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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtttgctagtgccactgcattttaaatagacctaactaccaattggtagtgcttaactctaacaggattcctttgtatatatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG

Basic information

species Zea mays
transcript GRMZM5G845755_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G845755_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 8
gtgtttgctagtgccactgc----------attttaaatagacctaactaccaattg-gtagtgcttaactctaacaggattcctttgtatatatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG
|| ||| | |||||| || |          ||   ||||  ||||| ||  || |   ||| |  |    |  |||| |||| |||| | ||| |   |||||||| |||||||| ||||||||| | || |||||||| ||||| || |||||||||||||||||||||
gtattt-ccagtgccccttcttcagaggttatcacaaatgtaccta-ctgtcattaaagtattaatggttttcaacatgatttcttt-tctatgt---tagGCCATCGATTTCCTTGACAAGCTTCTTCGCTATGATCACCAGGATAGACTTACTGCACGTGAAGCTATG

upper sequence: GRMZM5G845755_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 8
------gtgtttgctagtgccactg-cattttaaatagac---ctaactaccaattggtagtgcttaactctaacaggattcctttgtatatatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG
        | ||| ||||    |    | || || ||  |    ||  ||     | ||  |  ||   | |     ||||      | |   | || ||||  |||||||| | ||||||||| |||| ||||| ||||| || |||||||||||  | |||||||||
attctgtcgattgttagtcgtgcaaatacttcaattacgcactttagttagttccttgttttatttttatttttggtgattgtgccatgtgcctatgcagGCAGTAGATTTCTTGGACAAGCTTCTGCGGTATGACCATCAAGAAAGGCTTACTGCCAGGGAAGCTATG
















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|6465600|gb|AW191195.1|AW191195
EST:     CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG                         GCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
genomic: CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
EST: gi|5846756|gb|AI999839.1|AI999839
EST:     CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG                         GCCATAGATTTCCTCGACAAGCTTTTGCGTTAT
genomic: CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTAT
EST: gi|32846294|gb|CD985975.1|CD985975
EST:     CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG                         GCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
genomic: CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
EST: gi|194717129|gb|FK934282.1|FK934282
EST:     CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG                         GCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
genomic: CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
EST: gi|29945847|gb|CB815850.1|CB815850
EST:     CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG                         GCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
genomic: CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
EST: gi|94476026|gb|EB704984.1|EB704984
EST:     CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG                         GCCATAGATTTCCTCGCCAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
genomic: CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
EST: gi|31359089|gb|CD443446.1|CD443446
EST:     CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG                         GCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
genomic: CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
EST: gi|60354727|gb|DN221700.1|DN221700
EST:     CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG                         GCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
genomic: CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
EST: gi|32849734|gb|CD989415.1|CD989415
EST:     CCTGGACAAAGTTTATTAATACAGACAACCAACACCTAGTGTCTCATGAG                         GCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
genomic: CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
EST: gi|60345260|gb|DN212233.1|DN212233
EST:     CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG                         GCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
genomic: CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
EST: gi|4609748|gb|AI600587.1|AI600587
EST:     CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG                         GCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
genomic: CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
EST: gi|60350778|gb|DN217751.1|DN217751
EST:     CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG                         GCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
genomic: CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
EST: gi|61117731|gb|DN558692.1|DN558692
EST:     CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG                         GCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
genomic: CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
EST: gi|61117730|gb|DN558691.1|DN558691
EST:     CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG                         GCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
genomic: CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
EST: gi|61117732|gb|DN558693.1|DN558693
EST:     CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG                         GCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
genomic: CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
EST: gi|61117733|gb|DN558694.1|DN558694
EST:     CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAG                         GCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
genomic: CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
EST: gi|148990947|gb|EE032376.2|EE032376
EST:     CCTGGACAAAGTTTATTAATGCAGACAACCAACCCCTAGTGTTTCATGAG                         GCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT
genomic: CCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTT

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: 324

GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 170

GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 170

GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCTAGTGTCTCATGAGgtgtttgcta ... atatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactaccaattggtagtgcttaactctaacaggattcctttgtatatatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG
                       ctctaac  putative branch site (score: 170)
                                      tttgtatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtttgctagtgccactgcattttaaatagacctaactaccaattggtagtgcttaactctaacaggattcctttgtatatatctgtagGCCATAGATTTCCTCGACAAGCTTTTGCGTTATGATCATCAGGACAGGCTTACTGCACGTGAAGCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC