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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttattgcatttttttgtctatgcagaattttattttggatttctatgcctcttgttagtcaactatcaaagtgattttgacttcaatatcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC

Basic information

species Zea mays
transcript GRMZM2G000393_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000393_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os06g07905.2 (Oryza sativa), 3'ss of exon 8
ttttattgcatttttttgtcta-tgcagaattt--tattttggatttctatgcctcttgttagtcaactatcaaagtgattttgacttcaatatcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
     ||  || ||   |  || |     |||   ||  ||||||| || ||||  ||||||  |    ||  |||  | || ||   |||  ||||||||||||| |||||||||||||||||||| |||||||| |||||||||||||||||
--catttatatattcagggataatatttcattcagtacattggattgctttgccctttgttaacccgtcattgaagccactt-gataccaacttcaatttcagGGGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC

upper sequence: GRMZM2G000393_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA14G14000.1 (Glycine max), 3'ss of exon 8
---ttttattgcatttttttgtctatgcagaattttattttggatttcta--tgcctcttgttagtcaactatcaaagtgattttgacttcaatatcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
    || |||   | | ||| |||||  |   |   || ||| | ||     ||    ||   | |||||||  | ||  || ||   |  | | |   |||||||||  | | ||||||||||||||| |||||||||||||| |||  |||| |
aaagttcattat-tatatttttctataaactttcacatgttgaacttggggttgaggttttggattcaacta--atagccatcttatttggagtgtt--tttcagGGGAAAGCCATGGTATGAACCTGATTGGTGGAAATTTGGGGATGAAAAATC

upper sequence: GRMZM2G000393_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT4G32120.1 (Arabidopsis thaliana), 3'ss of exon 8
ttttattgcatttttttgtctatgcagaattt---tattttggatttc-----tatgcctcttgtt----agtc----aactatcaaagtgattttgacttcaa----------tatcaat-ttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
     | | || || |   ||||    | ||    || ||  ||||||     | || |  |||      ||||    || || ||   | ||| | |  | ||          | |   | ||||||||    ||||||||||| |||||||||||||||||||| ||    ||| |
---gttcgtatattctcaactatcttcagttcacataattgagatttcctagctgtgacaattgcccaaaagtctcataattaacattctcattctcatattaaatgggttgtttcttggtattcagGGGAAGTCAATGGTATGAGCCTGAGTGGTGGAAATTTGGGGACGACAAATC

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|32928477|gb|CF033289.1|CF033289
EST:     ACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGA                         GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
genomic: ACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
EST: gi|32846895|gb|CD986576.1|CD986576
EST:     ACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGA                         GGGCCAACAATGGTATGAACCTGAGTGGTGGAAACTTGGAGATTCAAAAAC
genomic: ACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
EST: gi|211130920|gb|FL136658.1|FL136658
EST:     CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGA                         GGGCCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAA
genomic: CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGG-CCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAA
EST: gi|33091019|gb|CF051013.1|CF051013
EST:     TACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGA                         GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTC-ACCTC
genomic: TACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
EST: gi|74246238|gb|DT654152.1|DT654152
EST:     CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGA                         GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
genomic: CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
EST: gi|32929367|gb|CF034179.1|CF034179
EST:     ACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGA                         GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
genomic: ACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
EST: gi|149005473|gb|EE040028.2|EE040028
EST:     CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGA                         GGGCCACCAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
genomic: CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
EST: gi|24765385|gb|CA400544.1|CA400544
EST:     CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGA                         GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
genomic: CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
EST: gi|50323552|gb|CO518678.1|CO518678
EST:     CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGA                         GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
genomic: CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
EST: gi|5124017|gb|AI745858.1|AI745858
EST:     CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGA                         GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
genomic: CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
EST: gi|21828587|gb|BQ703271.1|BQ703271
EST:     CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGA                         GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
genomic: CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
EST: gi|110200892|gb|EC882789.1|EC882789
EST:     CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGA                         GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
genomic: CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
EST: gi|15082759|gb|BI389443.1|BI389443
EST:     GGGATGGTCATAAGTGAAGA                         GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
genomic: GGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
EST: gi|113703856|gb|EE681360.1|EE681360
EST:     CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGA                         GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
genomic: CAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC

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: 48 (upstream exon), 47 (downstream exon)
Score: 103

CTGGGTTAATTGAGATGCTCGAAGGCCGTCGAGGTAGCCAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

CTGGGTTAATTGAGATGCTCGAAGGCCGTCGAGGTAGCCAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC


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

CTGGGTTAATTGAGATGCTCGAAGGCCGTCGAGGTAGCCAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 291

CTGGGTTAATTGAGATGCTCGAAGGCCGTCGAGGTAGCCAAGGATTGTACATGGGTTGTATGAAATCAGGGATGGTCATAAGTGAAGAgtatgtgctc ... tcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgcctcttgttagtcaactatcaaagtgattttgacttcaatatcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC
                               ttttgac  putative branch site (score: 291)
                                      ttcaatatcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttattgcatttttttgtctatgcagaattttattttggatttctatgcctcttgttagtcaactatcaaagtgattttgacttcaatatcaatttcagGGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - -ttgcatt
- - - - - - - - - -ctatgca