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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgactacttcaatccagtgacgtaacctaattttgccctgtggggtgggaaggtagctgatcattgccttctgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG

Basic information

species Zea mays
transcript GRMZM2G051004_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 12
gtgactacttc--aatccagtgacgtaacctaattttgccctgtggggtgggaaggtagc-tgatcattgccttctgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG
|| | ||||||   ||  |  || ||||  |  | |||  ||     | | |  | |  | | |      | ||||| ||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||
gtaagtacttctagatgtaccgatgtaaattg-tgttgtgctcaaaagggagtggttgacataactgcccctttctgcatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATTGGACTGAGCTCTTCCTTCATGAAGCTTGTGTCATGGTATGACAACGAGTGGGGCTACAG

upper sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 12
-------------gtgactacttcaatccagtgacgtaacctaattt--tgccctgtggggtgggaaggtagctgatc---attgccttctgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG
              |  ||  |||  |     ||  | ||  | ||   ||   | |    |  | |  |  ||  |    | ||  |||| |    ||||||||| |||||||||||||||||||| || | ||| ||  |||| ||  | ||||| || || ||||||||||| |||||||| |||||
aaattgaaccttcatttctctttccctagttagaatttactcatttggatgtattattatttaagtaaatgacttgttcaaaatgaattcttttctccagGTCAAGTATCTTTGATGCCAAGGCTGGCATTGCACTAAGTGCTTCCTTTGTTAAGCTGGTTTCGTGGTATGACAATGAGTGGGGTTACAG

upper sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT1G16300.1 (Arabidopsis thaliana), 3'ss of exon 12
----gtgactacttcaatccagtgacgtaacctaattttgccctgtggggtgggaaggtagctgatcattgccttctgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG
    || ||| ||| |||   ||  || | |   ||||       |||      ||||| | ||  ||||| |      || |||||||||| ||||||||||| || ||||| || ||| | |||   || |||||||| ||||| || |||||||||||||| ||||| |||||
gtatgtcact-cttaaatattgtagcggatc---atttaaaatcttggtactcaaaggttg-tggccattgtcaaaaaaat-tcagGTCAAGTATCTTTGATGCTAATGCTGGGATTGGATTAAGCAAGTCCTTCATGAAACTTGTCTCCTGGTATGACAACGAATGGGGTTACAG

upper sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 3'ss of exon 12
-------------------gtgactacttcaatccagtgacgtaacctaattttgccctgtggggtgggaaggtagctgatcattgccttctgtatat-cagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG
                   |   ||  || | |  |   || |   | ||      | | ||| |    |   |   |     ||  || || ||| | ||||||||| || |||||||| ||||| || || || |||||  |||| ||||||||||| ||  | |||||||||||||| ||||| |||||
ttcttgaattcccaggatcgaacctgatttattttatctacattttcaaag--catcatttggtggatcaccatttttatatgttctctgctttatttacagGTCAAGTATATTTGATGCAAAGGCCGGGATAGGGCTGAGTGCTTCCTTCATGAAGCTCGTTGCATGGTATGACAACGAATGGGGATACAG

upper sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 12
lower sequence: PP1S309_73V6.2 (Physcomitrella patens), 3'ss of exon 10
----gtgactacttcaatccagtgacgtaacctaattttgccctgtggg--gtgggaaggtagctgat--cattgccttctgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG
    ||   |       | |  ||    |   |   ||||     | ||   ||    ||   || ||   ||||   |||  ||| |||||| |||||||| ||||||||||| || || |   ||||       ||  | ||||| ||||| ||||||||||||||||||||||||||
gtaggtttttgtcgattttcgatgggacagattgtgtttgttgaattggtcatgtttgggatacttatggtattgaactcttgata-cagGTCGAGCATCTTCGATGCCAAGGCAGGAATTGCCTTGAGTGACAAGTTTGTCAAGCTGGTGTCGTGGTATGACAACGAGTGGGGCTACAG

upper sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 12
lower sequence: PP1S309_84V6.1 (Physcomitrella patens), 3'ss of exon 10
-----gtgactacttcaatccagtgacgtaacctaattttgccctgtggggtgggaaggtagctgatcattgccttctgtatat-cagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG
     ||   |  ||       | ||||  || |  || ||   |  |  | |    |  | || ||  |    |  |||  || |||||| |||||||| ||||| ||||| || || |   |||||      ||| ||||| | ||||| ||||||||||||||||||||||||||
gtaaggttgttgattttggatgg-gacg-gacttgtttgtggaattagtagcgtcgtgaca-ctaatggtgttgtaatgtcgatacagGTCGAGCATCTTCGATGCTAAGGCAGGAATTGCCTTGAGCGACAAGTTCGTGAAGTTGGTGTCGTGGTATGACAACGAGTGGGGCTACAG

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|211015683|gb|FL453044.1|FL453044
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|211407297|gb|FL458695.1|FL458695
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|148928089|gb|EC872534.2|EC872534
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTTTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|37397668|gb|CF636141.1|CF636141
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|67025324|gb|CO454073.1|CO454073
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|40337147|gb|CK371217.1|CK371217
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|84977532|gb|DW475954.1|DW475954
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GCCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|30306629|gb|CD001302.1|CD001302
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|31997624|gb|CD661686.1|CD661686
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|148944446|gb|EC889561.2|EC889561
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|6021812|gb|AW066740.1|AW066740
EST:     GGCTACCCAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTNTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT

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), 48 (downstream exon)
Score: 35

GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG


Block sizes: 38 (upstream exon), 46 (downstream exon)
Score: 13

GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 10

GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaattttgccctgtggggtgggaaggtagctgatcattgccttctgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG
                            agctgat  putative branch site (score: 87)
                                     ttgccttct  putative PPT
                                             tgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgactacttcaatccagtgacgtaacctaattttgccctgtggggtgggaaggtagctgatcattgccttctgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC