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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtaaaatgctattgggttatttttgcacatggtttgacagttatcatgcttgttactagcctacaaaattattattctatcttttgtatttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA

Basic information

species Zea mays
transcript GRMZM2G007283_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007283_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g02810.1 (Oryza sativa), 3'ss of exon 2
-ctgtaaaatgctattgggttatttttgcacatggtttgacagttatcatgcttgttactagcctacaaaattattattctatcttttgtatttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA
  |     ||  ||||   ||     | |  |   ||| |   || || |   |||||  ||  |    |   | ||    ||||||||| | | |||||||| || ||||  | ||| |||||| |||| |||||||| || || |||||||| || ||||||||||||||||||||  |||||||||| ||||||||||
tttcgggcatattattaacttggaaatccttaccttttcattcttgtcgt-tatgttataagaattatcaggaagtaactcatcttttgtttctttgtcagACTGAGGTTAGGTTCCTTGGGCAGCTAAGACATCCAAATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCA

upper sequence: GRMZM2G007283_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g02830.2 (Oryza sativa), 3'ss of exon 2
ctgtaaaatgctattgggttatttttgcac-atggtttgacagttatcatgcttgttactagcctacaaaattattattctatcttttgtatttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA
 |     ||  ||||   ||     | ||  |   ||| |   || || |   |||||  ||  |    ||  | ||    ||||||||| | | |||||||| || ||||  | ||| |||||| |||| |||||||| || || |||||||| || ||||||||||||||||||||  |||||||||| ||||||||||
ttcgggcatattattaacttggaaattcattaccttttcattcttgtcgt-tatgttagaagaattatcaagaagtaactcatcttttgtttctttgtcagACTGAGGTTAGGTTCCTTGGGCAGCTAAGACATCCAAATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCA

upper sequence: GRMZM2G007283_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G45200.1 (Glycine max), 3'ss of exon 2
ctgtaaaatgctattgggttatttttgcacat-ggtttgacagttatcatgcttgttactagcctacaaaattatt--attctatcttttgtatttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA
  || |  || |  | |  | |      || |   | |   | ||     || |  |   |  | | |   |||||  ||| | | | || |  |  || ||||| || || || |  || |||||| | |||||||| ||  ||||||||||||| || || |||||||||||||| ||  |||||||||| || |||||| 
-cgtgatgtgattgttgagtgtcaaaataccttaatgttgaaattgcagagcgtaatttgaaaccatacgtttatttaattttgtgtgttttggtggtg-caGACGGAGGTGAATTTTCTAGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGCTGCGAAGATGATCACAGGCTGCTTGTGTATGAGTTC-

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|67022281|gb|CO451030.1|CO451030
EST:     CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTT                         ACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTTgtgagttgat ... tttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG
EST: gi|148957429|gb|EC903492.2|EC903492
EST:     CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTT                         ACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTTgtgagttgat ... tttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG
EST: gi|78081509|gb|DV509921.1|DV509921
EST:     CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTT                         ACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTTgtgagttgat ... tttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG
EST: gi|148932585|gb|EC876437.2|EC876437
EST:     CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTT                         ACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTTgtgagttgat ... tttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG
EST: gi|211183056|gb|FK969613.1|FK969613
EST:     CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTT                         ACCGAAGTTAACTGCCTGGGGCAGTTGAGGCATCCAAACTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTTgtgagttgat ... tttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG
EST: gi|149102573|gb|EE188233.2|EE188233
EST:     CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTT                         ACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTTgtgagttgat ... tttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG
EST: gi|71437207|gb|DR818257.1|DR818257
EST:     CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTT                         ACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTTgtgagttgat ... tttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG
EST: gi|71315550|gb|DR794379.1|DR794379
EST:     CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTT                         ACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTTgtgagttgat ... tttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG
EST: gi|78082095|gb|DV510507.1|DV510507
EST:     AGTCAAGGTGCTCAACAAAGATGGACACCAAGGGGCACAGAGAATGGCTT                         ACCGAAGTTAACTGCCTGGGGGAGTTAAGGCATCC
genomic: AGTCAAGGTGCTCAACAAAGATGGACACCAAGGG-CACAGAGAATGGCTTgtgagttgat ... tttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCC
EST: gi|149094890|gb|EE180468.2|EE180468
EST:     CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTT                         ACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTTgtgagttgat ... tttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG
EST: gi|149000180|gb|EE037319.2|EE037319
EST:     CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTT                         ACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCCAACTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACACCAAGGGCACAGAGAATGGCTTgtgagttgat ... tttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgcttgttactagcctacaaaattattattctatcttttgtatttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA
                  tacaaaattattattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtaaaatgctattgggttatttttgcacatggtttgacagttatcatgcttgttactagcctacaaaattattattctatcttttgtatttatgtcagACCGAAGTTAACTGCCTGGGGCAGTTAAGGCATCCAAACTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT