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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgcgcccgccatctccgattgcttcccttcccttcccctcctcctcgactgtccgcagtcgcgcgcggcggccggcggcgagcgacccctgtatgtatgtatactggtatgtaatgggtaatgtaacgcgggcggcgggaatggtggtcgggcgcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGGCAAGGACCGCCACACCAACGAGACGATCGCGCTCAAGAAGATCCGCC

Basic information

species Zea mays
transcript GRMZM2G174596_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174596_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g03060.3 (Oryza sativa), 3'ss of exon 1
gtgagcgcgcccgccatctccgattgcttcccttcccttcccctcctcctcgactgtccgcagtcgcgcgcggcggccggcggcgagcgacccctgtatgtatgtatactggtatgtaatgggtaatgtaacgcgggcggcgggaatggtggtcgggcgcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGGCAAGGACCGCCACACCAACGAGACGATCGCGCTCAAGAAGATCCGCC
|||||| | ||| | | |||||   | |  |  | || |   ||    |    |  |||||      ||| || ||         |  |  | |||  ||      | ||| |   | ||| ||  |||   | | | ||| |||          || ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||| |||| || ||||||||||||||||||||||||||||||||||
gtgagcac-ccctcgacctccg--cgatgacgatgccctttgctgtatccgatccatccgcga----gcgtggagg--------aaatggtcgctgc-tgc-----tgctgctg-atgatgagtg-tgtt-tgtgtgtggctgga----------ggagcagTACGAGAAGGTGGAGAAGATCGGGGAGGGGACGTACGGGGTGGTGTACAAGGGCAAGCACCGGCATACCAACGAGACGATCGCGCTCAAGAAGATCCGCC

upper sequence: GRMZM2G174596_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G08330.1 (Glycine max), 3'ss of exon 1
gtgagcgcgcccgccatctccgattgcttcccttcccttcccctcctcctcgactgtccgcagtcgcgcgcggcggccggcggcgagcgacccctgtatgtatgtatactggtatgtaatgggtaatgtaacgcgggcggcgggaatggtggtcgggcgcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGGCAAGGACCGCCACACCAACGAGACGATCGCGCTCAAGAAGATCCGCC
                                                                                  |   |  |  |   |  || |  |  ||   ||   ||      |   |      ||       |     |     ||||||||||||||| |||||||| || ||||| || ||||| || || ||||||||    ||||||  |||||||||||| |||||  | |||||||| ||| 
----------------------------------------------------------------------------------gttggtaaaacgcatgcgttttgaagcttccattccatttcagtttcgatttt--cgattcttttccctctactctgcagTACGAGAAGGTTGAGAAGATAGGCGAGGGAACATACGGCGTCGTTTACAAGGGTCGCGACCGCTCCACCAACGAGACCATCGCCTTGAAGAAGATTCGCT

upper sequence: GRMZM2G174596_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 1
gtgagcgcgcccgccatctccgattgcttcccttcccttcccctcctcctcgactgtccgcagtcgcgcgcggcggccggcggcgagcgacccctgtatgtatgt---atactggtatgtaatgggtaatgtaacgcgggcggcgggaatggtggtcgggcgcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGGCAAGGACCGCCACACCAACGAGACGATCGCGCTCAAGAAGATCCGCC
                                                       || || ||   |||   ||   |  |      |||        |   | |   | |||    | |  ||   | ||     ||           | ||  |     |||||||||||||||||||||||| || ||||| || ||||| || || |||||||     ||||||  |||||| ||||| ||||| ||||||||||| ||||
-------------------------------------------------------gttcgtagcaccgcaatgca-tcatctctcttcgattttcagtttcctctcaaaaactcacttttcgtgaaaattggttttcgattttt-----ttgtttttttttgcagTACGAGAAGGTGGAGAAGATAGGCGAGGGAACATACGGCGTCGTTTACAAGGCTCGCGACCGCGTCACCAATGAGACCATCGCTCTCAAGAAGATTCGCC

upper sequence: GRMZM2G174596_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G25320.4 (Glycine max), 3'ss of exon 1
gtgagcgcgcccgccatctccgattgcttcccttcccttcccctcctcctcgactgtccgcagtcgcgcgcggcggccggcggcgagcgacccctgtatgtatgtatactggtatgtaatgggtaatgtaacgcgggcggcgggaatggtggtcgggcgcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGGCAAGGACCGCCACACCAACGAGACGATCGCGCTCAAGAAGATCCGCC
                                                       ||  | |    ||| | |||    |     |||  | | |  |  | ||  |   | |   |      || | |  ||   | |  | |  | |||       ||||||||||||||| |||||||| || || || || ||||| || || ||||||||    ||||||  |||||||||||| |||||| | |||||||| ||||
-------------------------------------------------------gttagtaaa-acgcactgcgttttg----aagcttcactttcacttttgagtttcgattctttccctctactctg-cgtatgtg-tgcgttttgtgaatttctgcagTACGAGAAGGTTGAGAAGATAGGCGAAGGAACATACGGCGTCGTTTACAAGGGTCGCGACCGCGTCACCAACGAGACCATCGCGTTGAAGAAGATTCGCC

upper sequence: GRMZM2G174596_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 1
gtgagcgcgcccgccatctccgattgcttcccttcccttcccctcctcctcgactgtccgcagtcgcgcgcggcggccggcggcgagcgacccctgtatgtatgtatactggtatgtaatgggtaatgtaacgcgggcggcgggaatggtggtcgggcgcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGGCAAGGACCGCCACACCAACGAGACGATCGCGCTCAAGAAGATCCGCC
                                                     |   || || |             |  |    |   ||   |   |  || |  |||    | | |            | |           ||  |  |     |||||||||||||||||||||||| || ||||| || ||||| || || |||||||     ||||||  |||||| ||||| ||||| || |||||||| ||||
--------------------------------------------------gttcctaccacaattcaatcttaacttcatcac--attaacattttcttcgattttcactttcctctcacaaact------cacttttcctttccattttttttttttgcagTACGAGAAGGTGGAGAAGATAGGCGAGGGAACATACGGCGTCGTTTACAAGGCTCGCGACCGCGCCACCAATGAGACAATCGCTCTGAAGAAGATTCGCC

upper sequence: GRMZM2G174596_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S281_23V6.1 (Physcomitrella patens), 3'ss of exon 2
gtgagcgcgcccgccatctccgattgcttcccttcccttcccctcctcctcgactgtccgcagtcgcgcgcggcggccggcggcgagcgacccctgtatgtatgtatactggtatgtaatgggtaatgtaacgcgggcggcgggaatggtggtcgggcgcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGGCAAGGACCGCCACACCAACGAGACGATCGCGCTCAAGAAGATCCGCC
                                           | ||   |  ||     | ||| |      |   | | | |||    ||| ||| |  |   |  |   | |    | | | |||        ||  | | |||| |||       ||||| || || ||||||||||| ||||| |||| |||||| ||||||||||||| |   ||||||   ||||| ||||| || || || ||||||||  | |
------------------------------------------ttgctatccatcttcaaactgtctcattttacattctgtgacgaa--gcccatgtgt-cactcac-ccaatctcctcttgatgatg--------gcaactgtaatg-tgg-------cagTATGAAAAAGTGGAGAAGATTGGGGAAGGCATGTACGGAGTGGTGTACAAGGCCCGAGACCGCGTTACCAATGAGACTATTGCTCTAAAGAAGATTAGGC

upper sequence: GRMZM2G174596_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ15022 (Selaginella moellendorffii), 3'ss of exon 1
gtgagcgcgcccgccatctccgattgcttcccttcccttcccctcctcctcgactgtccgcagtcgcgcgcggcggc-cggcggcgagcgacccctgtatgtatgtatactggtatgtaatgggtaatgtaacgcgggcggcgggaatggtggtcgggcgcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGGCAAGGACCGCCACACCAACGAGACGATCGCGCTCAAGAAGATCCGCC
                                                                   |  | |||   | ||      ||| | || |   | |     ||   || | |  | |  ||     |  ||||||               || |||| |||||||||||||| |||||||| ||||| ||||| || || ||||||| |  ||| |||  ||| || |||||||| ||||||||||||||||| |
-------------------------------------------------------------------gtactgcgaagccgcattcttcgatctctctcgttcttgccgctctgatcttactgttcttgcgcttcttgcggcg---------------cgtagTATGAGAAGGTGGAGAAAATCGGGGAAGGCACATACGGCGTCGTCTACAAGGCCCGGGATCGCATCACAAATGAGACGATTGCGCTCAAGAAGATCCGAC

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|88752963|gb|DY537104.1|DY537104
EST:     CCGCCGCCCGTTCCCGACCGATCCGGCCGGATCGCCCCGCCATGGACCAG                         TACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAG
genomic: CCGCCGCCCGTTCCCGACCGATCCGGCCGGATCGCCCCGCCATGGACCAGgtgagcgcgc ... tcgggcgcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAG
EST: gi|78103919|gb|DV522337.1|DV522337
EST:     CCGCCGCCCGTTCCCGACCGATCCGGCCGGATCGCCCCGCCATGGACCAG                         TACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAG
genomic: CCGCCGCCCGTTCCCGACCGATCCGGCCGGATCGCCCCGCCATGGACCAGgtgagcgcgc ... tcgggcgcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actggtatgtaatgggtaatgtaacgcgggcggcgggaatggtggtcgggcgcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGGCAAGGACCGCCACACCAACGAGACGATCGCGCTCAAGAAGATCCGCC
                  atgtaac  putative branch site (score: 3)
     tatgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcgcgcccgccatctccgattgcttcccttcccttcccctcctcctcgactgtccgcagtcgcgcgcggcggccggcggcgagcgacccctgtatgtatgtatactggtatgtaatgggtaatgtaacgcgggcggcgggaatggtggtcgggcgcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGGCAAGGACCGCCACACCAACGAGACGATCGCGCTCAAGAAGATCCGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG