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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcaaccgtctcatgctgcagtgccacaattgctgaacctgattgtgtctgactgtcttctgaccattcaaaatcaattaatcaaatatcctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTA

Basic information

species Zea mays
transcript GRMZM2G032267_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032267_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 7
----tttcaaccgtctcatgctgcagtgccacaattgctgaacctgat-tgtgtctgactgtcttctgaccattcaaaatcaattaatcaaatatcctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTA
     |    | ||  ||| ||||  ||| |    |     |  || | |   |||   |||  | |||        | | | ||      |  |    |  |||||||||||||| || ||||||||||| ||||||||||| ||||| |||||||||||||||||||||||||||||||| |||||||| |||||||||||||
ccttgtggggcagtgccatactgccatgctatttctctactatatggtataaatcttgatgtggtttgattt-----agttacttgtgaggaactttaatcgcagGTCCACATGTTAGACATTGAATGCTTCTCTTATCTTAATCGTGCTTTGGAGAGCCCATTATCACCAATTGTGATACTTGCTACGAACAGAGGAATATGTA

upper sequence: GRMZM2G032267_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 7
--tttcaaccgtctcatgctgcagtgccacaat-tgctgaacctgattgtgtctgactgtcttctgacc-attcaaaatcaattaatcaaatatcctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTA
  | | |    | |  | ||   || | || || || |  |    | | ||||| | |||  | |||   | | |      |||  |   |  |    || |||||||||||| | |||||||||||||| ||||||||||| |||||  ||||||||||||||||||||||||||||||| || || ||||||||||||||||
tgtataacttatttattactattgttctactatatggtaga----aatatgtcttaatgttgtttgatttaattacttattattgttaggaactttaattgcagGTCCACATGCTAGATATTGAATGCTTCTCTTATCTTAATCGTGCTCTGGAGAGCCCATTATCACCAATTGTGATACTTGCGACAAATAGAGGAATATGTA
















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|60342617|gb|DN209590.1|DN209590
EST:     TCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG                         GTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
genomic: TCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtatatcatt ... cctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
EST: gi|74241474|gb|DT649388.1|DT649388
EST:     TCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG                         GTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
genomic: TCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtatatcatt ... cctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
EST: gi|32842037|gb|CD981718.1|CD981718
EST:     ACCTGGTGTTTTGTTCATTGATGAG                         GTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
genomic: ACCTGGTGTTTTGTTCATTGATGAGgtatatcatt ... cctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
EST: gi|21331671|gb|BQ487052.1|BQ487052
EST:     TTGTACCTGGTGTTTTGTTCATTGATGAG                         GTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
genomic: TTGTACCTGGTGTTTTGTTCATTGATGAGgtatatcatt ... cctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
EST: gi|87157723|gb|DY402512.1|DY402512
EST:     TCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG                         GTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
genomic: TCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtatatcatt ... cctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
EST: gi|26559755|gb|CA831990.1|CA831990
EST:     CGACGAAGGAATCGCAGAGCTTGTACCTGNG-GTTTTGTTCATTGATGAG                         GTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
genomic: CGACGAAGGAATCGCAGAGCTTGTACCTG-GTGTTTTGTTCATTGATGAGgtatatcatt ... cctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
EST: gi|32840485|gb|CD980166.1|CD980166
EST:     ACCTGGTGTTTTGTTCATTGATGAG                         GTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
genomic: ACCTGGTGTTTTGTTCATTGATGAGgtatatcatt ... cctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
EST: gi|60356915|gb|DN223888.1|DN223888
EST:     TCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG                         GTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
genomic: TCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtatatcatt ... cctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
EST: gi|78103432|gb|DV521860.1|DV521860
EST:     TCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG                         GTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
genomic: TCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtatatcatt ... cctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
EST: gi|32842224|gb|CD981905.1|CD981905
EST:     ACCTGGTGTTTTGTTCATTGATGAG                         GTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG
genomic: ACCTGGTGTTTTGTTCATTGATGAGgtatatcatt ... cctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAG

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), 49 (downstream exon)
Score: 194

GTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtatatcatt ... cctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 66

GTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtatatcatt ... cctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 70

GTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtatatcatt ... cctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 82

GTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAGgtatatcatt ... cctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtctgactgtcttctgaccattcaaaatcaattaatcaaatatcctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTA
                                          tatcctttttc  CT-rich tract
                         aaaatcaattaatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcaaccgtctcatgctgcagtgccacaattgctgaacctgattgtgtctgactgtcttctgaccattcaaaatcaattaatcaaatatcctttttcagGTCCACATGTTGGATATTGAATGCTTTTCTTATCTTAACCGTGCATTGGAGAGCCCATTATCACCAATTGTGATACTCGCTACGAATAGAGGAATATGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA