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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCCAGCAGCATGAAGATCAAGGTGGTCGCTCCTCCAGAGAGGAAGTACAGTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAGgtaaaacaaacaaacaaatttcgcattcgcatttcctcaatcaaggtctgctcacgattttgcttgcgactgcag

Basic information

species Zea mays
transcript GRMZM2G152328_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152328_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g50885.1 (Oryza sativa), 5'ss of exon 3
TCCCAGCAGCATGAAGATCAAGGTGGTCGCTCCTCCAGAGAGGAAGTACAGTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAGgtaaa---acaaacaaacaaatttcgcattcgcatttcctcaatcaag---gtctgctcacgattttgcttgcgactgcag
||| |||||||||||||||||||||||||| ||||| || |||||||||||||||||||| |||||||||||| ||||||| |||||||| ||||||||||||||   |||||   |  ||| | |  |    |  || | ||         | |||| || || ||||||||   |||||
TCCTAGCAGCATGAAGATCAAGGTGGTCGCCCCTCCTGAAAGGAAGTACAGTGTCTGGATTGGAGGATCCATCTTGGCATCTCTCAGCACATTCCAGCAGgtaaatatacaaatgcagcaatgtagtgtgtttacctcatgaacttgatcaatttgcttacaatgttgcttgccgttgcag

upper sequence: GRMZM2G152328_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S337_26V6.1 (Physcomitrella patens), 5'ss of exon 4
TCCCAGC-AGCATGAAGATCAAGGTGGTCGCTCCTCCAGAGAGGAAGTACAGTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAGgtaaaacaaacaaacaaatttcgcattcgcatttcctcaatcaaggtctgct--cacgattttgc-ttgcgactgcag------------------------
  ||| | ||||||||||| |||||||| || || |||||||||||||||||||| ||||| ||||| || ||  ||||||| ||||| |||||||| ||||||   |    | |  |   | || |       | |  ||||    | |  |   ||  |||||| ||    |||||                         
-ACCATCGAGCATGAAGATAAAGGTGGTGGCGCCGCCAGAGAGGAAGTACAGTGTATGGATAGGAGGGTCTATTTTGGCATCTCTCAGTACCTTCCAACAGgtatttcttttatattacagttgcttagttgcatgcataatctgatttttatattacttttttgcattttatctgcattttgacgtgttggggtttttgcag

upper sequence: GRMZM2G152328_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 5'ss of exon 5
TCCCAGC-AGCATGAAGATCAAGGTGGTCGCTCCTCCAGAGAGGAAGTACAGTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAGgtaaaacaaacaaacaaatttcgcattcgcatttc----ctcaatcaaggtctgctcacgattttgcttgcgactgcag----------------------------------------------------------
  ||| | ||||||||||| |||||||| || || |||||||||||||||||||| ||||| ||||| || ||  ||||||| ||||| |||||||| |||||||   |    | |   | ||  | | |||||||     |   |  | |||| |      || |   | | | |||                                                            
-ACCATCGAGCATGAAGATAAAGGTGGTGGCGCCGCCAGAGAGGAAGTACAGTGTATGGATAGGAGGGTCTATTTTGGCATCTCTCAGTACCTTCCAACAGgtaatgtatttga-ctcgtgtctgagttgcatttcgtgtttttttttatgtcttcatgtctttgtttcttcaaatgctcgcgtttgtcgaggctgtaatctttctggaatttaatccgtttacttgttgtggtgcag

upper sequence: GRMZM2G152328_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S372_48V6.1 (Physcomitrella patens), 5'ss of exon 3
TCCCAGCAGCATGAAGATCAAGGTGGTCGCTCCTCCAGAGAGGAAGTACAGTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAGgtaaaacaaacaaaca----aatttcgcattcgcatttcctcaatcaaggtctgctcacgattttgc--ttgcgactgcag-----------------------------------------------------------
 ||    |||||||||||||||||||| || ||||| |||||||||||||| || ||||||||||| |||||| |||||||||||||||||||||||||||||||   |     ||    | ||||    | | |  |  | |||   |  || ||    | || ||  | |  | |  ||                                                           
GCCGTCAAGCATGAAGATCAAGGTGGTGGCGCCTCCGGAGAGGAAGTACAGCGTGTGGATCGGAGGCTCCATCTTGGCATCCCTCAGCACCTTCCAGCAGgtaaactgagtttgcatgatattttctacgttggacgtggtaaatattgaacttcttttcagttagcagtcggaatttgagtatgtttcgagaggttggttaattcggtgtttgcacatattgttctttctgtggtgcag

upper sequence: GRMZM2G152328_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ17401 (Selaginella moellendorffii), 5'ss of exon 3
TCCCAGCAGCATGAAGATCAAGGTGGTCGCTCCTCCAGAGAGGAAGTACAGTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAGgtaaaacaaacaaacaaatttcgcattcgcatttcctcaatcaaggtctgctcacgattttgcttgcgactgcag
||||||||||||||||||||||||||| |||||||| |||||||||||||| |||||||| ||||| || |||||||| || |||||||||||||| ||||||  ||||       | | |     |||  |||| |  ||||   |    |  |  ||| | ||    | |   
TCCCAGCAGCATGAAGATCAAGGTGGTTGCTCCTCCGGAGAGGAAGTACAGCGTCTGGATTGGAGGTTCTATCCTGGCTTCGCTCAGCACCTTCCAACAGgtaccacaac------attcttttgctcgtttttctt--atcagccttgtttttctttttcgtttctcgcag---

upper sequence: GRMZM2G152328_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ35077 (Selaginella moellendorffii), 5'ss of exon 3
TCCCAGCAGCATGAAGATCAAGGTGGTCGCTCCTCCAGAGAGGAAGTACAGTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAGgtaaaacaaacaaacaaatttcgcattcgcatttcctcaatcaaggtctgctcacgattttgcttgcgactgcag
||||||||||||||||||||||||||| |||||||| |||||||||||||| |||||||||||||| || |||||||| || |||||||||||||| ||||||  |||| ||  |   ||| ||       | |  |||  |  | | | ||     ||||  | ||        
TCCCAGCAGCATGAAGATCAAGGTGGTTGCTCCTCCGGAGAGGAAGTACAGCGTCTGGATCGGAGGTTCTATCCTGGCTTCGCTCAGCACCTTCCAACAGgtaccacaa-cattc---ttttgctcgtttttcttatcagccttgtttttctttttctttt-ttcgcag------

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|21330362|gb|BQ485743.1|BQ485743
EST:     GTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAG                         ATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGCCCATCCATCGNCCAC
genomic: GTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAGgtaaaacaaa ... gcgactgcagATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGCCCATCCATCGTCCAC
EST: gi|21331078|gb|BQ486459.1|BQ486459
EST:     GTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAG                         ATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGCCCATCCATCGACCAC
genomic: GTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAGgtaaaacaaa ... gcgactgcagATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGCCCATCCATCGTCCAC
EST: gi|7238178|gb|AW573400.1|AW573400
EST:     GTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAG                         ATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGCCCATCCATCGTCCAC
genomic: GTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAGgtaaaacaaa ... gcgactgcagATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGCCCATCCATCGTCCAC
EST: gi|6095303|gb|AW119970.1|AW119970
EST:     GTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAG                         ATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGNCCATCCATCGTCCAC
genomic: GTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAGgtaaaacaaa ... gcgactgcagATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGCCCATCCATCGTCCAC
EST: gi|21330872|gb|BQ486253.1|BQ486253
EST:     GTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAG                         ATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGCCCATCCATCGTCCAC
genomic: GTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAGgtaaaacaaa ... gcgactgcagATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGCCCATCCATCGTCCAC
EST: gi|32164926|gb|CD670244.1|CD670244
EST:     TGTCTGGATCGGAGGATCCATCCTGGCGATCC-TCAGCACCTTCCAGCAG                         ATGTGGATCGCC
genomic: TGTCTGGATCGGAGGATCCATCCTGGC-ATCCCTCAGCACCTTCCAGCAGgtaaaacaaa ... gcgactgcagATGTGGATCGCC

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: 593

TCCCAGCAGCATGAAGATCAAGGTGGTCGCTCCTCCAGAGAGGAAGTACAGTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAGgtaaaacaaa ... gcgactgcagATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGCCCATCCATCGTCCACAGGAAATGCTTCTAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 94

TCCCAGCAGCATGAAGATCAAGGTGGTCGCTCCTCCAGAGAGGAAGTACAGTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAGgtaaaacaaa ... gcgactgcagATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGCCCATCCATCGTCCACAGGAAATGCTTCTAA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 51

TCCCAGCAGCATGAAGATCAAGGTGGTCGCTCCTCCAGAGAGGAAGTACAGTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAGgtaaaacaaa ... gcgactgcagATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGCCCATCCATCGTCCACAGGAAATGCTTCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1778

TCCCAGCAGCATGAAGATCAAGGTGGTCGCTCCTCCAGAGAGGAAGTACAGTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAGgtaaaacaaa ... gcgactgcagATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGCCCATCCATCGTCCACAGGAAATGCTTCTAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCCAGCAGCATGAAGATCAAGGTGGTCGCTCCTCCAGAGAGGAAGTACAGTGTCTGGATCGGAGGATCCATCCTGGCATCCCTCAGCACCTTCCAGCAGgtaaaacaaacaaacaaatttcgcattcgcatttcctcaatcaaggtctgctcacgattttgcttgcgactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT