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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actaattaagctaatttgttgcttattgcccatgctgcagtccttttacctgttaggtctgtcttttaataataataccctttttcctttcgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTA

Basic information

species Zea mays
transcript GRMZM2G169773_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169773_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 4
-actaattaagctaatttgttgctta--ttgcccatgctgcagtccttttacctgttaggtctgtcttttaataataataccctttttcctttcgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTA
  ||| |   ||||||||  ||||||  ||     || |||| ||  ||| ||  ||  ||   |  ||      |   || ||||   ||||  |||  ||||||| |||||||||||||| || || |||||||||||  | || |||||||||||||||||||| || ||||||||||| ||||| ||||||||||| ||
ggctattcttgctaattttgtgcttatgtttgttctgttgcaatctattttccattttagttgttgcttctgcctttcaactcttt---cttttatttttcagCTGGGATTGTCATTGAAGAGAAAAACTGGCCACCCTTCTTCCCTATTATTCATCATGACATTTCAAATGAGATACCAATCCACCTACAAAGGATGCAATA

upper sequence: GRMZM2G169773_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 5
actaattaagctaatttgttgcttattgcccatgctgcagtccttttacctgttaggtctgtcttttaataataataccctttttcctttcgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTA
  || || || | || | ||  |||| |   |  |  |     |  |  ||||    | ||  || |  |||   |    |||||  |||| |||| ||||||| || || || || || || ||||||||||| ||| | ||||| ||||||||||||||| | || || |||||| | || || |||||||| |||||
-gtatttgagttcatctattctttataga--aatcaactagagtgatgtctgt--attttggtttct--taactctttatttttttttttcatttg-cagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTCATCATGACATTGCAAAGGAAATACCAGTACATCTTCAAAGGATCCAGTA

upper sequence: GRMZM2G169773_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT1G03550.1 (Arabidopsis thaliana), 3'ss of exon 4
actaat-taagctaatttgttgcttattgcccatgctgcagtccttttacctgttaggtctgtcttttaataataataccctttttcctttcgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTA
  || |  || ||  | | |  ||| || |   | |    | ||||||||  |||   | |||   | | |  | ||||  || ||        |||||||||||  ||||||||||||| |||||||||||    ||| | ||  | ||||||||||||||| | || ||||| ||||||||  | || | ||| || ||
-gtagtgcaatcttctatatgtctttttacatcttccaatgaccttttacgggtt---tttgtagctaact--tgatacggttgtt--------ttggcagCTGGAGTTGTCATTGAAGAGAAGAATTGGCCGGAGTTTTTTCCTTTAATTCATCATGACATTCCAAATGAGATTCCAATTCATTTACAGAAGATCCAATA

upper sequence: GRMZM2G169773_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 4
actaattaagctaatttgttgcttattgcccatgctgcagtccttttacctgttaggtctgtcttttaata-ataat--accctttttcctttcgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTA
         | |  | ||||| ||||   |  |  || |    ||        |||   | || |  | |  | |||  |    |  | ||||| |||||||||||| |||||||| || || || ||||||||||| ||| | ||| ||||||||||||||||| | || || |||||||| || |  || | | |||||||
---------gtttgtctgttgtttat-atcattagtgaatcaattaggttgagtagtgttttcatgcagtctacaatctaaatatcattctttc-tttggcagCTGGAATTGTCATAGAGGAGAAAAATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTA

upper sequence: GRMZM2G169773_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S50_114V6.4 (Physcomitrella patens), 3'ss of exon 5
actaattaag--ctaatttgttgcttattgcc-catgctgcagtccttttacctgttaggtctgtcttttaataataataccctttttcctttcgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTA
   ||||  |  ||   || |  | |    |    |  ||  |    ||  |    |    | |  |  || | ||  |  | ||||      | || | ||||||||||| ||||||| || || ||||||||||| ||| | || ||| ||||||| |||||| | || || ||||||   ||    ||     | |||||
---aatttggacctgcattttgacatgccactgtctaatgtggatggttccctacatcaagcaggatggtattgattgtttctttttggtgggctttggtcagCTGGTATTCTCATTGAGGACAAAAATTGGCCACCGTTTGTTCCAATTCTTCATCACGACATTGCTAATGACATACCAGCACATACTCAGCAACTACAGTA

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|148980186|gb|EE026996.2|EE026996
EST:     GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG                         CTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
genomic: GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
EST: gi|211370168|gb|FL333601.1|FL333601
EST:     GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG                         CTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
genomic: GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
EST: gi|211265380|gb|FL345555.1|FL345555
EST:     GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG                         CTGGTATTGTCATTGAAGATAAG
genomic: GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAG
EST: gi|211534447|gb|FL327599.1|FL327599
EST:     GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCCAGAG                         CTGGTATTGTCATTGAAGATAAGA-TTGG
genomic: GAGCTGAAAAGAAAGGAGGAAGCTGCAGCC-AGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGG
EST: gi|76293307|gb|DV032875.1|DV032875
EST:     GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG                         CTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
genomic: GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
EST: gi|211525880|gb|FL340827.1|FL340827
EST:     GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG                         CTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
genomic: GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
EST: gi|211425017|gb|FL340245.1|FL340245
EST:     GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG                         CTGGTATTGTCATTG
genomic: GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTG
EST: gi|211196276|gb|FL364468.1|FL364468
EST:     GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG                         CTGGTATTGTCATTGAAGATAAGAAT
genomic: GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAAT
EST: gi|71429331|gb|DR810381.1|DR810381
EST:     GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG                         CTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
genomic: GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
EST: gi|211537608|gb|FL330675.1|FL330675
EST:     GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG                         CTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
genomic: GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
EST: gi|211231053|gb|FL343819.1|FL343819
EST:     GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG                         CTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
genomic: GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
EST: gi|71449251|gb|DR830301.1|DR830301
EST:     GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG                         CTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
genomic: GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
EST: gi|211012583|gb|FL327130.1|FL327130
EST:     GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG                         CTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
genomic: GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
EST: gi|78115059|gb|DV533447.1|DV533447
EST:     GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG                         CTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
genomic: GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
EST: gi|211067503|gb|FL350735.1|FL350735
EST:     GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG                         CTGGTATTGTCATTGAAGAT
genomic: GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGAT
EST: gi|78077114|gb|DV505548.1|DV505548
EST:     GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG                         CTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
genomic: GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
EST: gi|211146797|gb|FL347631.1|FL347631
EST:     GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAG                         CTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC
genomic: GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTC

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: 40 (upstream exon), 44 (downstream exon)
Score: 38

GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTA


Block sizes: 41 (upstream exon), 46 (downstream exon)
Score: 118

GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 236

GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 96

GAGCTGAAAAGAAAGGAGGAAGCTGCAGCCAGAGgtagattatt ... cgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacctgttaggtctgtcttttaataataataccctttttcctttcgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTA
                  ttttaat  putative branch site (score: 96)
                              taccctttttcctttc  putative PPT
                  ttttaataataatacc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actaattaagctaatttgttgcttattgcccatgctgcagtccttttacctgttaggtctgtcttttaataataataccctttttcctttcgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - tgttgct
- - - - - - - - - - - - - - - - -gctgcag