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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagatattctaagatgttttgcacaagtaaaagttacccgttattcatttcatcttttattgtactgtagtctcataccatttcgtaaatgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTTTCTTTGGACTTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATA

Basic information

species Zea mays
transcript GRMZM2G067546_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G067546_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g21720.1 (Oryza sativa), 3'ss of exon 10
atagatattctaag---atgttttgcacaagtaaaagttacccgttattcatttcatcttttat-tgtactg--tagtctcataccatttcgtaaatgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTTTCTTTGGACTTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATA---
     | | || |    |||  ||| ||||||||||||    |    ||  || || ||||| | | | ||   ||  || || |  |||| |||| ||| ||||||||| ||||   || |  |  ||||||||||||| || || |||||||||||||||||||||||| |||| ||||| |||||||| || ||||| |||||   
-----tctactgaactaatggcttgaacaagtaaaagtgtggcaaatttttttacaccttttgtatattctacctaccctaatgctgtttc-taaacgatatgcagGCAAGGAGG---CTACGTCAGCTGTTGGCTGGAGTTTTCTGTGGGTTATTTTCTTTGGACTTGTTCTTGCTGGGGTCGGAGCATATGCGGTGTATAAATACAG
















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|211108137|gb|FL478050.1|FL478050
EST:     CAATATGCTATACATGAGAGAGCATGACACTTGCATCA                         GCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
genomic: CAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
EST: gi|74242229|gb|DT650143.1|DT650143
EST:     CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCA                         GCAAAGAGGGAACTGCCACTACTGTTG
genomic: CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTG
EST: gi|6828165|gb|AW331808.1|AW331808
EST:     AATATGCTATACATGAGAGAGCATGAC-CTTGCATCA                         GCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
genomic: AATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
EST: gi|67015635|gb|CO444384.1|CO444384
EST:     CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCA                         GCAAAGAGGGAACTGCCACTACTGTCGGCTGGAGCTTCCTCTGGGTTATTT
genomic: CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
EST: gi|6227124|gb|AW155653.1|AW155653
EST:     CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCA                         GCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
genomic: CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
EST: gi|148962555|gb|EE013431.2|EE013431
EST:     GTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCA                         GCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
genomic: GTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
EST: gi|60396640|gb|DN229508.1|DN229508
EST:     CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCA                         GCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
genomic: CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
EST: gi|33100298|gb|CF060258.1|CF060258
EST:     CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCA                         ACAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
genomic: CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
EST: gi|30032111|gb|CB833962.1|CB833962
EST:     GATGACAATATGCTATACATGAGAGAGCATGACNCTTGCATCA                         GCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
genomic: GATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
EST: gi|60401526|gb|DN234333.1|DN234333
EST:     CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCA                         GCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
genomic: CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
EST: gi|148966624|gb|EE017666.2|EE017666
EST:     CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCA                         GCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
genomic: CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
EST: gi|67019769|gb|CO448518.1|CO448518
EST:     CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCA                         GCAAAGAGGGAACTGCCACTACTGTCGGCTGGAGCTTCCTCTGGGTTATTT
genomic: CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
EST: gi|211348715|gb|FL063226.1|FL063226
EST:     CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCA                         GCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
genomic: CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
EST: gi|149099685|gb|EE185734.2|EE185734
EST:     CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCA                         GCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
genomic: CTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
EST: gi|29544790|gb|CB605398.1|CB605398
EST:     GATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCA                         GCAAAGAGGGAACTGCCGCTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT
genomic: GATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTT

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: 48 (upstream exon), 46 (downstream exon)
Score: 111

CAGTGCAAGGGTTGCAGCTGCAAGAATACGTGGGGAAGCTATGAATGCAGCTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTTTCTTTGGACTTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 608

CAGTGCAAGGGTTGCAGCTGCAAGAATACGTGGGGAAGCTATGAATGCAGCTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTTTCTTTGGACTTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 845

CAGTGCAAGGGTTGCAGCTGCAAGAATACGTGGGGAAGCTATGAATGCAGCTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTTTCTTTGGACTTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 385

CAGTGCAAGGGTTGCAGCTGCAAGAATACGTGGGGAAGCTATGAATGCAGCTGTGGTGATGACAATATGCTATACATGAGAGAGCATGACACTTGCATCAgtgagtagct ... tgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTTTCTTTGGACTTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttcatcttttattgtactgtagtctcataccatttcgtaaatgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTTTCTTTGGACTTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATA
       atcttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagatattctaagatgttttgcacaagtaaaagttacccgttattcatttcatcttttattgtactgtagtctcataccatttcgtaaatgatgtgcagGCAAAGAGGGAACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTTTCTTTGGACTTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - -tgttttg
- - - - - - - - - - - - -aagtaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catacca