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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgatctaattaaacttctttagacagttgactgcctttctatgtagatttacatattcccttgcttgtttaacaacttttggaaaacttgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTGGTGGTGGCCTAGGTGTTCCAAATGCTCCTAATG

Basic information

species Zea mays
transcript GRMZM2G127101_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127101_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g03920.1 (Oryza sativa), 3'ss of exon 6
cttgatctaattaaacttctttagacagttgactgcctttctatgtagatttacatattcccttgcttgtttaacaacttttggaaa-acttgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTGGTGGTGGCCTAGGTGTTCCAAATGCTCCTAATG
 ||    |  | ||   |   |||    |    ||    |  ||  | ||| |  ||      |  |  |   || |||| ||  |  |||| ||| | |||||||   ||||||||||   |||||| ||||||||| ||||| |||||||||||||||||||||||||| | ||| || ||||
tttagattgttgaattattgatagtatatattttggtgcttcattgaaattaatttagaatact-ttaatggcacgacttatgagagtactttaatgccagGCAATACTAACCTCAACAATCTGATGAGCATGTTCAGTGGGCTCGGTGCTGGTGGTGGCCTAGGTGTTCCTAGTGCACCCAATG
















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|76916495|gb|DV166414.1|DV166414
EST:     GGAGCGGACACAATCAGGCTCTGGTGCAG                         GCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
genomic: GGAGCGGACACAATCAGGCTCTGGTGCAGgtatctcctg ... tgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
EST: gi|211253494|gb|FL469932.1|FL469932
EST:     GGAGCGGACACAATCAGGCTCTGGTGCAG                         GCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
genomic: GGAGCGGACACAATCAGGCTCTGGTGCAGgtatctcctg ... tgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
EST: gi|211119111|gb|FL479446.1|FL479446
EST:     GGAGCGGACACAATCAGGCTCTGGTGCAG                         GCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
genomic: GGAGCGGACACAATCAGGCTCTGGTGCAGgtatctcctg ... tgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
EST: gi|31351028|gb|CD435385.1|CD435385
EST:     GGAGCGGACACAATCAGGCTCTGGTGCAG                         GCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
genomic: GGAGCGGACACAATCAGGCTCTGGTGCAGgtatctcctg ... tgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
EST: gi|78107355|gb|DV525773.1|DV525773
EST:     GGAGCGGACACAATCAGGCTCTGGTGCAG                         GCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
genomic: GGAGCGGACACAATCAGGCTCTGGTGCAGgtatctcctg ... tgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
EST: gi|148983365|gb|EE029351.2|EE029351
EST:     GGAGCGGACACAATCAGGCTTTGGTGCAG                         GCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
genomic: GGAGCGGACACAATCAGGCTCTGGTGCAGgtatctcctg ... tgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
EST: gi|31352246|gb|CD436603.1|CD436603
EST:     GGAGCGGACACAATCAGGCTCTGGTGCAG                         GCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
genomic: GGAGCGGACACAATCAGGCTCTGGTGCAGgtatctcctg ... tgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
EST: gi|86468765|gb|DY235135.1|DY235135
EST:     GGAGCGGACACAATCAGGCTCTGGTGCAG                         GCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
genomic: GGAGCGGACACAATCAGGCTCTGGTGCAGgtatctcctg ... tgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
EST: gi|67019053|gb|CO447802.1|CO447802
EST:     GGAGCGGACACAATCAGGCTCTGGTGCAG                         GCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
genomic: GGAGCGGACACAATCAGGCTCTGGTGCAGgtatctcctg ... tgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
EST: gi|149094648|gb|EE180187.2|EE180187
EST:     GGAGCGGACACAATCAGGCTCTGGTGCAG                         GCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
genomic: GGAGCGGACACAATCAGGCTCTGGTGCAGgtatctcctg ... tgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
EST: gi|4804587|gb|AI665610.2|AI665610
EST:     GGAGCGGACCCAATCAGGCTCTGGTGCAG                         GCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG
genomic: GGAGCGGACACAATCAGGCTCTGGTGCAGgtatctcctg ... tgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTG

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: 156

GGAGCGGACACAATCAGGCTCTGGTGCAGgtatctcctg ... tgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTGGTGGTGGCCTAGGTGTTCCAAATGCTCCTAATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 194

GGAGCGGACACAATCAGGCTCTGGTGCAGgtatctcctg ... tgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTGGTGGTGGCCTAGGTGTTCCAAATGCTCCTAATG


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

GGAGCGGACACAATCAGGCTCTGGTGCAGgtatctcctg ... tgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTGGTGGTGGCCTAGGTGTTCCAAATGCTCCTAATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 170

GGAGCGGACACAATCAGGCTCTGGTGCAGgtatctcctg ... tgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTGGTGGTGGCCTAGGTGTTCCAAATGCTCCTAATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagatttacatattcccttgcttgtttaacaacttttggaaaacttgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTGGTGGTGGCCTAGGTGTTCCAAATGCTCCTAATG
                       gtttaac  putative branch site (score: 170)
     ttacatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgatctaattaaacttctttagacagttgactgcctttctatgtagatttacatattcccttgcttgtttaacaacttttggaaaacttgaatcctagGCAATGTCAACCTCAACACCTTGATGAACATGTTCAGCGGGCTTGGTGCTGGTGGTGGCCTAGGTGTTCCAAATGCTCCTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - -tgactgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaact