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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatctgcttggcaactatactcatttgaatttcatcactattgtattttgctttatgcactattgccatcagttaaattgacatgaaactggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGACTTTGTCCGAGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAA

Basic information

species Zea mays
transcript GRMZM2G107575_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107575_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g41510.1 (Oryza sativa), 3'ss of exon 3
gtatgcatctgcttggcaactatactcatttgaatttcatcactattgtattttg-----ctttatgcactat----tgccatcagtt-aaattgacatgaaactggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGACTTTGTCCGAGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAA
|||| ||||| |||  |||| || |||| ||   ||   | | ||   |||| ||      || | |||| |     | | |||| || ||||| |||   ||  | |||||||||||||||||||||| ||||| ||||||||||| ||||| || |||||||||||||| |||||| ||||||| ||||||||||| |||||||||||||| |
gtatccatctccttatcaaccattctcacttaggttctgttagtaa-atattctgagtgctttcaggcacaaccttattctatcacttgaaatttacacagaatggaccttgcagATATTTGACCTTTTTGATGTGAAGAAAAGGGGGGTCATCGACTTTGGTGACTTTGTTCGAGCTTTAAATGTATTTCATCCAAACATCCCAATGGAAGAGA

upper sequence: GRMZM2G107575_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv02s0236g00140.t01 (Vitis vinifera), 3'ss of exon 4
gtatgcatctgcttggcaactatactcatttgaatttcatcactattgt--attttgct--ttatgcactattgccatcagttaaattgacatgaaactggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGACTTTGTCCGAGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAA
  ||||| ||||  |   | ||| ||  |    |||| |  |||  | |   |||||    |    || | ||   |||||  ||||||  ||   | ||  ||||||||| ||||| ||||| ||||| |||   | ||| |||||||||||||||||||||||| |  | |||||||| || |||||||||  ||||   ||||| |
--atgca-ctgcaagc--attattcttttcaccatttaaatacttctatttgttttgaaagtggaacaattttttaatcag--aaattgggatc--attgaacttgcagATCTTTGATCTTTTTGATGTTAAGCGGAAGGGAGTCATTGATTTTGGTGACTTTGTCAGGTCACTAAATGTTTTCCATCCAAATGCCCCACAAGAAGACA

upper sequence: GRMZM2G107575_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv02s0236g00150.t01 (Vitis vinifera), 3'ss of exon 4
gtatgcatctgcttggcaactatactcatttgaatttcatcactattgt--attttgc--tttatgcactattgccatcagttaaattgacatgaaactggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGACTTTGTCCGAGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAA
  ||||| ||||  |   | ||| ||  |    |||| |  |||  | |   |||||   ||     | | ||   |||||  ||||||  ||   | |   ||||||||| ||||| ||||| ||||| |||   | ||| |||||||||||||||||||||||| |  | |||||||| || |||||||||  ||||   ||||| |
--atgca-ctgcaagc--attattcttttcaccatttaaatacttctatttgttttgaaattggaataattttttaatcag--aaattgggatc--attaaacttgcagATCTTTGATCTTTTTGATGTTAAGCGGAAGGGAGTCATTGATTTTGGTGACTTTGTCAGGTCACTAAATGTTTTCCATCCAAATGCCCCACAAGAAGACA

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|86466680|gb|DY233050.1|DY233050
EST:     AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG                         ATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
genomic: AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
EST: gi|86468277|gb|DY234647.1|DY234647
EST:     AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG                         ATATTTGACCTTTTCGATGTCAAGAAAA
genomic: AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTTCGATGTCAAGAAAA
EST: gi|149079633|gb|EE168627.2|EE168627
EST:     AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG                         ATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
genomic: AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
EST: gi|101388735|gb|EB816351.1|EB816351
EST:     AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG                         ATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
genomic: AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
EST: gi|91053272|gb|EB163690.1|EB163690
EST:     AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG                         ATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
genomic: AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
EST: gi|78085933|gb|DV514326.1|DV514326
EST:     AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG                         ATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
genomic: AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
EST: gi|14203857|gb|BG837534.1|BG837534
EST:     GCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG                         ATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
genomic: GCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
EST: gi|211199934|gb|FL305445.1|FL305445
EST:     AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG                         ATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
genomic: AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
EST: gi|149016909|gb|EE045638.2|EE045638
EST:     AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG                         ATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
genomic: AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
EST: gi|211202489|gb|FL305452.1|FL305452
EST:     AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG                         ATATTTGACCTTTTCGATGTCAAGAAAAGGG-TGTCATTGATTTTGGTGAC
genomic: AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
EST: gi|76018012|gb|DT945182.1|DT945182
EST:     AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG                         ATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
genomic: AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
EST: gi|71427887|gb|DR808937.1|DR808937
EST:     AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG                         ATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
genomic: AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
EST: gi|20208081|gb|BQ134170.1|BQ134170
EST:     AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG                         ATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTCTGGTGAC
genomic: AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
EST: gi|211199933|gb|FL305444.1|FL305444
EST:     CTAGCACTATTNTAAGAATCAGAGGAAAGAAAATCCTTTTCGCCAATCGG                         ATATTTGACCTTTTTCGATGTC
genomic: CTAGCACTATT-TAAGAATCAGAGGAAAGAAAATC-TTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTT-CGATGTC
EST: gi|211199938|gb|FL305449.1|FL305449
EST:     AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG                         ATATT-GACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGA
genomic: AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGA
EST: gi|26456204|gb|CA827787.1|CA827787
EST:     AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG                         ATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGG
genomic: AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGG
EST: gi|91052665|gb|EB163083.1|EB163083
EST:     AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG                         ATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
genomic: AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
EST: gi|71317611|gb|DR795553.1|DR795553
EST:     AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG                         ATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC
genomic: AGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGGgtatgcatct ... ggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgctttatgcactattgccatcagttaaattgacatgaaactggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGACTTTGTCCGAGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAA
                              aattgac  putative branch site (score: 3)
                         agttaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcatctgcttggcaactatactcatttgaatttcatcactattgtattttgctttatgcactattgccatcagttaaattgacatgaaactggccttgcagATATTTGACCTTTTCGATGTCAAGAAAAGGGGTGTCATTGATTTTGGTGACTTTGTCCGAGCTCTAAATGTGTTTCATCCAAATATCCCAATGGAAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA