAGAGCAATCTCGAGACAATAACTCAAATGGCCCCTCAAACTTCACTCTT


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 36

ATGTGCTGCTTTCTGTAGATAGGCACCTAGTTCAGACTATTGTTCCAGGGACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTTAGAGCAATCTCGAGACAATAACTCAAATGGCCCCTCAAACTTCACTCTT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 28

ATGTGCTGCTTTCTGTAGATAGGCACCTAGTTCAGACTATTGTTCCAGGGACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTTAGAGCAATCTCGAGACAATAACTCAAATGGCCCCTCAAACTTCACTCTT


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 6

ATGTGCTGCTTTCTGTAGATAGGCACCTAGTTCAGACTATTGTTCCAGGGACTAGATTAACTGTTGTTGGCATCTACAGCGTGTACCAAGCATCCACAACgtatgatgaa ... cattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTTAGAGCAATCTCGAGACAATAACTCAAATGGCCCCTCAAACTTCACTCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtctgaacttggccatgtacatgattaataatgccattgaaaaacattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTTAGAGCAATCTCGAGACAATAACTCAAATGGCCCCTCAAACTTCACTCTT
                       gattaat  putative branch site (score: 6)
                  tacatgattaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatgaatctagaagttgttttgtttttattagtctgaacttggccatgtacatgattaataatgccattgaaaaacattttgcagCCAGAAGGGTGCTGTTGGTGTTAAGCAGCCTTACATTAGAGTTGTGGGTTTAGAGCAATCTCGAGACAATAACTCAAATGGCCCCTCAAACTTCACTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA