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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgaaagcatgcgggttagtattattatacttaactcgctaatttgttgccttctgttgtacatcagctttaattttcgcaatccatctatgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG

Basic information

species Zea mays
transcript GRMZM2G047093_T01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047093_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os01g43030.2 (Oryza sativa), 3'ss of exon 20
gttgaaagcatgcgggttagtattattatact-taactcgctaatttgttgccttctgttgtacatcagcttta-attttcgc---aatccatctatgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG-------------------------------------------
        || |   |  ||||||| |  ||  | | | ||||  || |        |   |   |  | | || ||||  |     |||  ||| || || |||||||| || ||||||||||| ||||||||| |||  || |||||||| |||||||||                                           
-----gcacaagtaaggcagtattaatgaacaatgaatagctatattatcttaaatggacatttctttgttatatatttatgtttttatctttctttgattccagGCAGTCAAGCAGCTCATTAAGTTGGATGAAAATAGCCCTGACAGTCATCGTTGTTTGGTGAGTATAAAAAATATGGTTTTCACTTAAGCTATTCATTTGT

upper sequence: GRMZM2G047093_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os01g43030.1 (Oryza sativa), 3'ss of exon 20
gttgaaagcatgcgggttagtattattatact-taactcgctaatttgttgccttctgttgtacatcagcttta-attttcgca---atccatctatgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG
        || |   |  ||||||| |  ||  | | | ||||  || |        |   |   |  | | || ||||  |     |||  ||| || || |||||||| || ||||||||||| ||||||||| |||  || |||||||| |||||||||
-----gcacaagtaaggcagtattaatgaacaatgaatagctatattatcttaaatggacatttctttgttatatatttatgtttttatctttctttgattccagGCAGTCAAGCAGCTCATTAAGTTGGATGAAAATAGCCCTGACAGTCATCGTTGTTTG
















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|20300007|gb|BQ162950.1|BQ162950
EST:     TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|32924622|gb|CF029434.1|CF029434
EST:     TTTCATNTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|32924627|gb|CF029439.1|CF029439
EST:     TTTCATNTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|32923660|gb|CF028472.1|CF028472
EST:     TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|211305933|gb|FL095827.1|FL095827
EST:     TCATTTGAGCTAAGCATGGAAAAAGCAAAAGGTTTTACTTGNTTTTCCAG                         GCAGTTAAAC-GCTCATTTAAATTTGGATGAA
genomic: TCATTTGAGCTAAGCATG-AGAAAGCAAAAGGTTTTACTTGCTTT-CCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATT-AAATT-GGATGAA
EST: gi|32944990|gb|CF049809.1|CF049809
EST:     TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|60345123|gb|DN212096.1|DN212096
EST:     TTTGAGCT-AGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|32924181|gb|CF028993.1|CF028993
EST:     TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|32924574|gb|CF029386.1|CF029386
EST:     TTTCATNTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|32924629|gb|CF029441.1|CF029441
EST:     TNTCATNTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|32923887|gb|CF028699.1|CF028699
EST:     TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|32923761|gb|CF028573.1|CF028573
EST:     TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|60398052|gb|DN230868.1|DN230868
EST:     TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|60340635|gb|DN207608.1|DN207608
EST:     TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|31355959|gb|CD440316.1|CD440316
EST:     TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|67014809|gb|CO443558.1|CO443558
EST:     TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|33093540|gb|CF053534.1|CF053534
EST:     TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|60349287|gb|DN216260.1|DN216260
EST:     TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|32934431|gb|CF039243.1|CF039243
EST:     TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
EST: gi|32923755|gb|CF028567.1|CF028567
EST:     TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAG                         GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT
genomic: TTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGT

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: 46 (upstream exon), 49 (downstream exon)
Score: 217

CTTGAAGCTTCTGCAGAATAACTCGTCAGACTCATTAGAGACCCATATACTTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 264

CTTGAAGCTTCTGCAGAATAACTCGTCAGACTCATTAGAGACCCATATACTTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 287

CTTGAAGCTTCTGCAGAATAACTCGTCAGACTCATTAGAGACCCATATACTTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 147

CTTGAAGCTTCTGCAGAATAACTCGTCAGACTCATTAGAGACCCATATACTTTCATTTGAGCTAAGCATGAGAAAGCAAAAGGTTTTACTTGCTTTCCAGgtatgttatt ... atgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgccttctgttgtacatcagctttaattttcgcaatccatctatgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG
                       ctttaat  putative branch site (score: 147)
                                              tgttttc  putative PPT
                        tttaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgaaagcatgcgggttagtattattatacttaactcgctaatttgttgccttctgttgtacatcagctttaattttcgcaatccatctatgttttcagGCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - agcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catcagc