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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagggacattttcctgaggcccattgatctttttttagtagcgcttgcctgtccttggcagcttgtgctgtatcgcgcttcggagttgccttttgctactgagccatatcatatcacacacatatatatcatctggctcgtcacgctcctccccttgcgacgctgatgtggaaacgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGATGCAAAAACACGTGGGGAAGCTACGAGTGCGGCTGCAGCGGGGGCCTGCT

Basic information

species Zea mays
transcript GRMZM2G347541_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G347541_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 9
gtaagggacattttcctgaggcccattgatctttttttagtagcgcttgcctgtccttggcagcttgtgctgtatcgcgcttcggagttgccttttgctactgagccatatcatatcacacacatatatatcatctggctcgtcacgctcctccccttgcgacgctgatgtggaa--acgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGATGCAAAAACACGTGGGGAAGCTACGAGTGCGGCTGCAGCGGGGGCCTGCT
                         |     |   |||   | | ||   | |   ||||     |||||| |  |   || |  || |     ||  || |||        |||||||   || ||| | |      || ||   || | |  ||    |   |||||||| ||      | || |||| |||||||||| |||||||||||||  ||||||||| | ||||||| |||||| ||||| ||||||||||| || ||||| ||||| || ||| ||||
------------------------gtaagaatcgatttgtgaaccctgttcagctgttgga----tgtgct-tgccatcctgcaaagcttgtagtt-ttagtgaa-------atatcacttgca-atacacc------cttgttgtgcacttgaccccttg-tactgatgtgaaatattttgtgaaagATATTGATGAATGCAAGGAAAGGACTGCATGCCAGTGCAAGGAATGCAAATGCAAGAACACATGGGGAAGCTATGAATGCGGTTGCAGTGGCGGCTTGCT

upper sequence: GRMZM2G347541_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 9
gtaagggacattttcctgaggcccattgatctttttttagtagcgcttgcctgtccttggcagcttgtgctgtatcgcgcttcggagttgccttttgctactgagccatatcatatcacacacatatatatcatctggctcgtcacgctcctccccttgcgacgctgatgtggaa--acgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGATGCAAAAACACGTGGGGAAGCTACGAGTGCGGCTGCAGCGGGGGCCTGCT
                         |     |   |||   | | ||   | |   ||||  |    |||  |   ||         |||   |||  || |||        |||||||   || ||| | |      || ||   || | |  ||    |   |||||||| ||        || |||| |||||||||| |||||||||||||  ||||||||| | ||||| | |||||| ||||| ||||||||||| |||||||| ||||| || ||| ||||
------------------------gtaagaatcgatttgtgaaccctgttcagctgttggatgtacttgccatcctgca----aagcttgtagttt--tagtgaa-------atatcacttgca-atacacc------cttgttgtgcacttgaccccttg-tactgatgtgaaatattttatgaaagATATTGATGAATGCAAGGAAAGGACTGCATGCCAGTGCAAGGAATGTAAATGCAAGAACACATGGGGAAGCTATGAGTGCGGTTGCAGTGGCGGCTTGCT
















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|149112915|gb|EE295714.2|EE295714
EST:     CTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAG                         ATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT
genomic: CTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAGgtaagggaca ... cgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT
EST: gi|32935750|gb|CF040562.1|CF040562
EST:     CTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAG                         ATATTGATGAATGTAAGGAAAGGACTGCGTGCCAGTGCGAAGAATGCAGAT
genomic: CTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAGgtaagggaca ... cgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT
EST: gi|67021468|gb|CO450217.1|CO450217
EST:     CTGCAGATGCCCTGACGGACTCAAGGGTGATGGCAAGCACAAATGTGAAG                         ATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT
genomic: CTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAGgtaagggaca ... cgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT
EST: gi|33099496|gb|CF059456.1|CF059456
EST:     CTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAG                         ATATTGATGAATGTAAGGAAAGGACTGCGTGCCAGTGCGAAGAATGCAGAT
genomic: CTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAGgtaagggaca ... cgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT
EST: gi|211224453|gb|FL435606.1|FL435606
EST:     CTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAG                         ATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT
genomic: CTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAGgtaagggaca ... cgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT
EST: gi|71423918|gb|DR806180.1|DR806180
EST:     TGGCAAGCACAAATGTGAAG                         ATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT
genomic: TGGCAAGCACAAATGTGAAGgtaagggaca ... cgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT
EST: gi|67028179|gb|CO456928.1|CO456928
EST:     GCAGATGCCCTGACGNGACTCA-GGGTGATGGCAAGCANCAA-TGTGAAG                         ATGTTGATGAATGTAANGAAAGGACTGTGTGCCANTGCGAAAAATGCA
genomic: GCAGATGCCCTGACG-GATTCAAGGGTGATGGCAAGCA-CAAATGTGAAGgtaagggaca ... cgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCA
EST: gi|76292778|gb|DV032346.1|DV032346
EST:     CTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAG                         ATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT
genomic: CTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAGgtaagggaca ... cgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT
EST: gi|76288308|gb|DV027876.1|DV027876
EST:     CTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAG                         ATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT
genomic: CTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAGgtaagggaca ... cgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT
EST: gi|50336834|gb|CO531960.1|CO531960
EST:     ACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAG                         ATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT
genomic: ACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAGgtaagggaca ... cgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT
EST: gi|211301945|gb|FL333154.1|FL333154
EST:     CTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAG                         ATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT
genomic: CTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAGgtaagggaca ... cgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGAT

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: 256

GATGATGGCTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAGgtaagggaca ... cgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGATGCAAAAACACGTGGGGAAGCTACGAGTGCGGCTGCAGCGGGGGCCTGCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 120

GATGATGGCTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAGgtaagggaca ... cgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGATGCAAAAACACGTGGGGAAGCTACGAGTGCGGCTGCAGCGGGGGCCTGCT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 67

GATGATGGCTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAGgtaagggaca ... cgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGATGCAAAAACACGTGGGGAAGCTACGAGTGCGGCTGCAGCGGGGGCCTGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

GATGATGGCTGCAGATGCCCTGACGGATTCAAGGGTGATGGCAAGCACAAATGTGAAGgtaagggaca ... cgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGATGCAAAAACACGTGGGGAAGCTACGAGTGCGGCTGCAGCGGGGGCCTGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctggctcgtcacgctcctccccttgcgacgctgatgtggaaacgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGATGCAAAAACACGTGGGGAAGCTACGAGTGCGGCTGCAGCGGGGGCCTGCT
                               cgctgat  putative branch site (score: 232)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagggacattttcctgaggcccattgatctttttttagtagcgcttgcctgtccttggcagcttgtgctgtatcgcgcttcggagttgccttttgctactgagccatatcatatcacacacatatatatcatctggctcgtcacgctcctccccttgcgacgctgatgtggaaacgcgcgacagATGTTGATGAATGTAAGGAAAGGACTGTGTGCCAGTGCGAAGAATGCAGATGCAAAAACACGTGGGGAAGCTACGAGTGCGGCTGCAGCGGGGGCCTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG