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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACACCACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAGgtgcgcgagtggtgtggcccttcttcttttgtcctcgcattgcctgtgaatccgcgatcctctgcgactgacgtctgtggctgtggctgtggtttcag

Basic information

species Zea mays
transcript GRMZM2G152135_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152135_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g48880.1 (Oryza sativa), 5'ss of exon 5
ATACACCACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAGgtgcgcgagtggtgtggcccttcttcttttgtcctcgcattgcctgtg---aatccgcgatcctctgcgactgacgtctgtg-gctgtggctgtggtttcag-----------------------
|||||||||| |||||||||||  ||||| ||||||||||| || || ||||| |||||||| || |||||   |  | | | | | |||      | || ||||   | | |  ||          |||   ||  ||  | ||      | | |||                        
ATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGACCCAAGgtgcgtgactggtgc--ctatgcatttgtcgtctatatgt-gcttgtgaccagtacatgacaaagcaatcctggtttccttgtaccgtcttctcgatctcaacgtgtgtgtggtcgtgcgtgcag
















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|211131936|gb|FL382998.1|FL382998
EST:     ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAG                         GAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
genomic: ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAGgtgcgcgagt ... gtggtttcagGAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
EST: gi|15554267|gb|BI644265.1|BI644265
EST:     ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAG                         GAGCTGGAGGAGGTTGGTGGCC-GGACGAGCTTGTTAGCAGTCCGGTGAGT
genomic: ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAGgtgcgcgagt ... gtggtttcagGAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
EST: gi|211378788|gb|FL471300.1|FL471300
EST:     ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAG                         GAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
genomic: ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAGgtgcgcgagt ... gtggtttcagGAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
EST: gi|149204930|gb|ES700526.1|ES700526
EST:     ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAG                         GAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
genomic: ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAGgtgcgcgagt ... gtggtttcagGAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
EST: gi|211485805|gb|FL428178.1|FL428178
EST:     ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAG                         GAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
genomic: ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAGgtgcgcgagt ... gtggtttcagGAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
EST: gi|211047719|gb|FL481049.1|FL481049
EST:     CATGGACAAGTTCGGCGGCGTCCCGTATTGGGCTCTTCCTGGGACCAAAG                         GAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTTGTTAGCAGTCCGGTGAG
genomic: CATGGACAAGTTCGGCGGCGTCCCGTA-TGGGCTCTTCCTGGGACCAAAGgtgcgcgagt ... gtggtttcagGAGCTGGAGGAGGTTGGTGGCCTGGACGAGC-TTGTTAGCAGTCCGGTGAG
EST: gi|18181362|gb|BM382572.1|BM382572
EST:     ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAG                         GAGCTGAAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
genomic: ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAGgtgcgcgagt ... gtggtttcagGAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
EST: gi|211354968|gb|FL469254.1|FL469254
EST:     ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAG                         GAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
genomic: ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAGgtgcgcgagt ... gtggtttcagGAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
EST: gi|148929072|gb|EC874391.2|EC874391
EST:     ACATGGACAAGTTCGGCGGGGTCCCGTATGGGCTCTTCCTGGGACCAAAG                         GAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
genomic: ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAGgtgcgcgagt ... gtggtttcagGAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
EST: gi|194717072|gb|FK934225.1|FK934225
EST:     ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAG                         GAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
genomic: ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAGgtgcgcgagt ... gtggtttcagGAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
EST: gi|211070680|gb|FL369853.1|FL369853
EST:     ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAG                         GAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT
genomic: ACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAGgtgcgcgagt ... gtggtttcagGAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGT

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 1 RNA-Seqlibrary.


Block sizes: 46 (upstream exon), 24 (downstream exon)
Score: 3

ATACACCACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAGgtgcgcgagt ... gtggtttcagGAGCTGGAGGAGGTTGGTGGCCTGGACGAGCTTGTTAGCAGTCCGGTGAGTGAAGCTACTGATACTGAAGACGCAGGAGAAGAAAAGACGCGTCCAGTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACACCACATGGACAAGTTCGGCGGCGTCCCGTATGGGCTCTTCCTGGGACCAAAGgtgcgcgagtggtgtggcccttcttcttttgtcctcgcattgcctgtgaatccgcgatcctctgcgactgacgtctgtggctgtggctgtggtttcag

- - - - CATGGA