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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTGACATGGGTGGTGGTACATGGGAACGTGATACTGTTGTTCGTGCTCTACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagttttatgttaactttattattttatcaatgcattgcagcttcattctgcctctgatgtgttcatttgtttcttttattttctgaaaaacatgctg...

Basic information

species Zea mays
transcript GRMZM2G035417_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035417_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os06g15360.1 (Oryza sativa), 5'ss of exon 6
TCTTGACATGGGTGGTGGTACATGGGAACGTGATACTGTTGTTCGTGCTCTACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagttttatgtt-aactttattattttatcaatgca--ttgcagcttcattctgcctctgatgtgttcatttgtttcttttat-tttctgaaaaacatgctg
|||||||||||||||||| || ||||||||||| |  ||||| |||||| | ||||||||||| || ||||| ||||||||||| ||||| ||||||||||||||||  | |||  |   | |  ||| |  ||||||  || |        |  |    ||      ||||||       |||| ||| | || |  ||    
TCTTGACATGGGTGGTGGCACCTGGGAACGTGACATGGTTGTCCGTGCTTTGCGTGCTGCATATAACAACCCTGAGAGAGCTATTGACTATCTGTATTCTgtaagttccacgtttgataatttcttttcacaaatgcacatttctatgctgatggggaattggaaaactcatttaaagaacttatgtttttaaagagaat----

upper sequence: GRMZM2G035417_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S58_148V6.4 (Physcomitrella patens), 5'ss of exon 6
TCTTGACATGGGTGGTGGTACATGGGAACGTGATACTGTTGTTCGTGCTCTACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagttttatgttaactttattattttatcaatgca--ttgcagcttcattctgcctctgatgtgttcatttgtttcttttattttctgaaaaacatgctg
| | || |||||||| ||||  ||||| ||||| ||||| || |||||  |||||||||||| ||| || |||||| ||||| | || ||| | ||||||||||||      ||| | || |     | | || | |  |||  | |      ||        | ||   ||     ||   || |  |||   | ||    
TATGGATATGGGTGGGGGTAGCTGGGATCGTGACACTGTAGTGCGTGCATTACGTGCTGCATTCAACAATCCCGAGCGAGCTGTGGAGTACTTATATTCTgtaagtgcacgcttatcattctgtaactgtaaacgaaatttgtggatattgaatgatatattcgagtaacttcacacctcagatgtattgagtcatatat--
















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|60356802|gb|DN223775.1|DN223775
EST:     TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCT                         GGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
genomic: TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
EST: gi|211524990|gb|FL195258.1|FL195258
EST:     TACGTGCTGCATACAATAACCCTGAGAGAGCTATAGACTACCTGTATTCT                         GGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
genomic: TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
EST: gi|5932681|gb|AW057042.1|AW057042
EST:     TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCT                         GGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
genomic: TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
EST: gi|71448259|gb|DR829309.1|DR829309
EST:     TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCT                         GGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
genomic: TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
EST: gi|78121958|gb|DV540342.1|DV540342
EST:     TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCT                         GGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
genomic: TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
EST: gi|120480604|gb|EH210908.1|EH210908
EST:     TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCT                         GGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
genomic: TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
EST: gi|211521980|gb|FL195242.1|FL195242
EST:     TACGTGCTGCATACAATAACCCTGAGAGAGCTATAGACTACCTGTATTCT                         GGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
genomic: TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
EST: gi|78107573|gb|DV525991.1|DV525991
EST:     TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCT                         GGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
genomic: TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
EST: gi|33102654|gb|CF062614.1|CF062614
EST:     TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCT                         GGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
genomic: TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
EST: gi|33095687|gb|CF055681.1|CF055681
EST:     TACGTGCTGCATACAATAACCCTGAGAGAGCTATAGACTACCTGTATTCT                         GGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
genomic: TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
EST: gi|33091803|gb|CF051797.1|CF051797
EST:     TACGTGCTGCATACAATAACCCTGAGAGAGCTATAGACTACCTGTATTCT                         GGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
genomic: TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
EST: gi|91876714|gb|EB406671.1|EB406671
EST:     TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCT                         GGAATTCCTGAGAATGTGGAGGCTCAGCCCTGT-GCCCGAGCACCTGCTGC
genomic: TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTGAGAATGTGGAGGCTCAGCC-TGTTGCCCGAGCACCTGCTGC
EST: gi|74244160|gb|DT652074.1|DT652074
EST:     TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCT                         GGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
genomic: TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCT
EST: gi|76908411|gb|DV162927.1|DV162927
EST:     TACGTGCTGCATACCATAACCCCGAGAGAGCTATAGACTACCTGTATTCT                         GGAATTC-TGGAGAAATGTGGAGGCTCAGCCTGTTGC
genomic: TACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTG-AGAA-TGTGGAGGCTCAGCCTGTTGC

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: 388

TCTTGACATGGGTGGTGGTACATGGGAACGTGATACTGTTGTTCGTGCTCTACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCTGGCCAACAAACAAATCAGCAGGCCGCATCACCCGCTCAGCCAGCAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 559

TCTTGACATGGGTGGTGGTACATGGGAACGTGATACTGTTGTTCGTGCTCTACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCTGGCCAACAAACAAATCAGCAGGCCGCATCACCCGCTCAGCCAGCAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 552

TCTTGACATGGGTGGTGGTACATGGGAACGTGATACTGTTGTTCGTGCTCTACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCTGGCCAACAAACAAATCAGCAGGCCGCATCACCCGCTCAGCCAGCAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 424

TCTTGACATGGGTGGTGGTACATGGGAACGTGATACTGTTGTTCGTGCTCTACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagtttta ... ttcctggtagGGAATTCCTGAGAATGTGGAGGCTCAGCCTGTTGCCCGAGCACCTGCTGCTGGCCAACAAACAAATCAGCAGGCCGCATCACCCGCTCAGCCAGCAGTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTGACATGGGTGGTGGTACATGGGAACGTGATACTGTTGTTCGTGCTCTACGTGCTGCATACAATAACCCCGAGAGAGCTATAGACTACCTGTATTCTgtaagttttatgttaactttattattttatcaatgcattgcagcttcattctgcctctgatgtgttcatttgtttcttttattttctgaaaaacatgctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaaca