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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttaacttccatgctcattcatgtttatcgtcacatgtctcgtgcttgcgacgctctttgttcactcactcatcacctgattattttactaagcttcccttaaagcttgatttgcaattcgccatttcttagGTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACTCTTCTTGGTGACAG

Basic information

species Zea mays
transcript GRMZM2G011893_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011893_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv16s0050g01140.t01 (Vitis vinifera), 3'ss of exon 3
gtatgcttaacttccatgctcattcatgtttatcgtcac-atgtctcgtgcttgcgacgctctttgttcactcactcatcacctgattattttactaagcttcccttaaagcttgatttgcaattcgccatttcttagGTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACTCTTCTTGGTGACAG
                   |   | |||||| | |||||  ||     |||||| || |   | | |||         | | |    | ||||| |        || |||| ||  ||    ||||   || |   |||||  || |   ||  ||||||| |    |   |||||||| |||||||||||||||||||| ||
-------------------tttgtgatgtttttagtcactgtgagaattgcttgagatgtaatatattc-------tgttatccagctgttttaat--------ctaaaagtttctttc---attctgtatgtac-agGTTGAGGCTCTTCAGAAAATGGATGATTCTTATTTTGGAGAGGGTTTAACTCTTCTTGGTGAAAG
















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|37425230|gb|CF650352.1|CF650352
EST:     TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA                         GTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACT
genomic: TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAAgtatgcttaa ... catttcttagGTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACT
EST: gi|18964079|gb|BM660797.1|BM660797
EST:     TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA                         GTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACT
genomic: TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAAgtatgcttaa ... catttcttagGTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACT
EST: gi|19057799|gb|BM736466.1|BM736466
EST:     TCTTCAGTTCGAAAGGGTGAGCTTCAGACCGGAAAA                         GTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGGTTAACT
genomic: TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAAgtatgcttaa ... catttcttagGTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACT
EST: gi|211421218|gb|FL403241.1|FL403241
EST:     TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA                         GTTTTGGTTAACCACCAAATGGACGGAGATGTGTTT
genomic: TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAAgtatgcttaa ... catttcttagGTTTTGGTTAACCACCAAATGGACGGAGATGTGTTT
EST: gi|8383251|gb|BE056194.1|BE056194
EST:     TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA                         GTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACT
genomic: TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAAgtatgcttaa ... catttcttagGTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACT
EST: gi|211087671|gb|FL396338.1|FL396338
EST:     TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA                         GTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACT
genomic: TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAAgtatgcttaa ... catttcttagGTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACT
EST: gi|71446780|gb|DR827830.1|DR827830
EST:     TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA                         GTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACT
genomic: TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAAgtatgcttaa ... catttcttagGTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACT
EST: gi|149102642|gb|EE287999.2|EE287999
EST:     TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA                         GTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACT
genomic: TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAAgtatgcttaa ... catttcttagGTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACT
EST: gi|78122304|gb|DV540688.1|DV540688
EST:     TCTTCAGTTCAAAAGGTTGATCTTCAGACCGGAAAA                         GTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTATCT
genomic: TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAAgtatgcttaa ... catttcttagGTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACT

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: 42 (upstream exon), 47 (downstream exon)
Score: 74

TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAAgtatgcttaa ... catttcttagGTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACTCTTCTTGGTGACAG


Block sizes: 36 (upstream exon), 46 (downstream exon)
Score: 71

TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAAgtatgcttaa ... catttcttagGTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACTCTTCTTGGTGACAG


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 82

TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAAgtatgcttaa ... catttcttagGTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACTCTTCTTGGTGACAG


Block sizes: 36 (upstream exon), 46 (downstream exon)
Score: 47

TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAAgtatgcttaa ... catttcttagGTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACTCTTCTTGGTGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattattttactaagcttcccttaaagcttgatttgcaattcgccatttcttagGTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACTCTTCTTGGTGACAG
                                            ccatttctt  CT-rich tract
     attttactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttaacttccatgctcattcatgtttatcgtcacatgtctcgtgcttgcgacgctctttgttcactcactcatcacctgattattttactaagcttcccttaaagcttgatttgcaattcgccatttcttagGTTTTGGTTAACCACCAAATGGACGGAGATGTGTTTGGAGAAGGTTTAACTCTTCTTGGTGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA