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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcacttgtgtccattatagtcttttgcaactcccgttttattttttcaatatcaaacacctacggattatttgatatttttcatgtttattattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTTGGCAATTTGATGGCCCTTGGAAG

Basic information

species Zea mays
transcript GRMZM2G032314_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032314_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g35640.1 (Oryza sativa), 3'ss of exon 2
ttgcacttgtgtccattatagtcttttgcaactcccgttttattt---tttcaata---tcaaacacctacggattatttgatatttttcatgtttattattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTTGGCAATTTGATGGCCCTTGGAAG
 |   |||  |    |    ||||    ||| |   ||| | |||   ||||| |    || | |  ||  || ||||||||||||||| || |  |||   ||||||||||||||| ||||||||||| |||||||| |||||| ||||||||||||||||||||||||| ||||||||
-tattcttcagattttctctgtctac--caatttttgttgtgtttgattttcatttccctccagccactgtgggttatttgatatttttgatctccatt---gcagTCAATGCTTGTTTTCTTCAATCCTGTGAAATTCGGGGTAACATTCACCCTTGGCAATTTGATGGCACTTGGAAG

upper sequence: GRMZM2G032314_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv07s0130g00230.t01 (Vitis vinifera), 3'ss of exon 2
-ttgcacttgtgtccattatagtcttttgcaactcccgttttattttttcaatatcaaacacctacggattatttgatatttttcatgtttattattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTTGGCAATTTGATGGCCCTTGGAAG
 |      ||      |  |  |  | |  ||||   | |  || ||       |  || |  |     ||   | || ||| |  | |    | |  |||||||||||||| |||||||||||| | || || ||| || |||||||| ||||||||||| | || ||||| ||
gtcatggctggaaaattggttttactatcaaactggagatggatattagtggccttgaaaaaatctaacttgcct-atttttgttctttcccctgtgacagTCAATGCTTGTTTTCTTCAATCCAATCAAGTTCGGGATAACATTCACCTTTGGCAATTTGCTTGCACTTGGGAG
















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|211123230|gb|FL167317.1|FL167317
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211123228|gb|FL167315.1|FL167315
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211122445|gb|FL167296.1|FL167296
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211121673|gb|FL167292.1|FL167292
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTYTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211123226|gb|FL167313.1|FL167313
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211121675|gb|FL167294.1|FL167294
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211122444|gb|FL167295.1|FL167295
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211122456|gb|FL167307.1|FL167307
EST:     TCTATGGTTTCGCGATAT--TTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211121674|gb|FL167293.1|FL167293
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211123232|gb|FL167319.1|FL167319
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211121670|gb|FL167289.1|FL167289
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGT
EST: gi|211122448|gb|FL167299.1|FL167299
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211123225|gb|FL167312.1|FL167312
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211122458|gb|FL167309.1|FL167309
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211123224|gb|FL167311.1|FL167311
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211122453|gb|FL167304.1|FL167304
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTT
EST: gi|211122447|gb|FL167298.1|FL167298
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211123229|gb|FL167316.1|FL167316
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211122446|gb|FL167297.1|FL167297
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211122451|gb|FL167302.1|FL167302
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211121669|gb|FL167288.1|FL167288
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211123223|gb|FL167310.1|FL167310
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
EST: gi|211122455|gb|FL167306.1|FL167306
EST:     TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTG                         TCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT
genomic: TCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTT

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: 155

AGGCTCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTTGGCAATTTGATGGCCCTTGGAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 107

AGGCTCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTTGGCAATTTGATGGCCCTTGGAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 101

AGGCTCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTTGGCAATTTGATGGCCCTTGGAAG


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

AGGCTCTATGGTTTCGCGATATGCTTGGCTGCCGGACTGACGTGCACATTCTTGgtgagtttca ... attattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTTGGCAATTTGATGGCCCTTGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcaatatcaaacacctacggattatttgatatttttcatgtttattattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTTGGCAATTTGATGGCCCTTGGAAG
                         atttgat  putative branch site (score: 121)
                      attatttgatattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcacttgtgtccattatagtcttttgcaactcccgttttattttttcaatatcaaacacctacggattatttgatatttttcatgtttattattgcagTCAATGCTTGTCTTCTTCAATCCAGTGAAATTTGGGGTAGCATTCACCCTTGGCAATTTGATGGCCCTTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
-tgcactt
- - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacctac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttt