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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcctgaatttatctatagagtttttttgttctgaaaatgaacacttcactttcaattgattgtttatgccattatctattcatttttttttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCA

Basic information

species Zea mays
transcript GRMZM5G836910_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g55420.1 (Oryza sativa), 3'ss of exon 7
gtcctgaatttatctatagagtttttttgttctgaaaatgaacact-tcactttcaattgattgtttatgccattatc-tattcatttttttttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCA
| | |||| |||| | || | | | | | | | | | |||| || ||| ||| || | |||| |||| | | || ||| ||||||| || || || |||||||||||||| |||||||| |||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||
cttgtctgttta-ctattgttaattgtcaattttctgtttactattgttaatttctatgtgttgagtattggtttgtgatattgatttgtgtgtc-caatagGCTGCCCCAGATGGATCTTTTGTTCTGCTGCATGGTTGCGCTCACAACCCAACTGGAATAGACCCAACTCCGGAACAATGGGAGAAAATTGCAGATGTCA

upper sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA14G13480.1 (Glycine max), 3'ss of exon 7
-gtcctgaatttatctatagagtttt-tttgttctgaaaatgaacacttcactttcaattgattgtttatgccat-tatctattcatttttttttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCA
| | | || || | | | |||| | | || | ||||| | | | | | | || | | ||||| | | ||| | ||||| ||||| |||||| | | || ||||| |||||||| ||||| ||||| || || ||||| |||||||||||||| ||||| || ||||| |
agacgtacataggaacatgaattctcatttgatttaaaggt---tccttcaatccaatataaaattgaacaatgcctaattgtacatttctacattttttcagTCAGCTCCGGAAGGATCTTTTATCTTACTTCATGGATGTGCTCATAACCCTACTGGTATCGATCCAACACCTGAACAGTGGGAAAAAATAGCTGATGTAA

upper sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 8
gtcctgaatttatctatagagtttttttgttctgaaaatgaacacttcactttcaattgattgtttatgccattatctattcatttttttttcaca---acagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCA
| ||| | | | ||| | | | | ||| ||| || | || |||| | | | | | | | | || | | | | ||||| ||||| ||||| || || | |||| || || ||||||||||||||||||||||| |||||||| || |||||||||| |||||||| |||||||
-tactgtctgtgtg-ataaaacgagtacttgtttaaagacaacgtgaaaccct-gatggattataatggttaatcttgaatttctgttatgtaaaatgtacagGAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGGATGTGCTCACAACCCAACTGGAATTGACCCAACACCAGAACAGTGGGTAAAAATTGCTGATGTCA

upper sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 9
gtcctgaatttatctatagagtttttttgttctgaaa--atgaacacttc-actttcaattgattgtttatgccattatctattcatttttttttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCA
| || || | | | | | ||||| | | || || ||| | | |||| | | || || |||| ||||| ||||| || || ||||| |||||||| |||| ||||| |||||||||||||||||||| || || |||||||||||||||||||| || ||||| |||||||
---caaaagtttgttcttgcttggtattgtttcaatataattttcatttccaggctaaattcacttctttaattcaagagagtttatttatttttgtttccagGCAGCCCCAGAAGGATCTTTTGTGTTGCTTCATGGCTGTGCTCACAACCCAACTGGTATTGATCCAACTCCTGAACAGTGGGAAAAGATTGCTGATGTCA

upper sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S245_98V6.1 (Physcomitrella patens), 3'ss of exon 7
gtcctgaat-ttatctatagagtttttttgtt--ctgaaaatgaacacttcactttcaattgattgtttatgccattatctattcatttttttttcaca--acagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCA
|| | || | |||| | | || | || | | | || | | | | | ||| | || | || | | | | || || ||||||||||| || | |||| ||||| ||||| |||||||||||||| |||||||| || || || || |||||||| || || || | |
-----gagtgttgttctgagagaagtcgtattagcagagatttagcagtaccagggccgtgaggttgttactttactaaggacaatattgtgtatgatgttgtagAACGCACCTGAAGGTTCAATTATCTTGCTGCATGGGTGTGCACACAACCCAACTGGCATAGACCCTACACCCGAGCAATGGGAGAAGATCGCCGACCTTA

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|32845644|gb|CD985325.1|CD985325
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGATATTGAG                         GCTGCTCCTGAAGGATCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|26557436|gb|CA829671.1|CA829671
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAG                         GCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|32863795|gb|CF003477.1|CF003477
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGATATTGAG                         GCTGCTCCTGAAGGATCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|32802835|gb|CD955071.1|CD955071
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGATATTGAG                         GCTGCTCCTGA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGA
EST: gi|5342983|gb|AI795288.1|AI795288
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGATATTGAG                         GCTGCTCCTGAAGGATCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|32844188|gb|CD983869.1|CD983869
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGATATTGAG                         GCTGCTCCTGAAGGATCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|32921476|gb|CF026288.1|CF026288
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAG                         GCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|13515691|gb|BG517967.1|BG517967
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAG                         GCTGCTCCTGAAGGNTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|32926958|gb|CF031770.1|CF031770
EST:     ATTTTGAGGGAATGATAGCTGATATTGAG                         GCTGCTCCTGAAGGATCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
genomic: ATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|32920753|gb|CF025565.1|CF025565
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAG                         GCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|149107658|gb|EE189537.2|EE189537
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGGATGATAGCTGACATTGAG                         GCTGCTCCCTGA-GGTTCCTTTG
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCC-TGAAGGTTCTTTTG
EST: gi|32925729|gb|CF030541.1|CF030541
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGATATTGAG                         GCTGCTCCTGAAGGATCTTTTGTTCTGCTACACGGTTGTGCTCACAACCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|32921723|gb|CF026535.1|CF026535
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAG                         GCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|13150003|gb|BG320325.1|BG320325
EST:     ACCCCAAGACTGTT-GGKTGGATTTTGAGGGAATGATAGCTGACATTGAG                         GCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGG-TGTGCTCACAACCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|32843163|gb|CD982844.1|CD982844
EST:     CAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGATATTGAG                         GCTGCTCCTGAAGGATCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
genomic: CAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|32921739|gb|CF026551.1|CF026551
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGGGGGAATGATAGCTGACATTGAG                         GCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|32788347|gb|CD940583.1|CD940583
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGATATTGAG                         GCTGCTCCTGAAGG
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGG
EST: gi|32925063|gb|CF029875.1|CF029875
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGATATTGAG                         GCTGCTCCTGAAGGATCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|32925965|gb|CF030777.1|CF030777
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGATATTGAG                         GCTGCTCCTGAAGGATCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|78114229|gb|DV532618.1|DV532618
EST:     ACCCCTAGACTGTTGGGTTGGATTTTGAGGGGATGATAGCTGACATTGAG                         GCTGCTCCTGAAGGTTCTTTTTGT-CTGCTACATGGT
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTT-GTTCTGCTACATGGT
EST: gi|149000841|gb|EE038069.2|EE038069
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAG                         GCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACACCCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|32925664|gb|CF030476.1|CF030476
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGATATTGAG                         GCTGCTCCTGAAGGATCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|91056033|gb|EB166451.1|EB166451
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAG                         GCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
EST: gi|26557367|gb|CA829602.1|CA829602
EST:     ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAG                         GCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA
genomic: ACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCA

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: 101

GAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACCGGTATTATGACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 480

GAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACCGGTATTATGACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

GAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACCGGTATTATGACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 308

GAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACCGGTATTATGACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGCTGACATTGAGgtacttggat ... ttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcactttcaattgattgtttatgccattatctattcatttttttttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCA
         aattgat  putative branch site (score: 308)
 ttatctattcattttt  putative PPT
 attatctattcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcctgaatttatctatagagtttttttgttctgaaaatgaacacttcactttcaattgattgtttatgccattatctattcatttttttttcacaacagGCTGCTCCTGAAGGTTCTTTTGTTCTGCTACATGGTTGTGCTCACAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- cctgaat
- - - - - - - - - - - - - -tgttctg
- - - - - - - - - - - - - - - - - - - - - cacttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccatt