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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actttgtggttactgtgttgttgtattagtcaatttctttcgttagttgatgaattgctttgtggcttcagcaagattttaatacactgaagatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTAGGTTCACCTGAGGATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTC

Basic information

species Zea mays
transcript GRMZM2G057853_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057853_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g43250.1 (Oryza sativa), 3'ss of exon 5
actttgtggttactgtgttgttgtattagtcaatttctttcgt-tagttgatgaattgctttgtggcttcagcaagattttaatacactgaaga------tgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTAGGTTCACCTGAGGATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTC
  |||||  ||| || ||      || |||   ||||||| |  ||||| ||||  ||   | ||  |    ||  ||| ||||| | | | ||      |||||||||||||||||| ||||||||||| ||||| ||||| || ||||||||||| || |||||| ||||||  || |||| ||||  |||||||||||||||||
gttttgtatttagtgagta-----atcagtt--tttcttttgcctagttcatgagctgtcgtctgtttctgacactattctaataaaataatgaaaatggtgaacagATTTGGGAGTTCGAAGAAGCTCACCAGCGTTGGCTCCCCCTTGTTGAGCTTGGCTCACCTCAGGATAAGGGGGATATAGTGCATGCTGTAGCATGGGCTC
















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|148953595|gb|EC898949.2|EC898949
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|148930898|gb|EC873352.2|EC873352
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|93012339|gb|EB637859.1|EB637859
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|76294071|gb|DV033639.1|DV033639
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|93284260|gb|EB676524.1|EB676524
EST:     TTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGNTA-G                         ATTTGGGAGTTTGA
genomic: TTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTG-TAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGA
EST: gi|78080510|gb|DV508922.1|DV508922
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|76909537|gb|DV163411.1|DV163411
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|71772782|gb|DR970707.1|DR970707
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|89252106|gb|DY623892.1|DY623892
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTC-ACCTGTTGAGGCT
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAG-CT
EST: gi|71444110|gb|DR825160.1|DR825160
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|149107563|gb|EE189446.2|EE189446
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|71773952|gb|DR971840.1|DR971840
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|149107564|gb|EE189447.2|EE189447
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|148981980|gb|EE028040.2|EE028040
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|71439594|gb|DR820644.1|DR820644
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|149074196|gb|EE162559.2|EE162559
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|76286893|gb|DV026461.1|DV026461
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCACCTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|84976699|gb|DW475121.1|DW475121
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCTCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|71429467|gb|DR810517.1|DR810517
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|50331370|gb|CO526496.1|CO526496
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCT
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCT
EST: gi|148953594|gb|EC898948.2|EC898948
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|60353460|gb|DN220433.1|DN220433
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAG                         ATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTA
EST: gi|91051936|gb|EB162354.1|EB162354
EST:     GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCCACTCTTGTAAG                         ATTTGGGAGTTTG
genomic: GTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTG

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: 105

TTCTGCATCCATAGCATGGAATCCAAGAAGAGGTGGAAGCCAACAAGCTAGTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTAGGTTCACCTGAGGATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 67

TTCTGCATCCATAGCATGGAATCCAAGAAGAGGTGGAAGCCAACAAGCTAGTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTAGGTTCACCTGAGGATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 70

TTCTGCATCCATAGCATGGAATCCAAGAAGAGGTGGAAGCCAACAAGCTAGTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTAGGTTCACCTGAGGATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTC


Block sizes: 42 (upstream exon), 45 (downstream exon)
Score: 19

TTCTGCATCCATAGCATGGAATCCAAGAAGAGGTGGAAGCCAACAAGCTAGTTTTGCAATTGGCTTTAATTCAGATTCGCCTCATTTCAACTCTTGTAAGgtttgtgaga ... agatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTAGGTTCACCTGAGGATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgatgaattgctttgtggcttcagcaagattttaatacactgaagatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTAGGTTCACCTGAGGATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTC
                               ttttaat  putative branch site (score: 19)
                           aagattttaataca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actttgtggttactgtgttgttgtattagtcaatttctttcgttagttgatgaattgctttgtggcttcagcaagattttaatacactgaagatgaacagATTTGGGAGTTTGAAGAAGCTCATCAGCGCTGGCTTCCACTTGTTGAGCTAGGTTCACCTGAGGATACAGGAGATAAAGTGTGTGCTGTAGCATGGGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - -tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - -tgatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacactg