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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAGgttagttgcaaatgcaatgtgccttttgcacccatcaagcagcatcaatgccatgctatgaacattttattatccagtgcttgattcctatctgtttaatgtggtag

Basic information

species Zea mays
transcript GRMZM2G079256_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079256_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os09g10600.1 (Oryza sativa), 5'ss of exon 6
GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAGgttagttgcaa-atgcaatgtgc-cttttgcacccatcaagcagcatcaatgccatgctatgaacattttattatccagtgctt---gattcctatct---gtttaatgtggtag----------
||||||||||||||||| ||||||||| |||||||||||||||||||||| || ||||  ||||  | |   |  |   ||     ||     |    ||       | ||  | |   || | |  | ||      |||| | |    |  |||| ||              
GTTAAAGCAAACAAAAGGTATGCTGGATCTTCAAACTGGACTGTTAAGgtaagctgcagtatgccttttttgccatattacttggaaatagatacttgtgaaccatgaggattactaatttgtacgatcctcccaagttccaacccaaggcctaatctgtctttatttcatag
















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|60345537|gb|DN212510.1|DN212510
EST:     GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG                         GAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTA
genomic: GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAGgttagttgca ... aatgtggtagGAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTA
EST: gi|32907240|gb|CF012053.1|CF012053
EST:     GTTAAAGCACACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAA                         GAAGTTGTTGAGA
genomic: GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAGgttagttgca ... aatgtggtagGAAGTTGTTGAGA
EST: gi|78076466|gb|DV504900.1|DV504900
EST:     GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG                         GAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCTTTGTA
genomic: GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAGgttagttgca ... aatgtggtagGAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTA
EST: gi|32908286|gb|CF013099.1|CF013099
EST:     GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG                         GAAGTTGTTGAGA
genomic: GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAGgttagttgca ... aatgtggtagGAAGTTGTTGAGA
EST: gi|67011703|gb|CO440452.1|CO440452
EST:     GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG                         GAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTA
genomic: GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAGgttagttgca ... aatgtggtagGAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTA
EST: gi|87156317|gb|DY401106.1|DY401106
EST:     GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG                         GAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTA
genomic: GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAGgttagttgca ... aatgtggtagGAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTA
EST: gi|32911684|gb|CF016496.1|CF016496
EST:     GCTAAAGCAAACAAAAGATATGCTGGNAGCTTCAAACTGGACTGTTAAG                         C
genomic: GTTAAAGCAAACAAAAGATATGCTGG-AGCTTCAAACTGGACTGTTAAGgttagttgca ... aatgtggtag-
EST: gi|32911684|gb|CF016496.1|CF016496
EST:     GCTAAAGCAAACAAAAGATATGCTGGNAGCTTCAAACTGGACTGTTAAG                         C
genomic: GTTAAAGCAAACAAAAGATATGCTGG-AGCTTCAAACTGGACTGTTAAGgttagttgca ... aatgtggtag-
EST: gi|71332949|gb|DR803501.1|DR803501
EST:     GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG                         GAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTA
genomic: GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAGgttagttgca ... aatgtggtagGAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTA
EST: gi|211314447|gb|FL116841.1|FL116841
EST:     AAAGCAAACNAAAAGAAATGCTGGGAGCTTCAAACTGGACCTGGTTAAAG                         GAAGTTGTTGA
genomic: AAAGCAAAC-AAAAGATATGCTGG-AGCTTCAAACTGGAC-TG-TTAA-Ggttagttgca ... aatgtggtagGAAGTTGTTGA
EST: gi|22819573|gb|BU499663.1|BU499663
EST:     GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG                         GAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCT
genomic: GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAGgttagttgca ... aatgtggtagGAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCT
EST: gi|31356068|gb|CD440425.1|CD440425
EST:     GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG                         GAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTA
genomic: GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAGgttagttgca ... aatgtggtagGAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTA
EST: gi|211312415|gb|FL116823.1|FL116823
EST:     GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG                         GAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTA
genomic: GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAGgttagttgca ... aatgtggtagGAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTA

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), 48 (downstream exon)
Score: 242

GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAGgttagttgca ... aatgtggtagGAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTACACTCTCTCGCCAACGGTCCTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 143

GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAGgttagttgca ... aatgtggtagGAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTACACTCTCTCGCCAACGGTCCTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 77

GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAGgttagttgca ... aatgtggtagGAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTACACTCTCTCGCCAACGGTCCTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 156

GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAGgttagttgca ... aatgtggtagGAAGTTGTTGAGACTGTAAAGAATGACTTTGGTAGCATTGATATCCTTGTACACTCTCTCGCCAACGGTCCTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAGgttagttgcaaatgcaatgtgccttttgcacccatcaagcagcatcaatgccatgctatgaacattttattatccagtgcttgattcctatctgtttaatgtggtag

- - AAGCAA
- - - - - - - - -  ATGCTG
- - - - - - - - - -  GCTGGA
- - - - - - - - - - - - GGAGCT
- - - - - - - - - - - -  GAGCTT