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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgtaatccccatcttgaaactggaagtgtaatctcttcattatgtctaccattgaatgacccattatatagcacttttgattttctttctataaattttcagGAGCCTGAAAAACATGTGTTTCACCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATGC

Basic information

species Zea mays
transcript GRMZM2G076276_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G076276_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os06g49810.1 (Oryza sativa), 3'ss of exon 7
gttagtgtaatccccatcttgaaactggaagtgtaatctcttcattatgtctaccattgaatgacccattatatagcacttttgattttctttctataaattttcagGAGCCTGAAAAACATGTGTTTCACCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATGC
|| |||| ||||   |  |  ||  ||||| || ||| ||||    ||| ||   |   |   |  |  ||   |  |||  | |||||  | | ||       ||||||||||| |||||||| || || |||||||||||||| ||||||||||| || |||||||||||||||||| ||||||||||||| ||||| ||||| |
gtaagtgcaatctagagttc-aatttggaattgcaatttcttggcaatgactgagaaacatgtattcggta---aaaactgctcatttttctaccatg------cagGAGCCTGAGAAACATGTATTCCATCTTGTTACTGACAAGCTGAACTTTGGAGCAATGAACATGTGGTTTTTGTTGAATCCACCTGGAGATGCGACAATCC

upper sequence: GRMZM2G076276_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA09G40260.1 (Glycine max), 3'ss of exon 8
--------------------------------------------------------------------------gttagtgtaatccc-catcttgaaactggaa---gtgtaatctcttcattatgtctaccattgaatgacccattatatagcacttt----tgattttctt---------tctataaattttcagGAGCCTGAAAAACATGTGTTTCACCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATGC
                                                                            || | |   |   ||   |  |||  | |    | |  | | | || |   ||    | | | | |   ||   ||   |||||    | ||| ||||         |||  ||  || ||||| |||   || ||||||||||||||||||||||| ||||| || ||||| ||||||||||||||||||||| ||||||| |||||  | || |||||  
gtgacttaaacagtcttttaccataccagtgtgtatgtgcatgtctatatagatattcttttatatagatgatgaataatttgtgcttgcactgtacaacccggacatattttgtttgtgcagtgcatccctgactcagtaaataatataattaaactttgccttcattatcttatgtttgtgtcttcaacattgcagGATCCTTCGAAGCATGTGTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTTTGTTGAATCCTCCTGGAAAAGCTACAATCA

upper sequence: GRMZM2G076276_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA07G08910.1 (Glycine max), 3'ss of exon 5
gttagtgtaatccccatcttgaaactggaagtgtaatctc--ttcattatgtctaccattgaatgacccattatatagcacttttgattttctttctataaattttcagGAGCCTGAAAAACATGTGTTTCACCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATGC
    |    |     ||| || |  || |||||||       || | ||  |    | || ||   |       ||| |   ||||  ||  | |||  ||  || ||||| |||  ||| ||||| |||||||||||||| || ||||| || ||||| |||||||||||||||||| |  | || || ||||   | || ||||| |
----gcaccaaaaatatcgtgcatgtgaaagtgtatctatgatttagtaaattatacttttaaaaccaggcctcataac---tttg--ttattgtcttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC

upper sequence: GRMZM2G076276_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA18G45750.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------------------------------------------gttagtgtaatccc--catcttgaaactggaagtgtaatctcttcattatgtctaccattgaatgacccattatatagcacttttgattttctttctataaattttcagGAGCCTGAAAAACATGTGTTTCACCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATGC
                                                                                              ||  || ||   |||  |     ||   ||| |  |    ||  ||   ||  ||      ||      |  |  |  ||   ||    |  |  ||  ||  |||| |||   || ||||||||||||||||||||||| ||||| || ||||| ||||||||||||||||||||| ||||||| |||||  | || |||||  
gtgacttggactgtctttttccataccagtgtgtgtgtacatgtctgtatagtgaatttttttttatagatgatgaataatttgtgcttgcactgtacaacccggacatagtttgtttgcttgtgcatccctgacaaaataaataatataattaaactttgccttcattatcttatgttcgtgtcttccaacgttgtagGATCCTTCGAAGCATGTGTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTTTGTTGAATCCTCCTGGAAAAGCTACAATCA

upper sequence: GRMZM2G076276_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA03G02250.1 (Glycine max), 3'ss of exon 13
-----------------------------------------------------------------------------------gttagtgtaatccccatcttgaaactggaagtgtaatctcttcattatgtctaccattgaatgacccattatatagcacttttgattttctttctataaattttcagGAGCCTGAAAAACATGTGTTTCACCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATGC
                                                                                    | |   |  ||  ||| | |    ||  |  ||       | |||  ||  |  ||   || |   |  |     ||    | | ||||| |||  ||  || ||||| ||    ||  |||| ||||||||||||||||| ||||| || ||||| ||||||| |||||||||| |  | || || |||||  | || ||||| |
gtgacttgggctgtctttttaaccataccagtatttgtgtgcaagttcattgtttccttttatagattgcaaataagggtgccttgaccatggtcaacatatcgtgcatgtgaaagtgtatctatgatttagtaaattatattattaaa-accaggcctcataacttagtttctgtcttcaatgttgcagGATCCATCGAAGAATGTTTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAGCATGTGGTTTCTTTTAAACCCTCCTGGAAAAGCTACAATCC

upper sequence: GRMZM2G076276_T03 (Zea mays), 3'ss of exon 7
lower sequence: Vv15s0048g01300.t01 (Vitis vinifera), 3'ss of exon 8
gttagtgtaatccccatcttgaaactggaagtgtaatctcttcattatgtctaccattgaatgacccattatatagcacttttgattttctt--tctataaat--------tttcagGAGCCTGAAAAACATGTGTTTCACCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATGC
                | | || |   |||  |  || | ||    | |   |  |  | || ||  ||  | |  |  |||| |||  ||   | |   |||        || ||||| || ||||||||||| || || || |||||||| || ||||| ||||| |||||||| ||||||||| || |||| || || ||  | ||||| || |
----------------tttggataagcgaaaggggatttgttaggaaagcacaaaagggcatcacatatgttcttcc-tttttcattcactaagtttgctaataccctcgattgcagGAACCAGAAAAACATGTATTCCATCTGGTTACTGATAAGCTGAATTTTGGAGCCATGAATATGTGGTTTCTGTTGAACCCCCCAGGAAAAGCAACTATCC

upper sequence: GRMZM2G076276_T03 (Zea mays), 3'ss of exon 7
lower sequence: PP1S251_8V6.1 (Physcomitrella patens), 3'ss of exon 8
gttagtgtaatccccatcttgaaactggaagtgtaatctcttcattatgtctaccatt---gaatga-----cccattatatagcacttttgattttctttctataaattttcagGAGCCTGAAAAACATGTGTTTCACCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATGC
              |   |  | |    | || || | ||||  |  | |   |  ||   |||| |      |  |||| | |||      |  |  | |||      || ||||| ||    || ||||| |||||  ||||||| ||||||||||||| ||||||||||  ||||||||| ||||| || || || || | ||| || || |
-------------gctcttacatagcataggtctattttctttttagttttagcggtttgagaataagcttctctgttattttgcaaggcctaagtgttatctgctg--ttgcagGATCCCAGTAAGCATGTCTTTCATGTTGTTACAGACAAACTGAACTATGGGGCCATGCGCATGTGGTTCTTGCTCAACCCCCCCGGTGCTGCTACCATCC

upper sequence: GRMZM2G076276_T03 (Zea mays), 3'ss of exon 7
lower sequence: PP1S128_25V6.1 (Physcomitrella patens), 3'ss of exon 7
--------------------------------------------------------------------gttagtgtaatccccatcttgaa-actggaagtgtaatctcttcattatg-tctaccattgaatg-acccattatatagcacttttgattttctttctataaatttt-cagGAGCCTGAAAAACATGTGTTTCACCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATGC
                                                                     |||  |  |  | | |   | |  |||      | |  |  |   |||| || |   ||  ||| | |  | |||    ||   | ||||    | |||   | || |||||||| || ||||| || |||||| ||||||| ||||| || || ||||| |||||||  |||||||||||    ||||| || |||| |||    || |
gtatggagtctatcaagatctattcttttctgatagaggcctatggcctcagatattctatgttttgttttaaagcgacgctcgttaagtatgctgctgaaatgacttggtatatatgatcgagttttccatggatctgtcatagcaaacacct-atttcaactttatctttcttgcagGAGCCAGAGAAACACGTTTTTCACATTGTTACCGACAAGCTAAATTTTGGTGCCATGATGATGTGGTTTTTAGCAAATCCTCCCGGGGCTGCTGTCATAC

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|101385706|gb|EB814901.1|EB814901
EST:     ATGTTTTGGCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCGAAG                         GAGCCTGAAAAACATGTGTTTCACCTTGTTACTGACAAACTGACCTTTGGG
genomic: ATGTTTTGGCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCGAAGgttagtgtaa ... aaattttcagGAGCCTGAAAAACATGTGTTTCACCTTGTTACTGACAAACTGAACTTTGGG
EST: gi|71429642|gb|DR810692.1|DR810692
EST:     ATGTTTTGGCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCGAAG                         GAGCCTGAAAAACATGTGTTTCACCTTGTTACTGACAAACTGAACTTTGGG
genomic: ATGTTTTGGCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCGAAGgttagtgtaa ... aaattttcagGAGCCTGAAAAACATGTGTTTCACCTTGTTACTGACAAACTGAACTTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accattgaatgacccattatatagcacttttgattttctttctataaattttcagGAGCCTGAAAAACATGTGTTTCACCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATGC
                           ttttgat  putative branch site (score: 4)
                                                ttttc  putative PPT
                         acttttgattttcttt  TA-rich tract