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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatggaaggaaaacaatgttggtgtagccttgatggccatggactacagtttactgtatgatttgtgattatcggctttctgctgcctcttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG

Basic information

species Zea mays
transcript GRMZM2G018447_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018447_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 4
gaatggaaggaaaacaatgttggtgtagccttgatggccatggactacagtttactgtatgatttgtgattatcggctttc-tgctgcctcttgtc--tgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG
   ||     | | | | |  |||  | |    ||  |  | |  ||   ||||   || |  |  ||      |  | |  || ||  | |  ||  |||||||||||||||||| |||||||||||||| ||||| ||||| ||| |||| || || ||||| || ||| | || || ||| | | ||||
ttttgcttttagatccaag--ggtaca-ctcaaatttcagtagcttattatttaacataggcctcctggaagaagtatctgatgttgtgtatcatcgttgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG

upper sequence: GRMZM2G018447_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 4
gaatggaaggaaaacaatgttggtgtagccttgatggccatggactacagtttact-gtatgatttg-tgattatcggctttctgctgcctcttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG
   |   |  | |  |       | || ||    |     | |   | |||  | | | || ||  | | | |||          ||   || | | || ||||||| |||||||||| ||||||||||| ||||| ||||| || ||||| ||||| ||||| || ||| | || ||||| || | ||||
--gttacaatacataatcacgattatacccggcctcattttaggagaaagtccattaggattatgcgcttaatataacacactctctaattcctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG

upper sequence: GRMZM2G018447_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S193_49V6.1 (Physcomitrella patens), 3'ss of exon 4
--gaatggaaggaaaacaatgttggtgtagccttgatggccatggactacagtttactgtatgatttgtgattatcggctttctgctgc-ctcttgtctg--cagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG
    || ||| ||| |  |  | |  | || | ||| ||  | |   | ||  ||| ||    | |  ||||| |    | |  | |    | ||||     ||||||| ||||||||||| ||||| ||||| ||||| ||||||||  |||| ||||| ||||| |||||||| ||||||||  |||  |||
aatcatagaatgaagaacac-tcgacgcagtcatgagggaga-gtggtgcacgttaatg---aaatgatgatttttcattctgggatttatttttgttcaaccagATATATTGTATGACTCTTGGTCACCAGCAATGACTGTGAGCTCCATCTGCATCAGCATCCTCTCTATGTTATCTAGTTCAACAGTGAAG

upper sequence: GRMZM2G018447_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
---------gaatggaaggaaaacaatgttggtgtagccttgatggccatggactacagtttactgtatgatttgtgattatcggctttctgctgcctcttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG
          ||   || |||||| || |  |||||  |||||     |     | | ||||| | || || |  |   |     |||      || || | ||  |||||||| | |||||||| ||||| ||||| ||||||||||| ||| |||| ||||| |||||||| ||||||||||||||  | |  |||
acgagttcccaacttaacgaaaactatctctgtgta--cttgaatttaacatgttgc-gtttaat-taagactaatttctgcaaacttg-----gcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG

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|211421813|gb|FL084940.1|FL084940
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTANCNACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGT
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATG-ACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGT
EST: gi|18163588|gb|BM333427.1|BM333427
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|18172273|gb|BM347661.1|BM347661
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|17929384|gb|BM266344.1|BM266344
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|32869440|gb|CF009122.1|CF009122
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTTCAGCGATGACCGTGAGCTCTG
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTG
EST: gi|211424415|gb|FL084950.1|FL084950
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|211421809|gb|FL084936.1|FL084936
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|211424416|gb|FL084951.1|FL084951
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACC
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACC
EST: gi|76018971|gb|DT946141.1|DT946141
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|89756005|gb|DY686208.1|DY686208
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|211421806|gb|FL084933.1|FL084933
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|211424414|gb|FL084949.1|FL084949
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         G
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcag-
EST: gi|211424414|gb|FL084949.1|FL084949
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         G
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcag-
EST: gi|29947193|gb|CB816528.1|CB816528
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|76288121|gb|DV027689.1|DV027689
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|89246821|gb|DY618608.1|DY618608
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|211421814|gb|FL084941.1|FL084941
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|60352940|gb|DN219913.1|DN219913
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|211421802|gb|FL084929.1|FL084929
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|18166490|gb|BM336329.1|BM336329
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|211424417|gb|FL084952.1|FL084952
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|76288120|gb|DV027688.1|DV027688
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|211421805|gb|FL084932.1|FL084932
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|18169036|gb|BM338876.1|BM338876
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|116821688|gb|EC865015.1|EC865015
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|76018970|gb|DT946140.1|DT946140
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
EST: gi|211421808|gb|FL084935.1|FL084935
EST:     TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG                         ATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA
genomic: TCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAGgtaaaactgc ... ttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacagtttactgtatgatttgtgattatcggctttctgctgcctcttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG
                               ctttctgctgcctctt  CT-rich tract
            tatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatggaaggaaaacaatgttggtgtagccttgatggccatggactacagtttactgtatgatttgtgattatcggctttctgctgcctcttgtctgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - aaaacaa
- - - - - - - - -tgttggt
- - - - - - - - - - - - - - - -tgatggc
- - - - - - - - - - - - - - - - - - - catggac
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgatt