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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccccttatccaaactgcatgaaaagcacagttaacaagccgaattgttggaggatgcagcttcaatcctgcccaatgctgacacctatttggaaatttcattacagGTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG

Basic information

species Zea mays
transcript GRMZM2G141473_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141473_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 7
--gtaccccttatccaaactgc-atgaaaagcacagttaacaagccgaattgttggaggatgcagcttcaatcctgcccaatgctgacacct-atttggaaatttcattacagGTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG
   ||| |  ||  | |||    ||  |||  ||| | | || || |   ||    |  |||||  || ||||        |||  | |  | || || | | |    | ||||||||| | |||||||||||||| ||||| || || || ||||| ||||| || || || || ||||| ||| |||| |||||||||||||| ||||||
gtatacacactacacgaaccctgatccaaattaca-tcagcaggcagctctg----aaaatgcaattttaatcggaaatc-tgcatatatatgatatgaacactgttctccagGTGGAAGTCGATGTGCTGACAGGGGCAACCACCATCCTGAGGAGCGACCTCGTGTATGACTGTGGGCAGAGCCTGAATCCTGCTGTCGACTTAGGCCAG

upper sequence: GRMZM2G141473_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g57680.1 (Oryza sativa), 3'ss of exon 7
---------------------gtaccccttatccaaactgcatgaaaagcacagttaacaagccgaattgttgga----ggatgcagcttcaatcctgcccaatgctgacaccta-tttggaaattt-cattacagGTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG
                      |||   |||    |   ||    |||   || ||  | |||| | ||| ||         | |  ||  || |     || ||   |  |  | | || | ||   || | ||||||||| | ||||||||||| |||| ||| || || || ||||| ||||| || ||||| || ||||| ||| |||| |||||||| ||||||||||||
gtacacactaaagatacccagatacaaattacaacagaagctctgaaaatgcatttgccgagccaatttgctgagcttgatctccttctcaaagctaatgcattgtccatccaaaatctgcacatgaacactccagGTGGAAGTCGATGTGCTGACGGGAGAAACCACCATCCTGAGGAGCGACCTCGTGTACGACTGTGGGCAGAGCCTGAATCCTGCTGTGGACTTGGGCCAG
















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|5361195|gb|AI795615.1|AI795615
EST:     CTATTTAAACTACGGAGCTGGCATTAGTGAG                         GTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTT
genomic: CTATTTAAACTACGGAGCTGGCATTAGTGAGgtacccctta ... ttcattacagGTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTT
EST: gi|17921843|gb|BM259479.1|BM259479
EST:     CGGAGCTGGCATTAGTGAG                         GTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTT
genomic: CGGAGCTGGCATTAGTGAGgtacccctta ... ttcattacagGTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTT
EST: gi|32793565|gb|CD945801.1|CD945801
EST:     TAAACTACGGAGCTGGCATTCGTGAG                         GTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTT
genomic: TAAACTACGGAGCTGGCATTAGTGAGgtacccctta ... ttcattacagGTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTT
EST: gi|17921516|gb|BM259167.1|BM259167
EST:     GGAGCTGGCATTAGTGAG                         GTGGAAATTGATGTGCTGACAGGAGCATCAACAATTCTAAGGAGTGACCTT
genomic: GGAGCTGGCATTAGTGAGgtacccctta ... ttcattacagGTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTT
EST: gi|5005980|gb|AI712042.1|AI712042
EST:     CAGATCCAACTTTCAGAAGCTATTTAAACTACGGAGCTGGCATTAGTGAG                         GTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTT
genomic: CAGATCCAACTTTCAGAAGCTATTTAAACTACGGAGCTGGCATTAGTGAGgtacccctta ... ttcattacagGTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTT
EST: gi|17921574|gb|BM259225.1|BM259225
EST:     TAAACTACGGAGCTGGCATTAGTGAG                         GTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTT
genomic: TAAACTACGGAGCTGGCATTAGTGAGgtacccctta ... ttcattacagGTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTT
EST: gi|5895925|gb|AW037171.1|AW037171
EST:     CAGATCCAACTTTCAGAAGCTATTTAAACTACGGAGCTGGCATTAGTGAG                         GTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTT
genomic: CAGATCCAACTTTCAGAAGCTATTTAAACTACGGAGCTGGCATTAGTGAGgtacccctta ... ttcattacagGTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTT

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: 43 (upstream exon), 41 (downstream exon)
Score: 7

GCAAGTATGGCGAGTGTGAACTTATCGGCACATGCATACTGGACCCCAGATCCAACTTTCAGAAGCTATTTAAACTACGGAGCTGGCATTAGTGAGgtacccctta ... ttcattacagGTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 371

GCAAGTATGGCGAGTGTGAACTTATCGGCACATGCATACTGGACCCCAGATCCAACTTTCAGAAGCTATTTAAACTACGGAGCTGGCATTAGTGAGgtacccctta ... ttcattacagGTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 499

GCAAGTATGGCGAGTGTGAACTTATCGGCACATGCATACTGGACCCCAGATCCAACTTTCAGAAGCTATTTAAACTACGGAGCTGGCATTAGTGAGgtacccctta ... ttcattacagGTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG


Block sizes: 44 (upstream exon), 43 (downstream exon)
Score: 21

GCAAGTATGGCGAGTGTGAACTTATCGGCACATGCATACTGGACCCCAGATCCAACTTTCAGAAGCTATTTAAACTACGGAGCTGGCATTAGTGAGgtacccctta ... ttcattacagGTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatgcagcttcaatcctgcccaatgctgacacctatttggaaatttcattacagGTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG
                        tgctgac  putative branch site (score: 21)
                                            tttcatt  putative PPT
                                         aaatttcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccccttatccaaactgcatgaaaagcacagttaacaagccgaattgttggaggatgcagcttcaatcctgcccaatgctgacacctatttggaaatttcattacagGTGGAAATTGATGTGCTGACAGGAGCAACAACAATTCTAAGGAGTGACCTTGTCTACGATTGCGGGCAAAGCTTGAACCCTGCTGTCGACTTGGGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG