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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttgaaaactatacctaccattaagttttttgttttcttgaattatgcaacatgtcaaaataaattctcttcttacagtacactaatgacctaac...

Basic information

species Zea mays
transcript GRMZM2G047093_T01
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047093_T01 (Zea mays), 5'ss of exon 21
lower sequence: LOC_Os01g43030.1 (Oryza sativa), 5'ss of exon 21
GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttgaaaactatacctacca-ttaagttttttgttttcttgaattatgcaacatgtcaaaataaattctcttcttacagtacactaatgacctaac
||||| || ||||||||||| ||||||||| |||  || |||||||| ||||||||||| ||| | |||| |||   |  || ||||| | ||  |||   |    | |    | ||  |||||   |||      || | ||   || ||  |  ||
GCAGTCAAGCAGCTCATTAAGTTGGATGAAAATAGCCCTGACAGTCATCGTTGTTTGgtgagtataaaaaatatggttttcacttaagctattcatttgtatattctgtcagtcgtgataaaatttgttcgacctgtaaattatg-tactgtacctac
















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:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|32924622|gb|CF029434.1|CF029434
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|32924627|gb|CF029439.1|CF029439
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|32923660|gb|CF028472.1|CF028472
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|32944990|gb|CF049809.1|CF049809
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|60345123|gb|DN212096.1|DN212096
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|32924181|gb|CF028993.1|CF028993
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAACCAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|32924574|gb|CF029386.1|CF029386
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|32924629|gb|CF029441.1|CF029441
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|32923887|gb|CF028699.1|CF028699
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|32923761|gb|CF028573.1|CF028573
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|60398052|gb|DN230868.1|DN230868
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|60340635|gb|DN207608.1|DN207608
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|31355959|gb|CD440316.1|CD440316
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|67014809|gb|CO443558.1|CO443558
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|33093540|gb|CF053534.1|CF053534
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|60349287|gb|DN216260.1|DN216260
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|32934431|gb|CF039243.1|CF039243
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
EST: gi|32923755|gb|CF028567.1|CF028567
EST:     AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTG                         ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT
genomic: AACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCT

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: 242

GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 222

GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG


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

GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 145

GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttga ... tttttcgcagATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGTTAAACAGCTCATTAAATTGGATGAAGATAATCCAGACAGTCACCGTTGTTTGgtaagtttgaaaactatacctaccattaagttttttgttttcttgaattatgcaacatgtcaaaataaattctcttcttacagtacactaatgacctaac

- - - -  CAGCTC
- - - - - AGCTCA
- - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataaa