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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgatacttccttgcttactatctgtttgtccatttgtcgtaattattgctctctgcgtgggcag

Basic information

species Zea mays
transcript GRMZM2G133885_T01
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133885_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g72940.1 (Oryza sativa), 5'ss of exon 18
TTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgatacttcct--tgcttacta-----tctg------tttgtccatttgtcgtaattat-tgctctctgcgtgggcag---------------------------
||||| |||||| | ||||||||||| ||||| ||||||||||| |||||||||| ||  | ||  ||  |||| ||||     |||       || | | |    ||  ||||   ||| |  |   |                                 
TTTGGATATTTCGCTTTTGGAGGGAGCACAGTAATATGCGTCTTTGAGAAGgttt-ctatttctcgcttctgctgactaaaacatctagccgaattcgactacacatccaaattccatgcaccttatctatttctcaaattgtatcattcttttcatgacag
















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|5922429|gb|AW055718.1|AW055718
EST:     TTGGGTATTTCTCCTTTGGAGGGAGCCCAGTGATATGCGTCTTCGAGAAG                         GACGCCATCCAATTTGACGCTGATCT
genomic: TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgat ... gcgtgggcagGACGCCATCCAATTTGACGCTGATCT
EST: gi|6194556|gb|AW146660.1|AW146660
EST:     TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTTGAGAAG                         GACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
genomic: TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgat ... gcgtgggcagGACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
EST: gi|6021540|gb|AW066468.1|AW066468
EST:     TTGGGTATTTCTCCTTTGGAGGGAGCACAGTGATATGCGTCTTCGAGAAG                         GACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
genomic: TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgat ... gcgtgggcagGACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
EST: gi|37361294|gb|CF602583.1|CF602583
EST:     TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG                         GACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
genomic: TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgat ... gcgtgggcagGACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
EST: gi|32912653|gb|CF017465.1|CF017465
EST:     TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG                         GACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
genomic: TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgat ... gcgtgggcagGACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
EST: gi|33770671|gb|CF272965.1|CF272965
EST:     TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG                         GACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
genomic: TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgat ... gcgtgggcagGACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
EST: gi|32913231|gb|CF018043.1|CF018043
EST:     TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG                         GACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
genomic: TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgat ... gcgtgggcagGACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
EST: gi|211196234|gb|FL472452.1|FL472452
EST:     TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG                         GACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
genomic: TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgat ... gcgtgggcagGACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
EST: gi|32849096|gb|CD988777.1|CD988777
EST:     ACAGTGATATGCGTCTTCGAGAAG                         GACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
genomic: ACAGTGATATGCGTCTTCGAGAAGgtttgctgat ... gcgtgggcagGACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
EST: gi|60396723|gb|DN229588.1|DN229588
EST:     TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG                         GACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
genomic: TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgat ... gcgtgggcagGACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
EST: gi|78103985|gb|DV522403.1|DV522403
EST:     TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTTTTCGAGAAG                         GACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
genomic: TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgat ... gcgtgggcagGACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
EST: gi|40302877|gb|CK347264.1|CK347264
EST:     TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG                         GACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG
genomic: TTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgat ... gcgtgggcagGACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTG

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: 68

TTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgat ... gcgtgggcagGACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTGGAGACCCTTGTTTCTGTTGGTATGACCCTGGGCATCTCGACAAGGAACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 83

TTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgat ... gcgtgggcagGACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTGGAGACCCTTGTTTCTGTTGGTATGACCCTGGGCATCTCGACAAGGAACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 103

TTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgat ... gcgtgggcagGACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTGGAGACCCTTGTTTCTGTTGGTATGACCCTGGGCATCTCGACAAGGAACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 80

TTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgat ... gcgtgggcagGACGCCATCCAATTTGACGCTGATCTCGTGGCAAACAGCGAAAGGTCACTGGAGACCCTTGTTTCTGTTGGTATGACCCTGGGCATCTCGACAAGGAACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAGgtttgctgatacttccttgcttactatctgtttgtccatttgtcgtaattattgctctctgcgtgggcag

- - - - - - - - TTGGAG
- - - - - - - -  TGGAGG