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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttctctgaatgcattgggttcttcttgtttttgggtgctccttgttgtttcgtgacgcctgacggatgttcttcgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG

Basic information

species Zea mays
transcript GRMZM2G148176_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G148176_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g46280.3 (Oryza sativa), 3'ss of exon 2
--------------------gtgtg-ttctctgaatgcattgggttcttcttgtttttgggtgctccttgttgtttcgtgacgcctgacggatgttcttcgagga-acagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG
                    ||||| |||  ||| ||  ||   |  || ||||  || |  |    |  || | |  ||| || ||| || |||| || | ||    |||||||||||||||||||||||||||||||||||||||||||  ||||||||||||||||||| || ||||||||| 
gtgtgtaatgtgttatgtgtgtgtgattcggtgattgtgttttctcgttgttgtggtttgtggtgtttctttctcttttgatgcttgatggttgttgtttggggttgtagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTATAGATTTTCGATCTCTTGGTCAAGAATTTTCCCAA

upper sequence: GRMZM2G148176_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv14s0006g01790.t01 (Vitis vinifera), 3'ss of exon 2
---------------gtgtgttctctgaatgcattgggttcttcttgttt-ttgggtgctccttgttgtttcgtgacgcctgacggatgttcttcgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG
               | |  ||   ||| |  ||        |    ||   | | ||  |  |    ||| ||      | |  | ||||    |     ||||||||| || |||||||||| |   ||   |||||||| ||||||||||| ||||| ||||| ||||||||||| |
aatcatcatgatattgagcattggttga-tatatcataacagtaccattcactagttggcctattccatttagtatt--tttattgttgttacctgtttg-cagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCCATCTCCTGGTCAAGGATTTTCCCTG
















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|78107679|gb|DV526097.1|DV526097
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         AAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|76291670|gb|DV031238.1|DV031238
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|78078041|gb|DV506456.1|DV506456
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|76014466|gb|DT941636.1|DT941636
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGAT
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGAT
EST: gi|20300625|gb|BQ163568.1|BQ163568
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGGTTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|149013970|gb|EE043477.2|EE043477
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|89248541|gb|DY620327.1|DY620327
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|78082093|gb|DV510505.1|DV510505
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|78090492|gb|DV518866.1|DV518866
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|76018965|gb|DT946135.1|DT946135
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|93281963|gb|EB674227.1|EB674227
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACCAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTT
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTT
EST: gi|149072852|gb|EE161103.2|EE161103
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|94476899|gb|EB705857.1|EB705857
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|50339599|gb|CO534725.1|CO534725
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|50338381|gb|CO533507.1|CO533507
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|149089118|gb|EE178296.2|EE178296
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|76932675|gb|DV173111.1|DV173111
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|211311075|gb|FL268871.1|FL268871
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAG
EST: gi|149070068|gb|EE158468.2|EE158468
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|91049509|gb|EB159927.1|EB159927
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|93012162|gb|EB637682.1|EB637682
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|71333297|gb|DR803704.1|DR803704
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
EST: gi|149073325|gb|EE161620.2|EE161620
EST:     CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAG                         GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG
genomic: CTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCG

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: 137

GGACCATCCCTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 119

GGACCATCCCTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 31

GGACCATCCCTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 54

GGACCATCCCTAACAATGCCACCGCTGACGTGACGGTCGACGAGTATCATCGGTACAAGgtgtgttctc ... cgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgggtgctccttgttgtttcgtgacgcctgacggatgttcttcgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG
                            gcctgac  putative branch site (score: 54)
                                      tgttcttc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttctctgaatgcattgggttcttcttgtttttgggtgctccttgttgtttcgtgacgcctgacggatgttcttcgaggaacagGAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT