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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGTgtgagtgccatttcttcttatcatcaatttggagtgtacagtgtcctagtagttaaatcagacggtgtggatgcag

Basic information

species Zea mays
transcript GRMZM2G341404_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G341404_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g10180.2 (Oryza sativa), 5'ss of exon 6
GCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGTgtgagtgccatttcttcttatcatcaa-tttggagtgtacagtgtcctagtagttaaatcagacggtgtggatgcag
||||||||||||||| |||||||| || || || ||||| ||| |||||||||||||||| ||||| ||||||||| |||||||||| ||||||||||||   |||||||  ||||| ||| || || |  ||| |  || ||||| |   |||| | |||||| ||||||
GCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAAAGCATATTTTGGGTTGAAAAATCTTGTGAAGAAGACTAAGAGTgtgagtatgatttctttgtatcaacaaattaggggcttactgcatcatagtaataggatcaaatggtgtgcatgcag

upper sequence: GRMZM2G341404_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g74580.2 (Oryza sativa), 5'ss of exon 5
GCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGTgtgagtgccatttcttcttatcatcaa-tttggagtgtacagtgtcctagtagttaaatcagacggtgtggatgcag
||||||||||||||| |||||||| || || || ||||| ||| |||||||||||||||| ||||| ||||||||| |||||||||| ||||||||||||   |||||||  ||||| ||| || || |  ||| |  || ||||| |   |||| |||||||| ||||||
GCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAAAGCATATTTTGGGTTGAAAAATCTTCTGAAGAAGACTAAGAGTgtgagtatgatttctttgtatcaacaaattaggggcttactgcatcatagtaataggatcaaacggtgtgcatgcag
















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|148940996|gb|EC885847.2|EC885847
EST:     TGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGT                         GCAGAAGAATA-TGCTGCCAAGGGTAAGCTACGTGTGTCTGTTGAGGACTA
genomic: TGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGTgtgagtgcca ... gtggatgcagGCAGAAGA-TAATGCTGCCAAGGGTAAGCTACGTGTGTCTGTTGAGGACTA
EST: gi|71323581|gb|DR798459.1|DR798459
EST:     TGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGT                         GCAGAAGATAATGCTGCCTAGGGTAAGCTA
genomic: TGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGTgtgagtgcca ... gtggatgcagGCAGAAGATAATGCTGCCAAGGGTAAGCTA
EST: gi|78104565|gb|DV522983.1|DV522983
EST:     TGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGT                         GCAGAAGATAATGCTGCCAAGGGTAAGCTACGTGTGTCTGTTGAGGACTAC
genomic: TGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGTgtgagtgcca ... gtggatgcagGCAGAAGATAATGCTGCCAAGGGTAAGCTACGTGTGTCTGTTGAGGACTAC
EST: gi|149010182|gb|EE041997.2|EE041997
EST:     TGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGT                         GCAGAAAATAATGCTGCCAAGGGTAAGCT
genomic: TGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGTgtgagtgcca ... gtggatgcagGCAGAAGATAATGCTGCCAAGGGTAAGCT
EST: gi|148960799|gb|EE011462.2|EE011462
EST:     TGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGT                         GCAGAGGATAATGCTGCCAAGGGTAAGCTACGTGTGTCTGTTGAGGACTAC
genomic: TGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGTgtgagtgcca ... gtggatgcagGCAGAAGATAATGCTGCCAAGGGTAAGCTACGTGTGTCTGTTGAGGACTAC
EST: gi|67016841|gb|CO445590.1|CO445590
EST:     TGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACTAAGAGT                         GCAGAAGATAATGCTGCCAAGGGTAAGCTACGTGTGTCTGTTGAGGACTAC
genomic: TGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGTgtgagtgcca ... gtggatgcagGCAGAAGATAATGCTGCCAAGGGTAAGCTACGTGTGTCTGTTGAGGACTAC
EST: gi|148940390|gb|EC885183.2|EC885183
EST:     TGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGT                         GCAGAAGATAATGCTGCCAAGGGTAAGCTACGTGTGTCTGTTGAGGACTAC
genomic: TGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGTgtgagtgcca ... gtggatgcagGCAGAAGATAATGCTGCCAAGGGTAAGCTACGTGTGTCTGTTGAGGACTAC

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), 49 (downstream exon)
Score: 168

GCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGTgtgagtgcca ... gtggatgcagGCAGAAGATAATGCTGCCAAGGGTAAGCTACGTGTGTCTGTTGAGGACTACAAGGCAGCTCTAGCAATGGATCCAGACCATACTGCTTATAATGTACATC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 143

GCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGTgtgagtgcca ... gtggatgcagGCAGAAGATAATGCTGCCAAGGGTAAGCTACGTGTGTCTGTTGAGGACTACAAGGCAGCTCTAGCAATGGATCCAGACCATACTGCTTATAATGTACATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

GCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGTgtgagtgcca ... gtggatgcagGCAGAAGATAATGCTGCCAAGGGTAAGCTACGTGTGTCTGTTGAGGACTACAAGGCAGCTCTAGCAATGGATCCAGACCATACTGCTTATAATGTACATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 384

GCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGTgtgagtgcca ... gtggatgcagGCAGAAGATAATGCTGCCAAGGGTAAGCTACGTGTGTCTGTTGAGGACTACAAGGCAGCTCTAGCAATGGATCCAGACCATACTGCTTATAATGTACATC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGTgtgagtgccatttcttcttatcatcaatttggagtgtacagtgtcctagtagttaaatcagacggtgtggatgcag

- - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG