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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGACCTGGCTGTCTACTCTTCATTTTTGGCTGATCCCTCATCCAAGTATATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgcccttcttggcctttatgtttcctaggtatcccgttagcagtgagtgtgctaataatccatactatttcag

Basic information

species Zea mays
transcript GRMZM2G153569_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153569_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g42300.2 (Oryza sativa), 5'ss of exon 3
ATGACCTGGCTGTCTACTCTTCATTTTTGGCTGATCCCTCATCCAAGTATATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgcccttcttggcctttatgtttcctaggtatcccgttagcagtga-gtgtgctaataatccatactatttcag
||||| ||||||| |||||| ||||||   |||  ||||| || |  |||| |||||| || |||||||||| ||||||||||||||||||  | |||||||||||  || |   | ||| |  |||      ||    |   |||||  |||   |         |  ||||||||
ATGACTTGGCTGTGTACTCTGCATTTTCAACTGCGCCCTCTTCAAGCTATACCAATGTTGCTAGGTGGTTTACTCACATTGATGCACTCCTACGTCTGAGgtatgcatttttcccctttttttattctcttacattttatgttcagtgttgtgaattttctgaatgttgtatttcag
















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|211378085|gb|FL329648.1|FL329648
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGG
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGG
EST: gi|60339257|gb|DN206230.1|DN206230
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|76285318|gb|DV024886.1|DV024886
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|211291797|gb|FL131040.1|FL131040
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|13237021|gb|BG355035.1|BG355035
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|61117414|gb|DN558375.1|DN558375
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCTGCAGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|211291795|gb|FL131038.1|FL131038
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGGTTC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGG-TTC
EST: gi|32840968|gb|CD980649.1|CD980649
EST:     AATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCTGCAGTTCC
genomic: AATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|76926349|gb|DV170823.1|DV170823
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|67012865|gb|CO441614.1|CO441614
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|33093219|gb|CF053213.1|CF053213
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACCCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCTGCAGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|32846492|gb|CD986173.1|CD986173
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCTGCAGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|31557965|gb|CD527177.1|CD527177
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|211291796|gb|FL131039.1|FL131039
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|211437727|gb|FL330573.1|FL330573
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|67037468|gb|CO464282.1|CO464282
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCTGCAGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|32829957|gb|CD969635.1|CD969635
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCTGCAGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|211535307|gb|FL356762.1|FL356762
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|67016304|gb|CO445053.1|CO445053
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|8273074|gb|BE012169.1|BE012169
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|84977404|gb|DW475826.1|DW475826
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGACGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGAGTTAAGGTTGAGCCATCTGCAGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|211255757|gb|FL351785.1|FL351785
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|211232671|gb|FL320353.1|FL320353
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|60359229|gb|DN226202.1|DN226202
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC
EST: gi|33093139|gb|CF053133.1|CF053133
EST:     ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAG                         TGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCTGCAGTTCC
genomic: ATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgccctt ... actatttcagTGGAGTTACCGCAGAGGGCCTAGGTGTTAAGGTTGAGCCATCAGCGGTTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGACCTGGCTGTCTACTCTTCATTTTTGGCTGATCCCTCATCCAAGTATATCAATGTAGCAAGGTGGTTTAATCACATTGATGCACTCCTGAGGCTGAGgtatgcccttcttggcctttatgtttcctaggtatcccgttagcagtgagtgtgctaataatccatactatttcag

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