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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

Basic information

species Zea mays
transcript GRMZM2G300412_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os03g16980.3 (Oryza sativa), 3'ss of exon 7
gtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
                            ||||||  ||| |||||  ||| |||||  ||||||   |   || || |  || |  ||  |||   | |||   |||||| |||||||| ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||| ||||||||||||||||| || ||
--------------------------gtaatatttttagttcata--cctttttgtcttgtgatg--tactggattgtagttctccttaataagtat-tttccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os03g16980.5 (Oryza sativa), 3'ss of exon 8
gtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
                            ||||||  ||| |||||  ||| |||||  ||||||   |   || || |  || |  ||  |||   | |||   |||||| |||||||| ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||                             
--------------------------gtaatatttttagttcata--cctttttgtcttgtgatg--tactggattgtagttctccttaataagtat-tttccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTT-----------------------------

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 9
gtaacacttcatctttca---cttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
||||    |  |||||     |||| | ||   | |   |   |   || | | |    || | |||   |||  | || | |  |  ||    |   || | |||   || |     ||||||| || ||||| || || || ||||| ||||| ||  | ||||| ||||||||||| |||||||| ||||||||||||||||| ||  ||||
gtaatttattgtctttttttccttataatttcttctcgttttgtttaaggcatatccaata-gagatttttctttgttttttaactccttg---aggtgtttatatatcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGCAACTTCATTGCTCAAGCACTGCG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 8
--------------gtaacacttcatctttcacttaa----acttcaat-attagtagctca--tagtcctc--tttgttatg-tgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
               ||    ||| | ||   |||      |  ||| | |||    || ||   ||| | |  ||||   || || |||||        || | |   | |  |     | || || || | | |||  |||||| || ||||| || || |||||||| ||||| ||  | ||||| ||||||||||| |||||||| || |||||||||||||| ||  | ||
gtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcat-atttttctct-cagAAATACGCATTGCGAGAATCTTCAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTCAGTAACTTCATTGCTCAAGCAATTCG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 9
gtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgatttttt-ttcttaacagtgtttatcatctatgtc--tgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
||||    |  ||||    |    | |    |||  |  |||||  |  |      |||    ||    |     | || || ||   || |    ||||||||      | ||    ||||||| || ||||| || || || ||||| ||||| ||  | ||||| ||||||||||| |||||||||||||||||||||||||| ||  | ||
gtaatttcttgtcttctttt----ccttgtaatttctt-ctcattttgtttacacatatccagtagagatttatctttgtttcttaactccttgtggtgtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 8
gtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtct----gtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
||||   ||| ||| |   ||   |||||    |||| |    | |  ||| |||||||     |    | |   | |   | | |   ||||| | ||||   || | | | |     ||||||| ||  |||| || || || ||||| ||||||||  | ||||| ||||||||||| |||||||| ||||||||||||||||| ||  | ||
gtaa--tttcttctcttcttttttcttca----tagttgtctgttg--ctccttgttata----actggtagaaatttttctctgtaatttaactgagttttctatatttctttcaacatagAAATACGTGTTGCAAGAATCTTTAACACATATGGGCCGCGCATGAATATTGATGATGGACGTGTTGTCAGCAACTTCATTGCTCAAGCAATTCG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 8
---------gtaacacttcatctttcacttaaacttcaatattagtagct----catagtcctctttgttatgtgataactctgggcttatgattttttttc-----ttaacagtgtttatcatctatgtct----gtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
         |     |||    |   | ||    || | | ||  |   |    ||||||  |||||  |   |  | |     ||   |  ||||| |||      ||||| | |||| | || | | | |     ||||||| ||  |||| || || || ||||| ||||||||  | ||||| ||||||||||| |||||||| ||||||||||||||||| ||  | ||
gtaatttctgctcttcttttcttcatagttgttgttgattgttgttgttttcttcatagttgtcttttgttccttgttatagctggtagaaaattttcttttgtaagttaactgagttttttatatttctttcaacatagAAATACGTGTTGCAAGAATCTTTAACACATATGGGCCACGCATGAATATTGATGATGGACGTGTTGTCAGCAACTTCATTGCTCAAGCGATTCG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgata-actctgggcttatgattttttttcttaacagtgtttatcatctatgt-ctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
                            || |||| |  ||| |   ||  ||| ||      |    | |  ||||||    |  ||  |||  | | | |||  |||      |||||| || || || || ||||| |||||||| ||||| ||| | ||||||||||||||||| || ||||| ||||||||||||||||||||| |  |
--------------------------gtaaaattaatcactcttttaccattttcttgaaaactttgatttaagcttattggctgattagttattact-tctattgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtg-ataactctgggcttatgatttttt-ttcttaacagtgtttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
||||   | ||| ||   || |  ||              |||   | |||  ||| || || || |   |   || ||  |  ||| ||| | | | ||||| |  |   | | |||||||||||| ||||| || || |||||||| ||||| ||  | |||||||| ||||||||||||||||| |||||||||||||| || ||  | ||
gtaa-gttgcatttt---ctcaggctctcgc--------ttcaactttctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
       |   | ||  ||||   |   ||  | | |   |||   |  ||||| |   |||||  || |  | || | |||    |          |||| ||||       |||||||||||| ||||| || || |||||||| ||||| ||| | |||||||| |||||||| |||||||| ||||||||||||||||| ||  | ||
------gtcagttttctactt---ccctaaactcactgcatcacttttttctttatccagtgattcctttaagattctcattggcct----------gtttgtcat------ttgtagAAATCCGCATTGCTAGAATCTTCAACACATATGGTCCTCGAATGAACATCGATGATGGGCGTGTTGTGAGCAACTTCATTGCTCAAGCACTCCG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 8
---------------------------------------------------------------gtaa-cacttcatctttcacttaaacttcaatattagtagctcatag----tcctctttgttatgtgataactctgggctt--atg-atttt---ttttcttaacagtgtttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
                                                                 |  ||||   ||  | |    |  |  || |||  |  |||        |||   |   ||| ||| ||||||    |   ||| | | |   |||  ||   | || | ||| | ||       ||| || |||||||||||||| ||||| || ||||| ||  | ||||| |||||||| || |||||||| ||||| ||||||||||| ||  | ||
gtaaaattgggctccctctctctgatccatacacccaacacacagacacccccacacctacacacattcactcagtcactgatgggatgtgtaaaattgttcactcccttcccctccctctctctatctga-aactctactttccaatgcactctcactttattttgaaatggtgatcctata-----acagAGATACGGATTGCCAGGATATTCAATACTTATGGACCCCGAATGAATATTGATGACGGGCGTGTTGTCAGCAATTTCATTGCTCAAGCAATTCG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 8
gtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
                      |||||   | ||  |   |  || ||||        |   || | | ||   || | || | |       |   ||||| |      | |    |||||| || ||||| || ||||||||||| ||||||||  | ||||| ||||||||||| |||||||| ||||| ||||| ||||| ||  | ||
--------------------gtaacttttgtgtttttt-tttttaatcctgaacaaacttcaatgaatatgaagttttaatatgt-------atgttgtttctttatattttggacagAAATACGCATTGCTAGAATTTTCAACACATATGGGCCCCGCATGAATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCG

upper sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
lower sequence: EFJ17446 (Selaginella moellendorffii), 3'ss of exon 7
gtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
                                                       ||    |||  || | |  | ||||   |  |||| |     ||  |  |  | |      ||| ||  |||| ||  | ||||||||||| || |||||  ||||||| || || ||||| || || ||||||||||||||||| || ||| |  |
-----------------------------------------------------gtttgctcgattgctttagcttgatgacgctggttctga----cgtccagtaattct-----cagAGATAAGGATCGCTCGCATTTTCAACACTTACGGGCCCCGGATGAATATCGACGATGGACGGGTCGTTAGCAACTTCATTGCCCAAGCTCTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG
                        tcttaac  putative branch site (score: 2)
           ttatgattttttttct  TA-rich tract