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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgttttatcattgaattcctattgcaagttgtagtgttgatgccgatggtggtccgcatgctcacgcgtttaattgctgtttggggatgctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG

Basic information

species Zea mays
transcript GRMZM2G086805_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086805_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g43060.1 (Oryza sativa), 3'ss of exon 1
gtgttttatcattgaattcctattgcaagttgtagtgttgatgccgatggtggtccgcatgctcacgcgtttaattgctgtttgg-----ggatgctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG
   |||    |||| ||     |   || ||  ||| |||||  || ||||| |     ||||   || ||   ||  |   ||      | |||   ||  ||||||| |||| | |||||||| |||||||| || || || ||||| || || |||||||||||||||||||||||||||||||||||||| ||
---tttagggattgtatcttcgtgagaaatt--agttttgatttcgttggtgtttttgctgctgctgctttatttttttccctgataaccgtatggattgcacagTTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGG
















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|7844125|gb|AW787328.1|AW787328
EST:     CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAG                         TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
genomic: CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
EST: gi|211373132|gb|FL346967.1|FL346967
EST:     CCGAGCHGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAG                         TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
genomic: CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
EST: gi|211388869|gb|FL452911.1|FL452911
EST:     TGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAG                         TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
genomic: TGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
EST: gi|37378989|gb|CF626218.1|CF626218
EST:     CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAG                         TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
genomic: CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
EST: gi|4730597|gb|AI649763.1|AI649763
EST:     CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAG                         TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
genomic: CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
EST: gi|32943412|gb|CF048231.1|CF048231
EST:     CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAG                         TTCAGGGAG-ATTTTTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
genomic: CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
EST: gi|37375940|gb|CF624458.1|CF624458
EST:     CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAG                         TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
genomic: CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
EST: gi|91869839|gb|EB400567.1|EB400567
EST:     CCGAGCTGCGCGCCTGCCTCCGATCCCGCCTCGTCAAGACCTACGACCAG                         TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
genomic: CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
EST: gi|45847108|gb|CN071051.1|CN071051
EST:     CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTGCGGCCAG                         TTCAGGGAGAACGGCTGCGAAAAACTGCCCGTTTCTAGAGATGGACAGAGA
genomic: CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCG-AAAACTGCCCGTTTCTAGAGATGGACAGAGA
EST: gi|60339603|gb|DN206576.1|DN206576
EST:     CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAG                         TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
genomic: CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
EST: gi|211528033|gb|FL311002.1|FL311002
EST:     CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAG                         TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
genomic: CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
EST: gi|60398153|gb|DN230969.1|DN230969
EST:     CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAG                         TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
genomic: CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
EST: gi|211342808|gb|FL351909.1|FL351909
EST:     CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAG                         TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
genomic: CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
EST: gi|60351934|gb|DN218907.1|DN218907
EST:     CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAG                         TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
genomic: CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
EST: gi|32857871|gb|CD997552.1|CD997552
EST:     CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGGCCTACGACCAG                         TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
genomic: CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
EST: gi|7844126|gb|AW787329.1|AW787329
EST:     CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAG                         TTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG
genomic: CCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAG

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: 322

GGACGATGAAGAGAGGGTGGGCCATGCGGAGATCCCGACCAGTTTCGGTCCCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 246

GGACGATGAAGAGAGGGTGGGCCATGCGGAGATCCCGACCAGTTTCGGTCCCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 357

GGACGATGAAGAGAGGGTGGGCCATGCGGAGATCCCGACCAGTTTCGGTCCCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

GGACGATGAAGAGAGGGTGGGCCATGCGGAGATCCCGACCAGTTTCGGTCCCGAGCTGCGCGCCTGCCTCCGATGCCGCCTCGTCAAGACCTACGACCAGgtaccctcct ... ctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatggtggtccgcatgctcacgcgtttaattgctgtttggggatgctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG
                        tttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttttatcattgaattcctattgcaagttgtagtgttgatgccgatggtggtccgcatgctcacgcgtttaattgctgtttggggatgctgtgtgcagTTCAGGGAGAACGGCTGCGAAAACTGCCCGTTTCTAGAGATGGACAGAGAGCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - -ctattgc
- - - - - - - - - - - - - - - - - - - tgatgcc
- - - - - - - - - - - - - - - - - - - - - - -gatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgtt