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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttacttttattagtaataagattttaatatcaattagagaagtacagaatatgttttctgacggcggttattatttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG

Basic information

species Zea mays
transcript GRMZM2G153704_T07
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153704_T07 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g04190.1 (Oryza sativa), 3'ss of exon 10
gtaagtttacttttattagtaataagattttaatatcaattagagaagtacagaatatgttttctgacggcggttattatttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG
|| |||  |   |||      | |  ||| ||  |||||||            |||    ||||||| ||    ||| |||| || |||||||| ||| ||||||||||||| |||||||| ||||||||||| |||||||||||||||||||||||||| |||
gttagtccatgctta-----gaaagtattctagaatcaattt--------tgaaatggcctttctgatggtatatat-attt-ctgatagGTACAATGATTGCATCTTCTCTGATGGACAAGCAAGGAAGGAAGAGCCTTCTGATAACAAGCTTTTCTGGCATG

upper sequence: GRMZM2G153704_T07 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G07780.2 (Glycine max), 3'ss of exon 11
--------------------gtaagtttacttt-tatt-agtaataagattttaatatcaattagagaagtacagaatatgttttctgacggcggttattatttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG--------------------------
                      | ||||| | |  ||| ||||| |  |  ||| | |  ||     |   |||  |||| ||||||||  |  ||| ||||||      ||| |||    |||| || ||  ||||||||||||||||||||||||| || || || |||||||||  ||| |||                          
gttagtatttttattcttaaaaatgtttattgtgcattcagtaaaagaaggttattgtatatgttccacaaacatgatattttttctgattgaagtt-ttattt---tgcagGAACTTGTATTGCTTCCTCCTTAATGGACAAACAAGGAAGGAAAAGTCTCCTTATCACAAGCTTTAGTGGGATGGTAATAGATGTTTTCGGCACACATCT

upper sequence: GRMZM2G153704_T07 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G07780.1 (Glycine max), 3'ss of exon 10
--------------------gtaagtttacttt-tatt-agtaataagattttaatatcaattagagaagtacagaatatgttttctgacggcggttattatttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG
                      | ||||| | |  ||| ||||| |  |  ||| | |  ||     |   |||  |||| ||||||||  |  ||| ||||||      ||| |||    |||| || ||  ||||||||||||||||||||||||| || || || |||||||||  ||| |||
gttagtatttttattcttaaaaatgtttattgtgcattcagtaaaagaaggttattgtatatgttccacaaacatgatattttttctgattgaagtt-ttattt---tgcagGAACTTGTATTGCTTCCTCCTTAATGGACAAACAAGGAAGGAAAAGTCTCCTTATCACAAGCTTTAGTGGGATG

upper sequence: GRMZM2G153704_T07 (Zea mays), 3'ss of exon 8
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 10
--------gtaagtttacttttattagtaataagattttaatatcaattagagaagtacagaatatgttttctgacggcggttattatttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG
         |   ||  || | |||  |  ||| ||||| || |||         ||| ||||| | ||   |||| | | || | || | || | ||| ||     | ||||| ||| | |||||||  |||||||||||||| ||||| |||||||||||| |||| |||
gtaatcctttttattctctctgatttcttgtaaaattttgatttcatactt---tgtagagaatgttttacatgactg-gattttgatcttcttacagGCACAGCCATAGCATCCTCTTTGATGGACAGGCAAGGAAGGAAAAGTCTTCTAATAACAAGCTTTGCTGGGATG

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|60339792|gb|DN206765.1|DN206765
EST:     GTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: GTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|60400456|gb|DN233263.1|DN233263
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|211050169|gb|FL124870.1|FL124870
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGATTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|148981334|gb|EE027588.2|EE027588
EST:     AGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: AGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|101389575|gb|EB816720.1|EB816720
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|61119088|gb|DN560049.1|DN560049
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|67035008|gb|CO463541.1|CO463541
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|60339583|gb|DN206556.1|DN206556
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|211050165|gb|FL124866.1|FL124866
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGATTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|67037358|gb|CO464198.1|CO464198
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|149071544|gb|EE159937.2|EE159937
EST:     GATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: GATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|60355926|gb|DN222899.1|DN222899
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|116826239|gb|EC870015.1|EC870015
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGGGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|67011667|gb|CO440416.1|CO440416
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|7844519|gb|AW787741.1|AW787741
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|211050172|gb|FL124873.1|FL124873
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGATTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|211050170|gb|FL124871.1|FL124871
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGATTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|60351782|gb|DN218755.1|DN218755
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|60401429|gb|DN234236.1|DN234236
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|78179345|gb|DV549718.1|DV549718
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|211106867|gb|FL216747.1|FL216747
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGATTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|94472602|gb|EB701560.1|EB701560
EST:     GCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: GCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|60358931|gb|DN225904.1|DN225904
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|7844129|gb|AW787332.1|AW787332
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|60355312|gb|DN222285.1|DN222285
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|18963572|gb|BM660510.1|BM660510
EST:     GCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: GCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|148996906|gb|EE035710.2|EE035710
EST:     GCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: GCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
EST: gi|22545719|gb|BU098078.1|BU098078
EST:     TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTG                         GTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC
genomic: TGCATCTGATGTTGCTGCTAGTGCTCTTGTTGGAGCAGCCAATGTTTTTGgtaagtttac ... ttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaattagagaagtacagaatatgttttctgacggcggttattatttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG
                          ttctgac  putative branch site (score: 2)
                                            tttactc  putative PPT
                                      ttattatttactcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttacttttattagtaataagattttaatatcaattagagaagtacagaatatgttttctgacggcggttattatttactcatagGTACTATGGTTGCATCTTCTCTAATGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT