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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCACTCGTGAAGAATGTTTTTATTCCTCCGGACTTAGAAGAAGATGGTCTGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCTCCAgtatgttacaaagctatcagctgaattacaaagagttttagacatagacttattgcctaatggtaagatagttaatgggcag

Basic information

species Zea mays
transcript GRMZM2G141735_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141735_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g37120.2 (Oryza sativa), 5'ss of exon 4
TCCACTCGTGAAGAATGTTTTTATTCCTCCGGACTTAGAAGAAGATGGTCTGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCTCCAgtatgttacaaagctatcagctgaattacaaagagttttagacatagacttattgcctaatggtaagatag-ttaatgggcag
|||| | || || |||||||| || ||||| |||  |||||||||||| ||||||||||||||||||||||||||||||||||||| ||||||||| || ||||||||  |   ||| |   |  |||||    | |       |      ||    |||||| ||||||  || ||| ||||
TCCAGTTGTAAAAAATGTTTTCATCCCTCCAGACACAGAAGAAGATGGGCTGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTCTTTTTTGGCCCCTgtatgttatgatattataataagtgttacagtttgctgagtcattttgaacatgtaataatggcaagataaatttatgagcag
















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|91867746|gb|EB399779.1|EB399779
EST:     TGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCTCCA                         GTTGACACATGCAAGGATCAAATTGCTGCTGTCCTGGAGACACTGCGACCT
genomic: TGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCTCCAgtatgttaca ... taatgggcagGTTGACACATGCAAGGATCAAATTGCTGCTGTCCTGGAGACACTGCGACCT
EST: gi|76919350|gb|DV167672.1|DV167672
EST:     TGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCTCCA                         GTTGACACATGCAAGGATCAAATTGCTGCTGTCCTGNAGACACTGCGACCT
genomic: TGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCTCCAgtatgttaca ... taatgggcagGTTGACACATGCAAGGATCAAATTGCTGCTGTCCTGGAGACACTGCGACCT
EST: gi|78089289|gb|DV517663.1|DV517663
EST:     TGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCTCCA                         GTTGACACATGCAAGGATCAAATTGCTGCTGTCCTGNAGACACTGCGACCT
genomic: TGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCTCCAgtatgttaca ... taatgggcagGTTGACACATGCAAGGATCAAATTGCTGCTGTCCTGGAGACACTGCGACCT
EST: gi|148933679|gb|EC877578.2|EC877578
EST:     GCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCTTCC-                         GTTGACACATGCAAGGATCAAATTGCTGC
genomic: GCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCT-CCAgtatgttaca ... taatgggcagGTTGACACATGCAAGGATCAAATTGCTGC
EST: gi|76911768|gb|DV164422.1|DV164422
EST:     TGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCTCCA                         GTTGACACATGCAAGGATCAAATTGCTGCTGTCCTGGAGACACTGCGACCT
genomic: TGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCTCCAgtatgttaca ... taatgggcagGTTGACACATGCAAGGATCAAATTGCTGCTGTCCTGGAGACACTGCGACCT
EST: gi|74242909|gb|DT650823.1|DT650823
EST:     TGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGCCTCC-                         GTTGACACATGCAAGGATCAAATTGCTGCTGTCCTGGAGACACTGCGACCT
genomic: TGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCTCCAgtatgttaca ... taatgggcagGTTGACACATGCAAGGATCAAATTGCTGCTGTCCTGGAGACACTGCGACCT

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: 48

TCCACTCGTGAAGAATGTTTTTATTCCTCCGGACTTAGAAGAAGATGGTCTGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCTCCAgtatgttaca ... taatgggcagGTTGACACATGCAAGGATCAAATTGCTGCTGTCCTGGAGACACTGCGACCTACATCTTCATGGGAGAGAGGGGTTGCTTCTGGGCAGGAAGAGGATACTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 36

TCCACTCGTGAAGAATGTTTTTATTCCTCCGGACTTAGAAGAAGATGGTCTGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCTCCAgtatgttaca ... taatgggcagGTTGACACATGCAAGGATCAAATTGCTGCTGTCCTGGAGACACTGCGACCTACATCTTCATGGGAGAGAGGGGTTGCTTCTGGGCAGGAAGAGGATACTG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 42

TCCACTCGTGAAGAATGTTTTTATTCCTCCGGACTTAGAAGAAGATGGTCTGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCTCCAgtatgttaca ... taatgggcagGTTGACACATGCAAGGATCAAATTGCTGCTGTCCTGGAGACACTGCGACCTACATCTTCATGGGAGAGAGGGGTTGCTTCTGGGCAGGAAGAGGATACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 37

TCCACTCGTGAAGAATGTTTTTATTCCTCCGGACTTAGAAGAAGATGGTCTGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCTCCAgtatgttaca ... taatgggcagGTTGACACATGCAAGGATCAAATTGCTGCTGTCCTGGAGACACTGCGACCTACATCTTCATGGGAGAGAGGGGTTGCTTCTGGGCAGGAAGAGGATACTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCACTCGTGAAGAATGTTTTTATTCCTCCGGACTTAGAAGAAGATGGTCTGCCTGTTGCCCTTGAAGATGCCATGCCCCTACTTTGTTTTTTGGCTCCAgtatgttacaaagctatcagctgaattacaaagagttttagacatagacttattgcctaatggtaagatagttaatgggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG