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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacgaattgaaaatacatgcatactcttcaatacatgtcgttttcatattgtattaagacttaccgtcaatgaaacccattatttttttggtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCG

Basic information

species Zea mays
transcript GRMZM2G392975_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G392975_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g44630.2 (Oryza sativa), 3'ss of exon 3
-------aacgaattgaaaatacatgcatactcttc---aatacatgtcgttttcatattgtattaagacttaccgtcaatgaaacccattatttttttggtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCG
       ||  ||||||   ||   | ||| |       | || || | | |||  | | || ||             || | |   |  |  ||| |||||||||||||||||||||||||||||||||||| || |||||||||||||||||||| |||||||||||||||||||| || ||||||||||| || |||||||||||||
tttgctcaagaaattgactgtatgcgtatagttactggaagtatatatgggttttttgt-gtgttgca---------taacgtatttctgtcctttgttggtgaaaacagATCCTTGCCCCACTGCCAATTGGTTTTGCGGTGTTCCTGGTCCACCTGGCCACCATCCCCATCACCGGTACTGGCATCAACCCAGCCAGGAGCCTTGGCG

upper sequence: GRMZM2G392975_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA14G06680.1 (Glycine max), 3'ss of exon 2
aacgaattgaaaatacatgcatactcttcaatacat-gtcgttttcatattgtattaagacttaccgtcaatgaaacccattattttt--ttgg---tgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCG
    | |||  | || ||| ||| | |  | ||||| | | |    | |    |  |  | |||   | ||  ||| | | |  | |   |||    |   |  ||||  | || ||  |||||||||||||||| |||||| |||| ||| | || ||||||||||||||||| || || |||||||| ||| | || ||||| |
----atttgtgattagatg-ata-tgtaaattacatagccatcaaaaaaaaaaaaaaccatttattatgaactaaatctaattgtgtgggttgaatatatgagtagATTTTGGCACCCTTGCCAATTGGGTTCGCTGTGTTCTTGGTTCACTTGGCAACCATCCCCATCACCGGAACTGGTATCAACCCTGCTCGTAGTCTTGGTG

upper sequence: GRMZM2G392975_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G35030.1 (Glycine max), 3'ss of exon 2
--------------------------------aacgaattgaaaatacatgcatactcttcaatacat-gtcgttttcatattgtattaagacttaccg--tcaatgaaacccattatttttttggtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCG
                                 |   | | || || |||||| |   ||   || || |     |  ||  |  ||    ||| |  |  ||||||||  | || | |    || |     |||||  | || ||  |||||||||||||||| |||||| |||| ||| | ||||| ||||| ||||| || || || |||||||| ||  | || || || |
gtatgtgcatgccctcttctcttgtctcataatatataattaacatgcatgcaaaaaattacttaaatagatacatgtatgattcat-ggaactgaatgaatcaatgaa-tcaatgaatcaaatgat-----cagATTTTGGCACCCTTGCCAATTGGGTTCGCTGTGTTCTTGGTGCACTTGGCCACAATCCCAATCACTGGAACTGGTATCAACCCTGCACGAAGTCTCGGTG

upper sequence: GRMZM2G392975_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA14G06680.3 (Glycine max), 3'ss of exon 2
aacgaattgaaaatacatgcatactcttcaatacat-gtcgttttcatattgtattaagacttaccgtcaatgaaacccattattttt--ttgg---tgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCG
    | |||  | || ||| ||| | |  | ||||| | | |    | |    |  |  | |||   | ||  ||| | | |  | |   |||    |   |  ||||  | || ||  |||||||||||||||| |||||| |||| ||| | || ||||||||||||||||| || || |||||||| ||| | || ||||   
-ggaatttgtgattagatg-ata-tgtaaattacatagccatcaaaaaaaaaaaaaaccatttattatgaactaaatctaattgtgtgggttgaatatatgagTAGATTTTGGCACCCTTGCCAATTGGGTTCGCTGTGTTCTTGGTTCACTTGGCAACCATCCCCATCACCGGAACTGGTATCAACCCTGCTCGTAGTCTTG---

upper sequence: GRMZM2G392975_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G42220.3 (Glycine max), 3'ss of exon 2
--aacgaattgaaaatacatgcata--ctcttcaatacatgtcgttttcatattgtattaagact--taccgtcaatgaaacccattattttt--ttgg---tgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCG
  ||       |   |   |  | |  ||||| |||     |  |||   ||    |  || |||  |   ||  |  ||||| | |  | |   |||    |   |  ||||  | || ||  |||| |||||||||||||||||| |||| ||| | || |||||||| ||||||||||| || |||||||| ||| | || ||||| |
gtaagccccccaccctctgtcgaaaatctctttaat-tgctttttttcgttaaaaaaaaaatactatttttgtggactaaacctaattgtgtgggttgaatatatgagtagATTTTGGCACCTTTGCCTATTGGGTTCGCGGTGTTCTTGGTTCACTTGGCAACCATCCCTATCACCGGCACTGGTATCAACCCTGCTCGTAGTCTTGGTG

upper sequence: GRMZM2G392975_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0067g00220.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------aacgaattgaaaatacatgcatactcttcaatacatgtcgttttcatattgtattaagacttacc---gtcaatgaaacccat-tatttttttg---gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCG
                                 |  | |   |  |    |  ||||    |  ||  | ||  |||  ||  |||||   || ||   |||  ||      || |||| |||||   |||  || |||| || || ||  ||||||| |||||||| |||||| |||| ||| | |||||||||||||| || || |||||||||||||| ||| ||||||| || |
gtaagctatacatctctctgtctttctctttctcagactctcacgat-cacccactcaatcactcactttgtcatcaagtta-attaattattgcctttgtcggtgtgggtgatgtattattttgaatgtgttaa-agATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCCACCATCCCCATAACTGGAACCGGCATCAACCCAGCTCGGAGCCTGGGTG

upper sequence: GRMZM2G392975_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv15s0046g02410.t01 (Vitis vinifera), 3'ss of exon 2
aacgaattgaaaatacatgcatactcttcaatacatgtcgttttcatattgt-attaagacttaccgtcaatgaaacccattatttttttgg---tgaaa-acagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCG
   ||  |     | |   |  | | |||||  |||  |       ||||   | |  ||  |       |  | |||| |||||||    |   ||||   |||||  | || || || || |||||||| || |||||| |||| || || || ||||||||||||||||| |||||||||||||| |||||||| || || |
---gacgtcccctttcgctctcatttttcaac-catacctgagaattattacgaatgggatctgaaaatgac-acaccctttattttccctgaattgaactgcagATTTTGGCTCCTCTCCCGATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTCGGGG

upper sequence: GRMZM2G392975_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv02s0025g03390.t01 (Vitis vinifera), 3'ss of exon 2
aacgaattgaaaatacatgcatactcttcaatacatgtcgttttcata--ttgtattaagacttaccgtcaatgaaacccattatttttttggtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCG
      |||  | |    |  || |   || |||  |   | |  | |  |   ||  | |  |   || |    |||| |  | || ||   |  |  |||||  | ||||| || || |||||||| || |||||| |||| ||| | ||||||||||||||||| || || ||||| ||||| || ||||| ||||| |
ttttctttggtagttagagggtagttaccattactagaaatgtgaacaagtcccatacaaatcttgagttaccctaaccga--aattcttgaatatatgcagATTTTGGCCCCCCTCCCCATTGGGTTTGCAGTGTTCTTGGTTCACTTGGCCACCATCCCCATCACAGGAACTGGCATTAACCCAGCCAGGAGTCTTGGAG

upper sequence: GRMZM2G392975_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv15s0046g02420.t01 (Vitis vinifera), 3'ss of exon 2
aacgaattgaaaatacatgcatactcttcaatacatgtcgttttcatattgtattaagactta---ccgtcaatgaaac--ccattatttttttggtgaaaa----cagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCG
           | |     |  | | |||||    |   | |   || |  ||||   | |     | |  ||| | ||  || ||||||||   | |   |    |||||  | || || || || |||||||| || |||||| |||| || || || ||||||||||||||||| |||||||||||||| |||||||| || || |
---------ccattttcctctcatttttcaaccattcctgatggtatttattattgcaaatgggatctgaaaataacacgccctttatttttcctgcgttgaactgcagATTTTGGCTCCTCTCCCCATTGGGTTTGCAGTGTTCTTGGTTCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGG

upper sequence: GRMZM2G392975_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S1_535V6.2 (Physcomitrella patens), 3'ss of exon 2
---------------------aacgaattgaaaatacatgcatactcttcaatacatgtcgttttcatattgtattaagacttaccgtcaatgaaacccattat----ttttttggtgaaa--acagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCG
                       |   |      || ||     | | | |  || ||  |  |  || || |  ||   || || || |      | ||  ||     | || | || |    ||| | ||||| || || || || || ||||| || |||||||| ||| | |||||||| ||||||||||| || ||||||||||| ||  | || || || |
gtgagtacactccgtttccggtgcagttcagttctagattaccgcgcctgag-acgtgctggctg-atctt-tggtactcctcacagttagatggtctcaaaatgatgctcttcgatggacttgcagGTGCTTGCGCCTCTTCCCATCGGATTCGCAGTTTTCCTGGTGCACTTGGCCACCATTCCCATCACCGGAACTGGCATCAACCCCGCCCGTAGTCTAGGTG

upper sequence: GRMZM2G392975_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ18960 (Selaginella moellendorffii), 3'ss of exon 2
-------------------------------------------------------------------------------------------aacgaattgaaaatacatgcatac-tcttcaatacatgtcgttttcatattgtattaagacttaccgtcaatg--aaacccattatttttt-tggtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCG
                                                                                                  |     ||| | |     |||||     || || | | |   |  |    ||| |||   |   |   || | ||  |  |||   | |    |||| |  | || ||||| ||||| ||||| ||||||||||| |||||||||||||| ||||||||||| ||||| ||||||||||| ||  | || || ||| 
gtacgtttcttcttccatccaaagctttggttgattcccctctcatgaagttttgcttttcttcttcttatcttcttgtgtggttttcctagtttttcttgctgtacttcctcttatcttctccttatctcttctcctcctcatggatagatttaagatatgttccaagctcacaaactttggcgatttctacagCTTTTGGCTCCACTTCCAATCGGGTTTGCGGTGTTCCTCGTCCACCTTGCCACGATCCCCATCACTGGCACGGGCATCAACCCAGCGCGAAGTCTCGGCT

upper sequence: GRMZM2G392975_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ11572 (Selaginella moellendorffii), 3'ss of exon 2
---------------------------------------------------------------------------------------------aacgaattgaaaatacatgcatac-tcttcaatacatgtcgttttcatattgtattaagacttaccgtcaatg--aaacccattatttttt-tggtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCG
                                                                                                    |     ||| | |     |||||     || || | | |   |  |    ||| |||   |   |   || | ||  |  |||   | |    |||| |  | || ||||| ||||| ||||| ||||||||||| |||||||||||||| ||||||||||| ||||| ||||||||||| ||  | || || ||| 
gtacgtttctccttccatccaaagctttggttgattcccccctctcatgaagttttacttttcttcttcttatcttcttgtgtggttttcctagtttttcttgctgtacttcctcttatcttctccttatctcttctcctcctcatggatagatttaagatatgttccaagctcacaaactttggcgatttctacagCTTTTGGCTCCACTTCCAATCGGGTTTGCGGTGTTCCTCGTCCACCTTGCCACGATCCCCATCACTGGCACGGGCATCAACCCAGCGCGAAGTCTCGGCT

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|148936891|gb|EC881041.2|EC881041
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACT
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACT
EST: gi|76285262|gb|DV024830.1|DV024830
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCCACTTTGC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCC-ACCTTGC
EST: gi|149079702|gb|EE168703.2|EE168703
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACC
EST: gi|76923442|gb|DV169489.1|DV169489
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
EST: gi|148931929|gb|EC875151.2|EC875151
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCCATTGGGTTCGCGGTGTTCCTGGGTCCACCTTGC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGG-TCCACCTTGC
EST: gi|94472445|gb|EB701403.1|EB701403
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
EST: gi|211489110|gb|FL100837.1|FL100837
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCAATTGGGGGTTCGCGGTG
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGG--TTCGCGGTG
EST: gi|71330068|gb|DR801773.1|DR801773
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCCCTGCCAATTGGGTTCGCGG
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGG
EST: gi|149099303|gb|EE185339.2|EE185339
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
EST: gi|149111018|gb|EE294517.2|EE294517
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTC-ACCTTGCC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
EST: gi|31350056|gb|CD434413.1|CD434413
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
EST: gi|76012460|gb|DT939630.1|DT939630
EST:     TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCC                         ATCCTTGCCCCACTGCCCATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC
genomic: TCTTCTCGGCCACCGATGCCAAGAGGAACGCCAGGGACTCCCATGTCCCCgtaagtactc ... gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattgtattaagacttaccgtcaatgaaacccattatttttttggtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCG
            gacttac  putative branch site (score: 2)
                                 attatttttttggt  TA-rich tract