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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtcgagtgatgggaaatggaatccgctcgctgacttgtgcttagcttataaaataattcatggatggtgacgcgcctaacgtgcgtttgtaatgaacagGAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATCGCTACAAG

Basic information

species Zea mays
transcript AC217401.3_FGT002
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC217401.3_FGT002 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g49610.1 (Oryza sativa), 3'ss of exon 1
agtcgagtgatgggaaatggaatccgctcgctgacttgtgcttagcttataaa--ataattc----atggatggtgacgcgcctaacgtgcgtttgta-atgaacagGAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATCGCTACAAG
      | ||| |  |||    ||  ||   ||  |  |  | |  |  |  |  || ||      |   || |||| |     |  ||   |||    ||||||||| || ||||| | | | |  || ||||||||||| ||||||||||||||||||||||||
-----ggggatag--aatcagctcatctgattggatgatattaaattcgtggatcattatcttaaaaaaaatcgtgatgttgacattgtttttttccggatgaacagGGAATATTGCGGGAAATGGGAATGCAGATGTTACTACAGATGAATATCATCGCTACAAG
















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|211165132|gb|FK981035.1|FK981035
EST:     GTCCGGCGGCCGCGGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCG                         GAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATC
genomic: GTCCGGCGGCCGCGGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCGgtaacacacg ... taatgaacagGAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATC
EST: gi|211165138|gb|FK981041.1|FK981041
EST:     GTCCGGCGGCCGCGGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCG                         GAAAGAT-GCTGAAG
genomic: GTCCGGCGGCCGCGGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCGgtaacacacg ... taatgaacagGAAAGATTGCTGAAG
EST: gi|149081710|gb|EE170863.2|EE170863
EST:     GGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCG                         GAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATC
genomic: GGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCGgtaacacacg ... taatgaacagGAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATC
EST: gi|4753308|gb|AI657213.1|AI657213
EST:     GTCCGGCGGCCGCGGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCG                         GAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATC
genomic: GTCCGGCGGCCGCGGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCGgtaacacacg ... taatgaacagGAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATC
EST: gi|149081712|gb|EE170865.2|EE170865
EST:     GGGCCCTGCATCTGGTATCCCTTCGTCCACACCCCCG                         GAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATC
genomic: GGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCGgtaacacacg ... taatgaacagGAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATC
EST: gi|211165137|gb|FK981040.1|FK981040
EST:     GTCCGGCGGCCGCGGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCG                         GAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATC
genomic: GTCCGGCGGCCGCGGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCGgtaacacacg ... taatgaacagGAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATC
EST: gi|211165135|gb|FK981038.1|FK981038
EST:     GTCCGGCGGCCGCGGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCG                         GAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATC
genomic: GTCCGGCGGCCGCGGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCGgtaacacacg ... taatgaacagGAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATC
EST: gi|211165136|gb|FK981039.1|FK981039
EST:     GTCCGGCGGCCGCGGGCC-TGCATCTGGGATCCCTTCGTCCACACCCCCG                         GAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATC
genomic: GTCCGGCGGCCGCGGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCGgtaacacacg ... taatgaacagGAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATC
EST: gi|211165134|gb|FK981037.1|FK981037
EST:     GTCCGGCGGCCGCGGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCG                         GAAAGAT-GCTGAAGA
genomic: GTCCGGCGGCCGCGGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCGgtaacacacg ... taatgaacagGAAAGATTGCTGAAGA
EST: gi|149014535|gb|EE044169.2|EE044169
EST:     GGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCG                         GAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATC
genomic: GGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCGgtaacacacg ... taatgaacagGAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATC

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: 203

TTCGTCTTCGGGACGGCGACGTCCGCGTACCAGGTCGAGGGCGCGGCGACGTCCGGCGGCCGCGGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCGgtaacacacg ... taatgaacagGAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATCGCTACAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 80

TTCGTCTTCGGGACGGCGACGTCCGCGTACCAGGTCGAGGGCGCGGCGACGTCCGGCGGCCGCGGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCGgtaacacacg ... taatgaacagGAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATCGCTACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 62

TTCGTCTTCGGGACGGCGACGTCCGCGTACCAGGTCGAGGGCGCGGCGACGTCCGGCGGCCGCGGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCGgtaacacacg ... taatgaacagGAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATCGCTACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

TTCGTCTTCGGGACGGCGACGTCCGCGTACCAGGTCGAGGGCGCGGCGACGTCCGGCGGCCGCGGGCCCTGCATCTGGGATCCCTTCGTCCACACCCCCGgtaacacacg ... taatgaacagGAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATCGCTACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttataaaataattcatggatggtgacgcgcctaacgtgcgtttgtaatgaacagGAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATCGCTACAAG
                             gcctaac  putative branch site (score: 134)
     aaaataattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtcgagtgatgggaaatggaatccgctcgctgacttgtgcttagcttataaaataattcatggatggtgacgcgcctaacgtgcgtttgtaatgaacagGAAAGATTGCTGAAGACGCCAACGCAGATGTTACAACAGATGAATATCATCGCTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - -tgatggg
- - - - - - - - - - - - - - cgctgac
- - - - - - - - - - - - - - - - - - tgtgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - attcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatggtg