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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcacggtgtgagtcatccatgttttgactatgttgatctgtgcaataaaatgcaattatagcttcgaaaactacagaggcctatatcatattttttcagGTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG

Basic information

species Zea mays
transcript GRMZM2G180863_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180863_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S152_123V6.1 (Physcomitrella patens), 3'ss of exon 5
gtcacggtgtgagtcatccatgttttgactatgttgatctgtgcaa-taaaatgcaatta--tagcttcgaaaacta--cagaggccta--tatcatattttttcagGTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG
    ||   | |  |    |  | |   || ||  |||   || || |  |||| | | |  |  | | ||  ||||  |  || |||   |||      | | |||||||||||||| ||||| ||||| ||||||||||||||| || || | || |||||||| || || || |
----cgagataatacgctgacatat---ctttgaggatagatgaaactggaatgaactcagttgacatggacgactattcgcagccctgagtatggatgatgtacagGTCATGAATTTGATTGGAGACGTCAAAGGAAAAGTGGCTGTCATGGTGGACGACATGATAGACACTGCCG
















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|32793704|gb|CD945940.1|CD945940
EST:     CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAG                         GTCATGAATTTA
genomic: CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAGgtgagatctt ... attttttcagGTCATGAATTTA
EST: gi|60341300|gb|DN208273.1|DN208273
EST:     CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAG                         GTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT
genomic: CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAGgtgagatctt ... attttttcagGTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT
EST: gi|211094604|gb|FL027759.1|FL027759
EST:     CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAG                         GTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT
genomic: CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAGgtgagatctt ... attttttcagGTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT
EST: gi|149006975|gb|EE040194.2|EE040194
EST:     TCACACCATGTCAGAG                         GTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT
genomic: TCACAACATGTCAGAGgtgagatctt ... attttttcagGTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT
EST: gi|60358780|gb|DN225753.1|DN225753
EST:     GTTGATAAAAGAAGACAGGGTCACAACATGTCAGAG                         GTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT
genomic: GTTGATAAAAGAAGACAGGGTCACAACATGTCAGAGgtgagatctt ... attttttcagGTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT
EST: gi|149088668|gb|EE177786.2|EE177786
EST:     CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAG                         GTCATGAATTTAATTGGCGAC
genomic: CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAGgtgagatctt ... attttttcagGTCATGAATTTAATTGGCGAC
EST: gi|6626351|gb|AW257883.1|AW257883
EST:     CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAG                         GTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT
genomic: CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAGgtgagatctt ... attttttcagGTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT
EST: gi|211094605|gb|FL027760.1|FL027760
EST:     CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAG                         GTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT
genomic: CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAGgtgagatctt ... attttttcagGTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT
EST: gi|31354391|gb|CD438748.1|CD438748
EST:     CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAG                         GTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT
genomic: CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAGgtgagatctt ... attttttcagGTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT
EST: gi|50339734|gb|CO534860.1|CO534860
EST:     CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAG                         GTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT
genomic: CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAGgtgagatctt ... attttttcagGTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT
EST: gi|50322471|gb|CO517597.1|CO517597
EST:     CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAG                         GTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT
genomic: CCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAGgtgagatctt ... attttttcagGTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGAT

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: 46 (upstream exon), 45 (downstream exon)
Score: 105

TGTGGGTGGCGTTGTTAGAGCACGTGCATTCGCTAAGAAATTATTGAATGCCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAGgtgagatctt ... attttttcagGTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 227

TGTGGGTGGCGTTGTTAGAGCACGTGCATTCGCTAAGAAATTATTGAATGCCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAGgtgagatctt ... attttttcagGTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

TGTGGGTGGCGTTGTTAGAGCACGTGCATTCGCTAAGAAATTATTGAATGCCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAGgtgagatctt ... attttttcagGTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 143

TGTGGGTGGCGTTGTTAGAGCACGTGCATTCGCTAAGAAATTATTGAATGCCCGTTTAGCTATTGTTGATAAAAGAAGACAGGGTCACAACATGTCAGAGgtgagatctt ... attttttcagGTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaaatgcaattatagcttcgaaaactacagaggcctatatcatattttttcagGTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG
                                            tattttttc  CT-rich tract
                                     tatatcatattttttc  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcacggtgtgagtcatccatgttttgactatgttgatctgtgcaataaaatgcaattatagcttcgaaaactacagaggcctatatcatattttttcagGTCATGAATTTAATTGGCGACGTGAAAGGAAAAGTGGCTATCCTGATTGATGACATGATTGATACAGCAG

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