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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtagtggaatgaggctggaacccatcaatatcacttgtagagaaggggagcaaattttttattggtcaagattctcatgtaataattttttcctttcagTTGTTGGGAGATATGCTGCTGGATAGATCAAATGTTGCAGTGATGATGCGCTATGTTAGTTCCAAAGACAATCTTATGATTCTGATGAATCTCTTAAGG

Basic information

species Zea mays
transcript GRMZM2G351417_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G351417_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 7
---agtagtggaatgaggctggaacccatcaatatcacttgtagagaaggggagcaaattttttattggtcaagattctcatgtaataattttttcctttcagTTGTTGGGAGATATGCTGCTGGATAGATCAAATGTTGCAGTGATGATGCGCTATGTTAGTTCCAAAGACAATCTTATGATTCTGATGAATCTCTTAAGG
        || ||     |||       |  ||       ||| |   |   |  |  |||| || |  ||   | | | || |  || ||||  || ||||||| |||||||| |||||||| |||||||| ||   | |||| |||||||| ||||||||||| ||||| |||||||||||||| ||||||||||| || 
cttttccttgtaaaagtactgttttattttgatgctgtgagtacact-gtacactatgttttctaattttctgaagt-taatatt-tacttttcccccttcagTTCTTGGGAGACATGCTGCTTGATAGATCCAACTCTACAGTCATGATGCGTTATGTTAGTTCAAAAGATAATCTTATGATTCTCATGAATCTCTTGAGA

upper sequence: GRMZM2G351417_T03 (Zea mays), 3'ss of exon 3
lower sequence: EFJ36360 (Selaginella moellendorffii), 3'ss of exon 7
agtagtggaatgaggctggaacccatcaatatcacttgtagagaaggggagcaaattttttattggtcaagattctcatgtaataattttttcctttcagTTGTTGGGAGATATGCTGCTGGATAGATCAAATGTTGCAGTGATGATGCGCTATGTTAGTTCCAAAGACAATCTTATGATTCTGATGAATCTCTTAAGG
                             ||||| |      ||   |        || || ||| |||     |||     | ||| |||   |   || |  | || |||||||| ||||||| ||||||   |||||||||||||||||||||    || ||||| || |||   ||  ||||||||||  |  ||
----------------------------gtatcaatcactttgagacg-------cttctttttgttca-----ctc-caccaaaatctttgtttgctagCTTCTCGGGGATATGCTCCTGGATAAATCAAACACTGCAGTGATGATGCGCTATGTCGTGTCAAAAGAGAACCTTCGAATCATGATGAATCTTCTGCGG

upper sequence: GRMZM2G351417_T03 (Zea mays), 3'ss of exon 3
lower sequence: EFJ35844 (Selaginella moellendorffii), 3'ss of exon 7
agtagtggaatgaggctggaacccatcaatatcacttgtagagaaggggagcaaattttttattggtcaagattctcatgtaataattttttcctttcagTTGTTGGGAGATATGCTGCTGGATAGATCAAATGTTGCAGTGATGATGCGCTATGTTAGTTCCAAAGACAATCTTATGATTCTGATGAATCTCTTAAGG
                             ||||| |      ||   |        || || ||| |||     |||     | ||| |||   |   || |  | || |||||||| ||||||| ||||||   |||||||||||||||||||||    || ||||| || |||   ||  ||||||||||  |  ||
----------------------------gtatcaatcactttgagacg-------cttctttttgttca-----ctc-caccaaaatctttgtttgctagCTTCTCGGGGATATGCTCCTGGATAAATCAAACACTGCAGTGATGATGCGCTATGTCGTGTCAAAAGAGAACCTTCGAATCATGATGAATCTTCTCCGG

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|149103428|gb|EE288821.2|EE288821
EST:     TAGGTTGCTGTCATCAACCAACTATATAACAAAAAGGGCA-GCTATCAAG                         TTGGTTGGGAGATATGCTGCTGGGATAGAT
genomic: TAGGTTGCTGTCATCAACCAACTATATAACAAAAAGG-CAAGCTATCAAGgtactgctac ... ttcctttcagTTG-TTGGGAGATATGCTGCTGG-ATAGAT




















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: 147

TTTTTTGAAGAATTCAACTCTAGGTTGCTGTCATCAACCAACTATATAACAAAAAGGCAAGCTATCAAGgtactgctac ... ttcctttcagTTGTTGGGAGATATGCTGCTGGATAGATCAAATGTTGCAGTGATGATGCGCTATGTTAGTTCCAAAGACAATCTTATGATTCTGATGAATCTCTTAAGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 268

TTTTTTGAAGAATTCAACTCTAGGTTGCTGTCATCAACCAACTATATAACAAAAAGGCAAGCTATCAAGgtactgctac ... ttcctttcagTTGTTGGGAGATATGCTGCTGGATAGATCAAATGTTGCAGTGATGATGCGCTATGTTAGTTCCAAAGACAATCTTATGATTCTGATGAATCTCTTAAGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 252

TTTTTTGAAGAATTCAACTCTAGGTTGCTGTCATCAACCAACTATATAACAAAAAGGCAAGCTATCAAGgtactgctac ... ttcctttcagTTGTTGGGAGATATGCTGCTGGATAGATCAAATGTTGCAGTGATGATGCGCTATGTTAGTTCCAAAGACAATCTTATGATTCTGATGAATCTCTTAAGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 176

TTTTTTGAAGAATTCAACTCTAGGTTGCTGTCATCAACCAACTATATAACAAAAAGGCAAGCTATCAAGgtactgctac ... ttcctttcagTTGTTGGGAGATATGCTGCTGGATAGATCAAATGTTGCAGTGATGATGCGCTATGTTAGTTCCAAAGACAATCTTATGATTCTGATGAATCTCTTAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggggagcaaattttttattggtcaagattctcatgtaataattttttcctttcagTTGTTGGGAGATATGCTGCTGGATAGATCAAATGTTGCAGTGATGATGCGCTATGTTAGTTCCAAAGACAATCTTATGATTCTGATGAATCTCTTAAGG
                                      taattttttcctttc  CT-rich tract
                          attctcatgtaataat  TA-rich tract