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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgcattcagaatgaatggtgtgtatatgttcaaggaaatgttaatcactgtttgtttgtctgtgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAACCCGGAGTACCATGAAGAGTGAAACGCTTTAGCATGCCAAATAGCATGG

Basic information

species Zea mays
transcript GRMZM5G816609_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G816609_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 24
-----gtaagctgcattcagaatgaatggtgtgtatatgtt---caaggaaatgttaatcactgtttgtttgtctgtgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAACCCGGAGTACCATGAAGAGTGAAACGCTTTAGCATGCCAAATAGCATGG
        ||||  ||| | |||      | | || | |||   | | ||||  | || |    |  |||  | |  ||| ||||||||||| || |||||| ||||||| ||||||||||| ||| |||||||||||||||| ||  | || ||||||    | ||  || ||   |||  ||| 
gtaataagagctcaattaacaatatgccatttctacaagtttccccatgaaacctaaaacctgatccgttgttttacgttttgcagATACATTCCGCTGACTTCGGTATTGGAGGGCTTTGTAATTCTGAAGAAGAACCCGGAATATAACGAGGAGTGAGGGACATTTCCAGGCTTGATACAATGC
















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|67025197|gb|CO453946.1|CO453946
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|71764382|gb|DR962319.1|DR962319
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAATTAGCAACTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|31361134|gb|CD445491.1|CD445491
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAGAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|32866712|gb|CF006394.1|CF006394
EST:     CACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAANCTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGA
genomic: CACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAA-CTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGA
EST: gi|213175318|gb|FM194417.1|FM194417
EST:     GTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: GTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|78179098|gb|DV549471.1|DV549471
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|12046100|gb|BF728239.1|BF728239
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTT
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTT
EST: gi|14208421|gb|BG842099.1|BG842099
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|32866711|gb|CF006393.1|CF006393
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|50328506|gb|CO523632.1|CO523632
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|31361941|gb|CD446298.1|CD446298
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|5928889|gb|AW056181.1|AW056181
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|5296342|gb|AI783112.1|AI783112
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|5917434|gb|AW054237.1|AW054237
EST:     ACNCCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCCCTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|67013648|gb|CO442397.1|CO442397
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         A-ACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTNTGAAGAAGA-
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|60348885|gb|DN215858.1|DN215858
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|21809773|gb|BQ668091.1|BQ668091
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|33102907|gb|CF062867.1|CF062867
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|6760600|gb|AW324699.1|AW324699
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|5846964|gb|AW000043.1|AW000043
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|12968387|gb|BG265333.1|BG265333
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCGCTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
EST: gi|71764383|gb|DR962320.1|DR962320
EST:     ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAA                         ATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA
genomic: ACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAA

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: 290

TTGGTCAGGCAGGAAGGCCTAAGACAATTACCGGCTTTCAGACACACTCCACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAACCCGGAGTACCATGAAGAGTGAAACGCTTTAGCATGCCAAATAGCATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

TTGGTCAGGCAGGAAGGCCTAAGACAATTACCGGCTTTCAGACACACTCCACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAACCCGGAGTACCATGAAGAGTGAAACGCTTTAGCATGCCAAATAGCATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 264

TTGGTCAGGCAGGAAGGCCTAAGACAATTACCGGCTTTCAGACACACTCCACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAACCCGGAGTACCATGAAGAGTGAAACGCTTTAGCATGCCAAATAGCATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 273

TTGGTCAGGCAGGAAGGCCTAAGACAATTACCGGCTTTCAGACACACTCCACACCAGTCTTGCTTGCAGCAGGGGAGAGAGCTGAACTAGCAACTGAAAAgtaagctgca ... tgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAACCCGGAGTACCATGAAGAGTGAAACGCTTTAGCATGCCAAATAGCATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgtatatgttcaaggaaatgttaatcactgtttgtttgtctgtgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAACCCGGAGTACCATGAAGAGTGAAACGCTTTAGCATGCCAAATAGCATGG
                     tgttaat  putative branch site (score: 273)
                  aaatgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctgcattcagaatgaatggtgtgtatatgttcaaggaaatgttaatcactgtttgtttgtctgtgttgtgcagATACATCCCACTGACTCCGGTATTAGAGGGCTTTGTGATTTTGAAGAAGAACCCGGAGTACCATGAAGAGTGAAACGCTTTAGCATGCCAAATAGCATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA