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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACTgtaagtttgaatatttggttcatttttaggtatcattgtatgaaaaaggtgctgatgtttatgacttatgagtaactcttgttagtattaaatgatgaat...

Basic information

species Zea mays
transcript GRMZM2G701689_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G701689_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g41230.2 (Oryza sativa), 5'ss of exon 5
GCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACTgtaagtt----tgaatatttggttcatttttaggtatcattgtatg-aaaaaggtgctgatgtttatgacttatgagtaactcttgttagtattaaatgatgaat
 || ||||| || | |||||||||||| || |||||||||||||| ||||||||||| |||||| |||| |||||||||    |  |  ||   |||    ||   | ||||  |||| || |||      | ||| ||      |||  |||   |     ||||   || |    
ACACAAGTTCGACAATGGTGATGGCACGTCGTGCAAGCGTTGTAGCTGTAAGAAGTCAAAATGCTTGAAGCTgtaagttgttctacaccttcttttctcaattgtttctcataatatgcaacaagccaaccaggttaattcagagtgaa-aacatgtcaagatattggttggt----

upper sequence: GRMZM2G701689_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA20G28740.2 (Glycine max), 5'ss of exon 3
GCATAAGTTTGA--TAG-TGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACTgtaagtttgaatatttggttcatttttaggtatcattgtatga-----aaaaggtgctgatgtttatgacttatgagtaactcttgttagtattaaatgatgaat
||  ||||| ||   || ||| || ||    || ||||||||||||| ||||||||| || |||||  |||| |||||||||| || |     | |  ||||   |    ||| |  |     | | | |||    |  | ||| || |   ||  |  | ||| ||  || || |  | 
GCGCAAGTTGGAACCAGCTGGGGAAGGGGAGTCTTGCAAGCGTTGTAATTGTAAGAAATCAAAATGTTTGAAGCTgtaagtttaaagaaacactccccttttgttttgggttggaatactatcatatgttgcaatggcctttgattttta--tagtttcttttacta--aactgtttta-
















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|87156415|gb|DY401204.1|DY401204
EST:     GGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACT                         TTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG
genomic: GGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACTgtaagtttga ... tttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG
EST: gi|26559555|gb|CA831790.1|CA831790
EST:     TCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACT                         TTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG
genomic: TCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACTgtaagtttga ... tttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG
EST: gi|31359966|gb|CD444323.1|CD444323
EST:     GGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACT                         TTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG
genomic: GGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACTgtaagtttga ... tttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG
EST: gi|31349638|gb|CD433995.1|CD433995
EST:     GGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACT                         TTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG
genomic: GGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACTgtaagtttga ... tttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG
EST: gi|32932451|gb|CF037263.1|CF037263
EST:     GGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACT                         TTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG
genomic: GGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACTgtaagtttga ... tttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG
EST: gi|31357841|gb|CD442198.1|CD442198
EST:     GGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACT                         TTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG
genomic: GGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACTgtaagtttga ... tttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG
EST: gi|19351662|gb|BM896194.1|BM896194
EST:     GGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACT                         TTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG
genomic: GGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACTgtaagtttga ... tttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG
EST: gi|76915167|gb|DV165860.1|DV165860
EST:     GGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACT                         TTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG
genomic: GGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACTgtaagtttga ... tttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG
EST: gi|22715536|gb|BU197816.1|BU197816
EST:     CTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACT                         TTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG
genomic: CTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACTgtaagtttga ... tttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTG

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: 432

GCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACTgtaagtttga ... tttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTGTATCGGCTGTATGAACAACCAGAGTCATACGGAAACTGTTCTATCTACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 310

GCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACTgtaagtttga ... tttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTGTATCGGCTGTATGAACAACCAGAGTCATACGGAAACTGTTCTATCTACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 481

GCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACTgtaagtttga ... tttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTGTATCGGCTGTATGAACAACCAGAGTCATACGGAAACTGTTCTATCTACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 308

GCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACTgtaagtttga ... tttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTGTATCGGCTGTATGAACAACCAGAGTCATACGGAAACTGTTCTATCTACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATAAGTTTGATAGTGGTGATGGCACTTCATGCAAGCGTTGTAGTTGTAAGAAGTCCAAATGCCTGAAACTgtaagtttgaatatttggttcatttttaggtatcattgtatgaaaaaggtgctgatgtttatgacttatgagtaactcttgttagtattaaatgatgaat

- - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgaaaaa