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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgcatctcttttcttgctttgttttgtctttatatcattcccttttagtgtgtactatttcatcacaatttagtcactcctcttttcttgcactgtatgggcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGCTATTGTAAATGAAAGGAGGCAATTACCGTGTTTTGACGTATTCTTTGGG

Basic information

species Zea mays
transcript GRMZM2G082664_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082664_T01 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os06g30460.4 (Oryza sativa), 3'ss of exon 17
gtgtgcatctcttttcttgctttgttttgtctttatatcattcccttttagtgtgtactatttcatcacaatttagtcactcctcttttcttgcactgtatgggcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGCTATTGTAAATGAAAGGAGGCAATTACCGTGTTTTGACGTATTCTTTGGG
         |       |      | | || ||| |   |||  || | |   |   |  |     ||    ||| |   || |   || |||   |  |||||    |||||||||||||||||| ||| || | | ||||||  | ||||| ||||| |||||||||||||||||||   | | | | |||| ||| |  |||||| | ||
---------ttagactataaaacatgtagt-tttgtgaaatttactctaaacataatcactgattccatctcttaattcgtctttcctttttgtttttcatggg---aagcagGCAAGTTTTTCACAGAGTTGTCACAGAATTTTGGTGACATTAGGAGACTGCTATTGTAAATGAAAGTTAGTACTAATCGTGCTTTCAAATATTCTGTTGG
















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|71433813|gb|DR814863.1|DR814863
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|61119124|gb|DN560085.1|DN560085
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTANGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATT
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATT
EST: gi|149028360|gb|EE154632.2|EE154632
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|211174833|gb|FL413958.1|FL413958
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|76924990|gb|DV170231.1|DV170231
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|8930105|gb|BE224943.1|BE224943
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|211220365|gb|FL435932.1|FL435932
EST:     GAGCTTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|149003161|gb|EE038899.2|EE038899
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|60337715|gb|DN204688.1|DN204688
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|47961688|gb|CN844397.1|CN844397
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|211219083|gb|FL476026.1|FL476026
EST:     GACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGGGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|50331519|gb|CO526645.1|CO526645
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|37398003|gb|CF636310.1|CF636310
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|211274102|gb|FL440043.1|FL440043
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|148945040|gb|EC890224.2|EC890224
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|40337298|gb|CK371368.1|CK371368
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|50331482|gb|CO526608.1|CO526608
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|50331518|gb|CO526644.1|CO526644
EST:     GAGCCTGACACTATTTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|50331481|gb|CO526607.1|CO526607
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|91053971|gb|EB164389.1|EB164389
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
EST: gi|88758153|gb|DY542294.1|DY542294
EST:     GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG                         GCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC
genomic: GAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGC

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: 47 (upstream exon), 48 (downstream exon)
Score: 155

GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGCTATTGTAAATGAAAGGAGGCAATTACCGTGTTTTGACGTATTCTTTGGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 183

GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGCTATTGTAAATGAAAGGAGGCAATTACCGTGTTTTGACGTATTCTTTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 188

GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGCTATTGTAAATGAAAGGAGGCAATTACCGTGTTTTGACGTATTCTTTGGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 216

GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAGgtgtgcatct ... gcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGCTATTGTAAATGAAAGGAGGCAATTACCGTGTTTTGACGTATTCTTTGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttcatcacaatttagtcactcctcttttcttgcactgtatgggcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGCTATTGTAAATGAAAGGAGGCAATTACCGTGTTTTGACGTATTCTTTGGG
         acaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgcatctcttttcttgctttgttttgtctttatatcattcccttttagtgtgtactatttcatcacaatttagtcactcctcttttcttgcactgtatgggcgggagcagGCAAGTTTTTCACGGAGCTGGCGCTGAATTTCAGCGACATCAGGAGGCTGCTATTGTAAATGAAAGGAGGCAATTACCGTGTTTTGACGTATTCTTTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG