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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcgaaatatttgccaatgttttgatccactccatgaaccattatttatcttggcagagccttgcttcatacatagtgccttactttttattattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT

Basic information

species Zea mays
transcript GRMZM5G823484_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G823484_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g13590.2 (Oryza sativa), 3'ss of exon 18
aatcgaaatatttgccaatgttttgatccactccatgaaccattatttatcttggcagagccttgcttcatacatagtgccttactttttatta----ttgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT
                               ||| ||   |||| |  |  || | |  |  |  |||   | ||  || |  |  |  |||||    ||| ||||||||  ||||| |||||||||| || ||||| || ||||| ||||||||||||||||||||||| || |||||||| ||||| |||||| | |||||
----------------------------gtatccttgtgtcattttgcacattcgaaagggttatcttgtcaaatgctgaccaatgtcctattaatttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAAT
















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|93283185|gb|EB675449.1|EB675449
EST:     TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
genomic: TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
EST: gi|67013225|gb|CO441974.1|CO441974
EST:     TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
genomic: TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
EST: gi|60356127|gb|DN223100.1|DN223100
EST:     TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
genomic: TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
EST: gi|78027269|gb|DV495656.1|DV495656
EST:     AGAAGTTCACATTTAGTCCCAG                         TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
genomic: AGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
EST: gi|9566477|gb|BE475986.1|BE475986
EST:     TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
genomic: TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
EST: gi|4834925|gb|AI670151.1|AI670151
EST:     TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
genomic: TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
EST: gi|91878412|gb|EB408369.1|EB408369
EST:     TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
genomic: TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
EST: gi|9731461|gb|BE510213.1|BE510213
EST:     TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
genomic: TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
EST: gi|37392304|gb|CF633401.1|CF633401
EST:     TGCATAAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
genomic: TGCAT-AAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
EST: gi|9461397|gb|BE453712.1|BE453712
EST:     TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
genomic: TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
EST: gi|76012574|gb|DT939744.1|DT939744
EST:     TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
genomic: TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
EST: gi|6672239|gb|AW282405.1|AW282405
EST:     TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCCCATTTAGTCCCAG                         TGGTGGCCTACGGTTTAAACGTGACATAACTGAATATGGGGATTTCGTTCG
genomic: TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
EST: gi|37377535|gb|CF625382.1|CF625382
EST:     TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
genomic: TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
EST: gi|71434510|gb|DR815560.1|DR815560
EST:     TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCTCAG                         TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
genomic: TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
EST: gi|60396240|gb|DN229109.1|DN229109
EST:     TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
genomic: TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
EST: gi|5847426|gb|AW000505.1|AW000505
EST:     TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG
genomic: TTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCG

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), 47 (downstream exon)
Score: 164

GGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 139

GGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 131

GGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 158

GGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttct ... attattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatcttggcagagccttgcttcatacatagtgccttactttttattattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT
                                 gccttac  putative branch site (score: 158)
                                  ccttactttttatt  CT-rich tract
                                    ttactttttattattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcgaaatatttgccaatgttttgatccactccatgaaccattatttatcttggcagagccttgcttcatacatagtgccttactttttattattgtagTGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - -catgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catacat