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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtttgggaatagcagttggttctaagcttggcatcctagtggttaatgttgaacttgggaatttcataattcatatatgttccataacttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG

Basic information

species Zea mays
transcript GRMZM2G058498_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g07960.2 (Oryza sativa), 3'ss of exon 8
catgtttgggaatagca--gttggtt--ctaagcttggcatcctagtggttaatgttgaacttgggaatttcataattcatatatgttccataacttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG
     ||| ||| ||||  |  |  |  ||    || | |  || |   | |  |||      |  |  || |   ||   |||| ||| || || ||   ||||| |||||||| ||||||||||||||||| || || || || || |||||||||||||||||||| || || || |||
---cattgagaaaagcattgccgacttactggtttttgaagtctggaaatcatagtttgcggagttatatttaaggttt-catattttctatcacgtggcacagGTTCATCACACGTTTGCAACTGCTGGATCAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAG

upper sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G19260.1 (Glycine max), 3'ss of exon 7
-catgtttgggaatagcagttggttctaagcttggcatcctagtggtta-atgttgaacttgggaatttcataattcatatatgttccataacttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG
   |   |   |||   ||     ||  |  |      |  |||  ||  |  ||  | |     |||   |   ||| || | ||     ||    |  |||| || ||||||||||||||| |||| ||||| ||||||||||| || |||||||||||||| || ||| |||| |||
gtttacctataaatccaagggacatcagaaatcattgacaaagtatttccactttataatctattatt--gtttctcagatttttttttctacgatttttagGTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGGGATAAGGATAGTAAACAGCGGCTCAAG

upper sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA02G13780.1 (Glycine max), 3'ss of exon 7
----catgtttgggaatagcagttggttctaagcttggcatcctagtggttaatgttgaacttgggaatttcataattcatatatgttccataacttgc-tgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG
     |        |||| |    | | || |  ||    | ||||| ||  || |   | |      ||   ||||  |  | ||||       |||| | ||||| |||||||| |||||||||||||||||||| |||||||| || |||||||||||||| || || ||||| || |||
gtagtacaccatataatacccaa-gttacttaaatttattttctagttgtggatttgatattct---tttatgtaatctaattttgtttgtgtctttgcattcagGTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGGGATAAGGACAGTAAACAGAGACTCAAG

upper sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA01G09290.1 (Glycine max), 3'ss of exon 7
------catgtttgggaatagcagttggttctaagcttggcatcctagtgg--ttaatgttgaacttgggaatttcataattcatatatgttccataacttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG
      |||| |     ||   | ||  ||  | |  |       | ||||  ||||| ||    |  | ||| | ||  ||  | |||||      | ||     |||| |||||||| |||||||||||||||||||| |||||||| || ||||||||||| || || || ||||| || |||
gtagtacatgatataatatcaaaattacttaaatgtattttcaagttgtggatttaatattcttttatgtaatcttat--tttgtttatgtctttgcattt-----agGTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGGGATAAAGACAGTAAACAGAGACTCAAG

upper sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA15G05740.1 (Glycine max), 3'ss of exon 7
catgtttgggaatagcagttggttctaagcttggcatcctagtggtta-atgttgaacttgggaatttcataattcatatatgttccata-acttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG
  |   |   |||   |      ||  |  |      |  |||  ||  |  ||  | |    | | ||||   ||| || | |    |  |     |  |||| || ||||||||||||||| |||| ||||| ||||||||||| || |||||||||||||| || |||||||| |||
tttagctataaatccaacggacatcagaaatcattgacaaagtatttccactttataatct--attatcatttctcacatttttcttttctatgaattttagGTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGGGATAAGGATAGTAAACAGAGGCTCAAG

upper sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT1G80670.1 (Arabidopsis thaliana), 3'ss of exon 8
------catgtttgggaatagcagttggttctaagcttggcatcctagtggttaatgttgaacttgggaatttcataattcatatatgttccataacttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG
        | | |     ||     |  | ||  |  ||   || | |  |          |  | |     | | |||   | | ||     |       |  |||| |||  ||| |||||||||||||| || || ||||||||||| |||||||| || ||||| || || || || |||
gtaagctctatctatagttatactcttatactc-gtatgtattctttgaagccttcagcatatgttgagcgatgaaaatgattgtttgagttgttgtggatttaagGTACATGGCACTTTTGCAACTGCTGGGTCAGATGGTGCTTTCAATTTCTGGGACAAAGATAGTAAACAAAGACTCAAG

upper sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv09s0002g09150.t01 (Vitis vinifera), 3'ss of exon 7
-catgtttgggaatagcagt----tggttctaagcttggcatcctagtggttaatgttgaacttgggaatttcataattcatatatgttccataacttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG
  |   |||| ||   |  |    || ||||||      | |     |  || |  |||| ||  |    |  | |  | || ||  | ||    |||| | ||||| ||||| |||||||||||||| || ||||| |||||||| || || ||||| |||||||| || ||||| || |||
tgacaattggcaaggtctatactgtgattctaaaacactcgtttgtatc-tttacattgagctcagttgctcaagaccttatttaactgcc----cttgtttcagGTGCATCATACATTTGCAACTGCAGGGTCTGATGGTGCTTTTAATTTTTGGGACAAGGATAGTAAACAGAGACTTAAG

upper sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 8
catgtttgggaatagc-agttggttctaagcttggcatcctagtggtt----aatgttgaacttgggaatttcataattcatatatgttccataacttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG
     ||||  |||   ||||   |   |  |  |   |  |    ||      | ||    || | | | || | |    |   | ||      |||  | ||||| |||||||||||||| ||||| || |||||||||||||| || |||||||| |||||||| || ||||| || |||
-----ttggagatatttagtttagttataattcagtgccaaaccattttgaaggtcttttgatttgcattctcttgagaacttatttttgtgcctcttatttcagGTGCATCACACATTTGCCACTGCAGGCTCTGACGGTGCTTTTAATTTCTGGGACAAGGATAGTAAACAGAGACTCAAG

upper sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ25923 (Selaginella moellendorffii), 3'ss of exon 7
catgtttgggaatagcagttggttctaagcttggcatcctagtg-gttaatgttgaacttgggaatttcataattcatatatgttccataacttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG
                                         ||| || ||| |    ||| | |  |   |      ||  ||  |  ||   ||| ||||||   |   ||||| || ||  | || ||||| |||||||| ||||||||||| ||||| |||||||||||||| |||
-----------------------------------------gtgagtcaatctcttcctttgaagctgtgt------taactggccttta---tgc-gcagGTGTTTGGAACATTCGCTACATCAGGCTCTGATGGTGCTTTTAACTTCTGGGACAAGGACAGCAAGCAGAGGCTCAAG

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|71310172|gb|DR791375.1|DR791375
EST:     ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCT                         GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
genomic: ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
EST: gi|5055819|gb|AI734706.1|AI734706
EST:     CTCTGTCAATTCACTCAACTTCCACCCT                         GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
genomic: CTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
EST: gi|67019316|gb|CO448065.1|CO448065
EST:     CAGGGNAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCT                         GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCA-CTTCTGG
genomic: CAGGG-AAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
EST: gi|31355022|gb|CD439379.1|CD439379
EST:     ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCT                         GGTC-ATCACACATTTGCAACTGCTGGATCTGACGGTGCT
genomic: ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagG-TCCATCACACATTTGCAACTGCTGGATCTGACGGTGCT
EST: gi|548062|gb|T25262.1|T25262
EST:     ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCT                         GTCCATCACACATTTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTG
genomic: ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTT-GCAACTGCTGGATCTGACGGTGCTTTCAACTTCTG
EST: gi|71427496|gb|DR808546.1|DR808546
EST:     ACAGGGGAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCT                         GTCCATCACACATTTGCAACTGCTGGATCT
genomic: ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTTGCAACTGCTGGATCT
EST: gi|32838237|gb|CD977915.1|CD977915
EST:     ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCT                         GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
genomic: ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
EST: gi|78092605|gb|DV520979.1|DV520979
EST:     CAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCCACTTCCCACCCT                         GTCCATCACACATTTGCCACTGCTGGATC
genomic: CAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCC-ACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTTGCAACTGCTGGATC
EST: gi|78092604|gb|DV520978.1|DV520978
EST:     ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCT                         GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
genomic: ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
EST: gi|24769686|gb|CA404815.1|CA404815
EST:     AGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCT                         GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
genomic: AGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
EST: gi|71756690|gb|DR954627.1|DR954627
EST:     ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCT                         GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
genomic: ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
EST: gi|78023897|gb|DV492284.1|DV492284
EST:     ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCT                         GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
genomic: ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
EST: gi|67013709|gb|CO442458.1|CO442458
EST:     GATATATTCTCTGTCAATTCACTCAACTTCCACCCT                         GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
genomic: GATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
EST: gi|32789124|gb|CD941360.1|CD941360
EST:     ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCT                         GTCCATCACACATTTGCAACTGCTGGATC
genomic: ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTTGCAACTGCTGGATC
EST: gi|32945537|gb|CF050356.1|CF050356
EST:     ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCT                         GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG
genomic: ACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGG

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: 136

TCATCATATCGATGACGCACAGCAAAGCAAAAACTTCACATTCAAATGCCACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 155

TCATCATATCGATGACGCACAGCAAAGCAAAAACTTCACATTCAAATGCCACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

TCATCATATCGATGACGCACAGCAAAGCAAAAACTTCACATTCAAATGCCACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 68

TCATCATATCGATGACGCACAGCAAAGCAAAAACTTCACATTCAAATGCCACAGGGAAGGAAATGATATATTCTCTGTCAATTCACTCAACTTCCACCCTgtaagatttc ... cttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatgttgaacttgggaatttcataattcatatatgttccataacttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG
                                       ccataac  putative branch site (score: 68)
                 aatttcataattcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtttgggaatagcagttggttctaagcttggcatcctagtggttaatgttgaacttgggaatttcataattcatatatgttccataacttgctgcagGTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
catgttt
- - - - - - - gcagttg
- - - - - - - - - - - - - - - - -gcatcct
- - - - - - - - - - - - - - - - - - - - - - - - -tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcatat