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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttgatctgttctattttacttgtagttttacttttttcgcaaatcaacatagcattttaatgacctgaccttgcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTTAGGGCATATCATCATACTGCTCAAACAAAGGCCGACAAGCAACATTATT

Basic information

species Zea mays
transcript GRMZM2G039263_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039263_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 3'ss of exon 14
gttttgatctgttctattttacttgtagttttacttttttcgcaaatcaacatagcattttaatgacctgaccttgcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTTAGGGCATATCATCATACTGCTCAAACAAAGGCCGACAAGCAACATTATT
  |||||||  || | || ||  |||    |||| |  |     |   || |||  | | | | |   |||||||| |    ||||| || ||||| |||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| || |||||||| | ||
-gtttgatcacttgtgttctatgtgt----ttacatactggatgacataaaatattaatgtgaag-tgtgaccttgtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTTAGGGCATATCATCATACTGCTCAAACAAAGGCTGATAAGCAACACTTTT
















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|211469892|gb|FL096481.1|FL096481
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTA
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTA
EST: gi|149074900|gb|EE163348.2|EE163348
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|22935598|gb|BU571873.1|BU571873
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|21389952|gb|BQ528001.1|BQ528001
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|22521580|gb|BU080391.1|BU080391
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|67015007|gb|CO443756.1|CO443756
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|37400207|gb|CF637451.1|CF637451
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|32937857|gb|CF042676.1|CF042676
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|211088488|gb|FL432079.1|FL432079
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|7136143|gb|AW498446.1|AW498446
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCCAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|60350871|gb|DN217844.1|DN217844
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|44901279|gb|CK827824.1|CK827824
EST:     AACAATGGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|26559466|gb|CA831701.1|CA831701
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|32937830|gb|CF042649.1|CF042649
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|31405908|gb|CD484640.1|CD484640
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|211524479|gb|FK952707.1|FK952707
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|60343155|gb|DN210128.1|DN210128
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|211524476|gb|FK952704.1|FK952704
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAA-CTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|31406183|gb|CD484915.1|CD484915
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|211524475|gb|FK952703.1|FK952703
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTC
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|84977527|gb|DW475949.1|DW475949
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|14203032|gb|BG836709.1|BG836709
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAY                         GTACTKTCTGTTAATGCTGCAAAAGATGCKACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|67018449|gb|CO447198.1|CO447198
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|87157304|gb|DY402093.1|DY402093
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
EST: gi|166681286|gb|EG299731.1|EG299731
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGAT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGAT
EST: gi|60337774|gb|DN204747.1|DN204747
EST:     AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAG                         GTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatct ... gcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacttttttcgcaaatcaacatagcattttaatgacctgaccttgcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTTAGGGCATATCATCATACTGCTCAAACAAAGGCCGACAAGCAACATTATT
                                   acctgac  putative branch site (score: 3)
                          attttaatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttgatctgttctattttacttgtagttttacttttttcgcaaatcaacatagcattttaatgacctgaccttgcgcctacagGTACTATCTGTTAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTTAGGGCATATCATCATACTGCTCAAACAAAGGCCGACAAGCAACATTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA