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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaatatagattaggttttattatatttgtcccattaaaacctaattattttccagtgaaagctagtgtttttcttctaatttgttggagcatgttagcaatttatttgttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAGTGTGAGGCTC

Basic information

species Zea mays
transcript GRMZM2G107984_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107984_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g41715.1 (Oryza sativa), 3'ss of exon 4
gtcaatatagattaggttttattatatttgtcccattaaaacctaattattttccagtgaaagctagtgtttttcttctaatttgttggagcatgttagcaatttatttgttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAGTGTGAGGCTC
       |  ||   ||||  |   |||| |    ||  | | ||   |  ||      ||  ||| | |||    |  |||   ||  |     |||    || |||  ||    ||||| ||||| ||||||||||| |||||||| ||||||||||||||||| ||||| ||| |||||||  |||  ||| |||| |||||||||||  |||| |
------gtgaatgtagtttactgtcattttttatgtttgaccatatcgacctt-----aaatactaatttttactataaaatgctttaaa-----ttaattgttcattcattt---cagGAGCATGCAAAAGGTGGTAAATGCATTGTATTTACACAAACAAAAAGAGATGCTGATCGATTGTCCTACACCATGGGTCGGAGTTTCCAGTGCCAGGCCC

upper sequence: GRMZM2G107984_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G03760.1 (Glycine max), 3'ss of exon 4
gtcaatatagattaggttttattatatttgtcccattaaaacctaattattttccagtgaaagctagtgtttttcttctaatttgttggagcatgttagcaatttatttgttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAGTGTGAGGCTC
         || ||     || || |     || |||   |  ||   |    | ||| || |       || |      |||| ||   |  |  ||   || |||   ||  |  |||||||||| ||||| || |||||||||||||| || ||||||||| | ||||| ||| |||| ||| | |  |||    ||||| |  | ||||||||| 
--------ggactaaaagatagtaaac----cctatttttatttagaaaa--actagttaagg---aaacttcttgctggatttttttttgtctcctaaagatatatcctttgtt--agGAACATGCAAAAGGAGGAAAGTGCATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCATATACCATGGCAAGAAGTGTTAAATGTGAGGCTT

upper sequence: GRMZM2G107984_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
gtcaatatagattaggtt-ttattatatttgtcccattaaaacctaattattttccagtga------aagcta---gtgtttttcttctaatttgt----------tggagcatgttagcaat-ttatttgttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAGTGTGAGGCTC
||     |   |||  ||  ||||| |   ||   | | |||  |  |  || | |||| |      ||| ||   |||| ||| |||  | ||||          ||||    ||||  ||| | | || | | ||||||| ||||||||||| || || |||||||||||||||||||||||| | ||||| ||| |  | ||| |     ||  | |||| ||| | ||||| ||| 
gtatgctttccttactttgctattaaacgagtatgagttaaattttgt-gttattcagtaactgagtaagttatttgtgtattttttcggagttgtcagttgtatatggaaagagttaataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT

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|32838568|gb|CD978246.1|CD978246
EST:     TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAG                         GAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAGgtcaatatag ... gttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
EST: gi|60337954|gb|DN204927.1|DN204927
EST:     TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAG                         GAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAGgtcaatatag ... gttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
EST: gi|91056824|gb|EB167242.1|EB167242
EST:     TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAG                         GAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAGgtcaatatag ... gttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
EST: gi|87152778|gb|DY397567.1|DY397567
EST:     TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAG                         GAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAGgtcaatatag ... gttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
EST: gi|149061229|gb|EE157494.2|EE157494
EST:     CTCTTCGGAGAACCGTGAAAAACCAGCTGTCCCTTGGG-AATTGATTAAG                         GAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAA-CAAAAAGGGAT
genomic: CTCTTCGGAGAACCGTGAAAAACCAGCTGTCC-TTGGGGAATTGATTAAGgtcaatatag ... gttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
EST: gi|32837236|gb|CD976914.1|CD976914
EST:     TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAG                         GAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAGgtcaatatag ... gttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
EST: gi|19057890|gb|BM736557.1|BM736557
EST:     TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAG                         GAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAACCAAAAAGGGAT
genomic: TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAGgtcaatatag ... gttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
EST: gi|78113910|gb|DV532299.1|DV532299
EST:     TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAG                         GAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAGgtcaatatag ... gttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
EST: gi|32837729|gb|CD977407.1|CD977407
EST:     TGGGGAATTGATTAAG                         GAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TGGGGAATTGATTAAGgtcaatatag ... gttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
EST: gi|149089755|gb|EE179029.2|EE179029
EST:     TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAG                         GAACATGCCAA
genomic: TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAGgtcaatatag ... gttcatgcagGAACATGCCAA
EST: gi|32836838|gb|CD976516.1|CD976516
EST:     TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAG                         GAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAGgtcaatatag ... gttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
EST: gi|32839302|gb|CD978983.1|CD978983
EST:     TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAG                         GAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAGgtcaatatag ... gttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
EST: gi|71304548|gb|DR788393.1|DR788393
EST:     TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAG                         GAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAGgtcaatatag ... gttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
EST: gi|32837093|gb|CD976771.1|CD976771
EST:     TCTCTTCGGAGAACCGCGAAAAACCAGCTGTCCTTGGGGAATTGATTAAG                         GAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAGgtcaatatag ... gttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
EST: gi|19855082|gb|BQ060134.1|BQ060134
EST:     TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAG                         GAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAGAACCGTGAAAAACCAGCTGTCCTTGGGGAATTGATTAAGgtcaatatag ... gttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtgtttttcttctaatttgttggagcatgttagcaatttatttgttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAGTGTGAGGCTC
           ttctaat  putative branch site (score: 2)
                                          tttgttc  putative PPT
     tttttcttctaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaatatagattaggttttattatatttgtcccattaaaacctaattattttccagtgaaagctagtgtttttcttctaatttgttggagcatgttagcaatttatttgttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAGTGTGAGGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT