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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttccaatagcggaccttgattttcagatccttttttgggtgaattacagccatggaagcaacatggttattgaaaatctatatcttacaagaca...

Basic information

species Zea mays
transcript GRMZM5G823484_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G823484_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os12g13590.2 (Oryza sativa), 5'ss of exon 17
AATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttccaatagcggaccttgattttcagatccttttttgggtgaattacagccatgg--aagcaacatggttattga--aaatctatatcttacaagaca-
||||||||||||||| ||||||||||| ||||||||||||||||| || ||||| ||||| ||||||||||||||||||||||||||||||     | | |  | ||| |   |    |   | |||   |||| ||     |||   || ||| ||  |    ||  | |    |    ||    | | 
AATTGTAGCCTATCTATCTCGTGTTCTCGAGGTTGCATTCAGTGCTCTAGAAGGTCTCAATAAACAGTCCTTTTTGACTGAGCTGgtatgt-----aaatcttaacttcaaaattgtttttatgttttcatgaactaagaatatgagaaaccaatatattacgagattagaatagtgcactattgtatat
















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:     CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG                         GGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
genomic: CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttcc ... gtgcttttagGGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
EST: gi|67013225|gb|CO441974.1|CO441974
EST:     CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG                         GGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
genomic: CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttcc ... gtgcttttagGGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
EST: gi|60356127|gb|DN223100.1|DN223100
EST:     CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG                         GGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
genomic: CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttcc ... gtgcttttagGGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
EST: gi|9566477|gb|BE475986.1|BE475986
EST:     CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG                         GGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
genomic: CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttcc ... gtgcttttagGGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
EST: gi|91878412|gb|EB408369.1|EB408369
EST:     CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG                         GGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
genomic: CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttcc ... gtgcttttagGGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
EST: gi|32802642|gb|CD954878.1|CD954878
EST:     CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG                         GGAAATCGCTTGCATAAGGGGCTGCTTA
genomic: CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttcc ... gtgcttttagGGAAATCGCTTGCATAAGGGGCTGCTTA
EST: gi|37392304|gb|CF633401.1|CF633401
EST:     AAACAGTCC-TTTTGACTNGAGCTG                         GGAAATCGC-TGCATAAAGGGGCTGCTTAATCATTGGCAGAAGTTCACAT
genomic: AAACAGTCCTTTTTGACT-GAGCTGgtatgtttcc ... gtgcttttagGGAAATCGCTTGCAT-AAGGGGCTGCTTAATCATTGGCAGAAGTTCACAT
EST: gi|76012574|gb|DT939744.1|DT939744
EST:     TTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG                         GGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
genomic: TTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttcc ... gtgcttttagGGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
EST: gi|37377535|gb|CF625382.1|CF625382
EST:     GTCCTTTTTGACTGAGCTG                         GGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
genomic: GTCCTTTTTGACTGAGCTGgtatgtttcc ... gtgcttttagGGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
EST: gi|32804847|gb|CD957083.1|CD957083
EST:     CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG                         NGAAATCGCTTGCATAAGGGGCTACTTA
genomic: CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttcc ... gtgcttttagGGAAATCGCTTGCATAAGGGGCTGCTTA
EST: gi|71434510|gb|DR815560.1|DR815560
EST:     CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG                         GGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
genomic: CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttcc ... gtgcttttagGGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
EST: gi|60396240|gb|DN229109.1|DN229109
EST:     CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG                         GGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
genomic: CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttcc ... gtgcttttagGGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
EST: gi|5847426|gb|AW000505.1|AW000505
EST:     CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG                         GGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT
genomic: CATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttcc ... gtgcttttagGGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTT

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: 153

AATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttcc ... gtgcttttagGGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 135

AATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttcc ... gtgcttttagGGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 149

AATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttcc ... gtgcttttagGGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 154

AATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttcc ... gtgcttttagGGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTGgtatgtttccaatagcggaccttgattttcagatccttttttgggtgaattacagccatggaagcaacatggttattgaaaatctatatcttacaagaca

- - - - - - - - - - - - - - - - - - - - - - -  TTGAAG