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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtccatgatggttgctcaagccatgttttctatatccattcatctcttctttctctaggctacatgcatatttattctttattaatttcttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGGCGTTGTTATATGCCATCCGAATGGTAACACTGATGGATGTGACGAAGCC

Basic information

species Zea mays
transcript GRMZM2G163912_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G163912_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g58480.1 (Oryza sativa), 3'ss of exon 1
---tgtccatgatg--gttgctcaagccatgttttctatatccattcatctcttctttctctaggctacatgcatatttattctttat-taatttcttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGGCGTTGTTATATGCCATCCGAATGGTAACACTGATGGATGTGACGAAGCC
   | |  ||  ||  ||||||     |||| | | | |    | | |   ||| |     |   ||      ||| || |  || || || |||  |   |||||||||||| |||||||||||||||||||||| ||||| |||||||| || || || |||||||| |  ||  |||| |||| |||||   | || ||||||
ttctatatattgtgtagttgcttg---catgctatttgtggtgaataa---cttatgaggttgtacttttgttataattgtggttaatgtactttaatccttgcagTCCAATGGTGAAAGAGGCTGTGGAAATGTCCACAGACGAAGAATCAGACGGTGTCGTTATATGTCCACCAGATGGCAACAATGATGATCGAGAGGAAGCC
















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|148969207|gb|EE019955.2|EE019955
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|149026634|gb|EE046054.2|EE046054
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|211454809|gb|FL307043.1|FL307043
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|211164209|gb|FL365735.1|FL365735
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|149113175|gb|EE295923.2|EE295923
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|211265647|gb|FL357470.1|FL357470
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|211511984|gb|FL308788.1|FL308788
EST:     GCGGCGGCACGACGCCGGTGGGATCTCACCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|211342746|gb|FL350515.1|FL350515
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|91051871|gb|EB162289.1|EB162289
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|148940178|gb|EC884940.2|EC884940
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|26557716|gb|CA829951.1|CA829951
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|148993804|gb|EE033889.2|EE033889
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|211494831|gb|FL326697.1|FL326697
EST:     GCGGCGGCACGACGCCGGTGGGATCTCACCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|149104910|gb|EE290380.2|EE290380
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|211061316|gb|FL328106.1|FL328106
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|149001239|gb|EE038515.2|EE038515
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|148944987|gb|EC890160.2|EC890160
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|149099628|gb|EE185673.2|EE185673
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|211393901|gb|FL329727.1|FL329727
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|211425496|gb|FL357534.1|FL357534
EST:     GCGGCGGCACGACGCCGGTGGGATCTCACCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|211333886|gb|FL365385.1|FL365385
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|211401435|gb|FL321320.1|FL321320
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|211184259|gb|FL364400.1|FL364400
EST:     CGGCGGCACGCCGNCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGNGATG
genomic: CGGCGGCACGCCG-CCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCG-GATG
EST: gi|211430766|gb|FL360606.1|FL360606
EST:     GCGGCGGCACGACGCCGGTGGGATCTCACCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|211259897|gb|FL317730.1|FL317730
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|50333496|gb|CO528622.1|CO528622
EST:     GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: GCGGCGGCACGCCGCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
EST: gi|211095900|gb|FL320659.1|FL320659
EST:     CGGCGGCACGCCGCCCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCAC                         TCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG
genomic: CGGCGGCACGCCG-CCGGTGGGATCTCTCCAACAAGGGCCCCGACAGCACgtaatggcac ... ttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttctttctctaggctacatgcatatttattctttattaatttcttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGGCGTTGTTATATGCCATCCGAATGGTAACACTGATGGATGTGACGAAGCC
                                   tattaat  putative branch site (score: 2)
                              ttctttattaatttct  CT-rich tract
                   atgcatatttattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtccatgatggttgctcaagccatgttttctatatccattcatctcttctttctctaggctacatgcatatttattctttattaatttcttttctgcagTCCAATGTTGAAAGAGGCTGTGGAAATGTCTACAGATGAAGAATCGGATGGCGTTGTTATATGCCATCCGAATGGTAACACTGATGGATGTGACGAAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA