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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtagcatgctatactttggacattattgtagttatcagcatattctgatttcagtcgacctgttctcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTACAGAGACATGGCCTTGGCTGTGAAAAATCCATGCCATCTCAATATGGCTG

Basic information

species Zea mays
transcript GRMZM2G133624_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133624_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g05090.1 (Oryza sativa), 3'ss of exon 5
gttagtagcatgctatactttggacatta-ttgtagttatcagcatattctgatttcagtcgacctgttctcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTACAGAGACATGGCCTTGGCTGTGAAAAATCCATGCCATCTCAATATGGCTG
|||||| |  | ||  |  |    | | |  | | || |   ||  | ||  | | |   | | |||||||  | ||||||| |||||||||||||| |||||||||||||||||||| ||||| |||||||||||||||||||| |||||||||||||| ||||||||||| ||||| |
gttagttgtctactg-atgtcattcttcagctattgtaagatgctcaatcataatccc-cctagctgttcttctttacagGCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTACAGAGACATGGCCTTAGCTGTGAAAAATCCCTGCCATCTCAACATGGCCG

upper sequence: GRMZM2G133624_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G01080.1 (Glycine max), 3'ss of exon 5
-------------------------------gttagtagcatgctatactttggacattattgtag-ttatcagcatattctgattt---cagtcgacctgttctcttcta---------cagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTACAGAGACATGGCCTTGGCTGTGAAAAATCCATGCCATCTCAATATGGCTG
                                 || |     ||| | |||    |||     ||  || ||    |||| ||  ||         |  |||  |  |||          ||||| |||||||| ||||||||||| |||||||| || || ||||| ||||| ||||| |||||  |||| || || |||||||||||||| || ||||| |
gttacacacttatgtttcttgtgctcttcttaataattcttcgctgttcttaatccatggaaatatcttctctttttattttgggttatttgacaaatttgtgattgtcttggttcttgtcagGCCATTGCATATATGGGAGATGACTTCATGTTCCAGTTGTTTGGGAAGTATAGAGATATGGCTCTGGCAGTAAAGAATCCATGCCATCTTAACATGGCAG

upper sequence: GRMZM2G133624_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G36250.1 (Glycine max), 3'ss of exon 6
-----------------------------------gttagtagcatgctatactttggacattattgtagttatcagcatattctga-----tttcagtcgacctgttctcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTACAGAGACATGGCCTTGGCTGTGAAAAATCCATGCCATCTCAATATGGCTG
                                    ||  || |       | |||     || |  || |  |  |  |  | |||     ||   || | | || | |||| | ||||| || ||||| ||||||||||| |||||||| || || ||||| ||||| ||||| |||||  ||||||| || |||||||||||||| || ||||| |
gttacacacttatgtttcttgtgctcttctacataattcttaacccatggaaatttctttcttctcttattattttgggttgtttgacaaatttgtggttgtcttggt-tcttgt-cagGCCATAGCATATATGGGAGATGACTTCATGTTCCAGTTGTTTGGGAAGTATAGAGATATGGCTCTGGCTGTAAAGAATCCATGCCATCTTAACATGGCAG

upper sequence: GRMZM2G133624_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv13s0064g00580.t01 (Vitis vinifera), 3'ss of exon 6
gttagtagcatgct-atactttggacattattgtagttatcagcatattctgatttcagtc------------gacctgttctcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTACAGAGACATGGCCTTGGCTGTGAAAAATCCATGCCATCTCAATATGGCTG
    ||  ||| ||    | |  | || |||||  ||| | ||  ||| | |||||   ||               |  || | ||   ||||| || ||||| ||||||||||| |||||||| || || ||||| |||||| | |||||||| ||||||||||| ||||||||||| || || ||||| |
----gttacatacttgctcctcagtcaatattggtgttttgagtttatgcagattttcttcctcttttgacaaagtccctttttttaaccagGCCATAGCATATATGGGAGATGACTTCATGTTCCAGTTGTTTGGGAAGTACCGTGACATGGCTTTGGCTGTGAAGAATCCATGCCACCTTAACATGGCAG

upper sequence: GRMZM2G133624_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S364_48V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------gttagtagcatgctatactttggacattattgta-gttatcagcatattctgatttcagtcgacctgttctct--tctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTACAGAGACATGGCCTTGGCTGTGAAAAATCCATGCCATCTCAATATGGCTG
                     ||   || | |  | | || ||  ||| |||   ||| |||    | ||   ||  | |    |   |   |  |    ||||  | || |||||||| ||||| |||||||||||| | ||||| ||||||   ||||||||| | || || |||||||| || ||||||||  | ||| 
catttttggggcaaaagcgaattttgaggaag--acatttaggttattgttgggtgttgtcactccaatcaagttctaattccgcgagtggttggttggtagGCACTCGCTTACATGGGTGATGACTTCATGTTTCAACTCTTTGGCAAGTACCACGACATGGCCATTGCAGTAAAAAATCCGTGTCATCTCAACCTTGCTA

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|29130064|gb|CB380768.1|CB380768
EST:     CATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|60357904|gb|DN224877.1|DN224877
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|78108737|gb|DV527154.1|DV527154
EST:     AAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: AAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|71765927|gb|DR963864.1|DR963864
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTTCA-TTATTTTGGAA-GT
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTT-CAATTATTT-GGAAAGT
EST: gi|71299220|gb|DR785608.1|DR785608
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|71438300|gb|DR819350.1|DR819350
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|71768316|gb|DR966253.1|DR966253
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|71756680|gb|DR954617.1|DR954617
EST:     ATATTTCAAAGAAAAGAAGC-TGNAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: ATATTTCAAAGAAAAGAAGCTTG-AGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|78089641|gb|DV518015.1|DV518015
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|33104053|gb|CF064013.1|CF064013
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|71435312|gb|DR816362.1|DR816362
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|76021435|gb|DT948605.1|DT948605
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|149015212|gb|EE044997.2|EE044997
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGGTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|6526795|gb|AW216068.1|AW216068
EST:     GAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: GAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|71299221|gb|DR785609.1|DR785609
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|149076434|gb|EE165057.2|EE165057
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTTCA-TTATTTGGAAAGTA
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTT-CAATTATTTGGAAAGTA
EST: gi|76021436|gb|DT948606.1|DT948606
EST:     CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
EST: gi|71321226|gb|DR797322.1|DR797322
EST:     CATATTTCAAAGATAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATG                         GCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC
genomic: CATATTTCAAAGAAAAGAAGCTTGAGGAGGCCATGCAGCAATATGAAATGgttagtagca ... tcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattattgtagttatcagcatattctgatttcagtcgacctgttctcttctacagGCGATTGCATACATGGGAGATGATTTCATGTTTCAATTATTTGGAAAGTACAGAGACATGGCCTTGGCTGTGAAAAATCCATGCCATCTCAATATGGCTG
                      ttctgat  putative branch site (score: 3)
                                      cctgttctcttctac  putative PPT
        tagttat  TA-rich tract