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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAATGGGTGGTGCTGCCATGTATGAACTTGTTCGTGTCGGACATGATAACCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgcaacatggcagatcatctataataaattattcacccatgggcatgaaaagctcctttccagttgaatacacggtactaacctcgcgagtgccgtcatttgcgtgttgcag

Basic information

species Zea mays
transcript GRMZM2G421857_T04
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 2
GGAATGGGTGGTGCTGCCATGTATGAACTTGTTCGTGTCGGACATGATAACCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgcaaca---tggcagatcatctataataaattattcacccatgggcatgaaaagc---tcctttccagttgaatacacggt-----actaacctcgcgagtgccgtcatttgcgtgttgcag
|||||||| |||||||||||||||||||| || ||||| || || ||||| || ||||| |||||||| ||||||||||| |||||||||||||| |||||| || ||||       || |  | | |   | |  || ||  || | |     | |||   |   | || ||||||  ||  ||      ||||| ||   | ||  || ||||| || |  |||
GGAATGGGAGGTGCTGCCATGTATGAACTCGTCCGTGTTGGGCACGATAATCTTATTGGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAGgtgtggaacagctctttagtttctatctttaacagcatacagacacgagttctgatagcaattatatgcctgttgaaaccatagtcaatatctaacatcagaaatgttgttatttgtgtatcacag

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 2
GGAATGGGTGGTGCTGCCATGTATGAACTTGTTCGTGTCGGACATGATAACCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgt--------atgcaacatggcagatcatctataataaattattcacccatgggca--tgaaaagctcctttccagttgaatacacggtactaacctcgcgagtgccgtcatttgcgtgttgcag
|| |||| ||| ||||| ||||||||||| || ||||| || |||||||| |||||||| |||||||| ||||| || ||  |||| ||||| |||||||||        || |    ||  | || | |||    ||| || | ||  ||| | |  | |   | ||  | | | || |                                             
GGCATGGCTGGGGCTGCTATGTATGAACTCGTGCGTGTTGGTCATGATAATCTCATTGGTGAAATTATTCGTCTCGAAGGGAATTCTGCTACCATCCAAGgtgcattttcataccgtgtgcaatatta-ctacttcaaactaattacttatgagaaactcattggttctctgcaattttag--------------------------------------------

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 2
GGAATGGGTGGTGCTGCCATGTATGAACTTGTTCGTGTCGGACATGATAACCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgcaacatggcagatcatctataataaattattcacc--catgggcatgaaaagctcctttccagttgaatacacggtactaacctcgcgagtgccgtcatttgcgtgttgcag
|| |||| ||||||||| ||||||||||| || ||||| || |||||||| |||||||| |||||||| ||||| || || ||||| ||||| |||||||||      |    || | | ||| ||||   |     | |  |||     ||  || ||| ||    |||   |   |  |  ||                                
GGCATGGCTGGTGCTGCTATGTATGAACTCGTGCGTGTTGGTCATGATAATCTCATTGGTGAAATTATTCGTCTCGAAGGGGATTCTGCTACCATCCAAGgtgcatttc----cataccttctctaatgtttctgcaaactgcatccttctgcgaaactcattc---gtt--ctctgcaattttag-------------------------------

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT1G78900.1 (Arabidopsis thaliana), 5'ss of exon 3
GGAATGGGTGGTGCTGCCATGTATGAACTTGTTCGTGTCGGACATGATAACCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgcaacatggcagatcatctataataaattattcacccatgggcatgaaaagctcctttccagttgaatacacggta-ctaacctcgcgagtgccgtcatttgcgtgttgcag
|| ||||  |||||||| ||||||||  | || ||||| || ||||||||  | ||||| ||||| ||||||||||| || ||||| || || ||||||||| ||   | |      |  |   || |   | ||| ||     |||||   | |   | |  | || |||   | | || || | ||      || |  | |     || | |||
GGTATGGCCGGTGCTGCTATGTATGAGTTAGTGCGTGTTGGTCATGATAATTTGATTGGTGAAATCATCCGTCTTGAAGGAGATTCTGCCACCATCCAAGgtttgtttcttctattgtgcttcctagt--gtaatttactttacggcatcttatgtgacct--ctgtcgaa-gtaagatatcttaactgatatttggcaacttccttttgat-cag

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 2
GGAATGGGTGGTGCTGCCATGTATGAACTTGTTCGTGTCGGACATGATAACCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgc-aacatggcagatcatctataataaattattcacccatgggcatgaaaagctcctttccagttgaatacacggtactaacctcgcgagtgccgtcatttgcgtgttgcag
|||||||  || ||||| ||||||||||| || ||||| |||||||| ||||| ||||| |||||||| ||  | || || ||||| || |||||||| |||||    || |   | |   | | |  | | |  | ||  | |     || |    | ||||    ||| |   | |||  |||  |      |   ||  |||           
GGAATGGCAGGGGCTGCTATGTATGAACTGGTCCGTGTTGGACATGACAACCTTATTGGAGAAATTATTCGGTTAGAAGGAGATTCTGCCACAATCCAGGgtattttgacttttaaaacgttttcttgttactgttgcattcttctcactgta--tttactttaattttgga---aaggtcttaatgtatgtcttcttgtttttt-----------

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 2
GGAATGGGTGGTGCTGCCATGTATGAACTTGTTCGTGTCGGACATGATAACCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgcaacatggcagatcatctataataaattattcacccatgggcatgaaaagctcctttccagttgaatacacggtactaacctcgcgagtgccgtcatttgcgtgttgcag-
|||||||| || || |||||||| ||  | || ||||| ||||| ||||| || ||||| || ||||| ||||||||||| ||||||||||| || ||||||  | |  |  ||      || ||    |||| ||        || |||||  | |   ||  |||  ||  |||  | ||  |  |   |  | | || ||    | | |  | 
GGAATGGGAGGAGCAGCCATGTACGAGTTGGTCCGTGTAGGACACGATAAGCTGATTGGAGAGATTATTCGTCTTGAGGGTGATTCAGCTACCATTCAAGgtgcggagaa--gctttcagtcgatgg--aattttt--------ggaatgaacggattagtt--agtccaa-gcacatttctttctccattaa-gtcttcgttgttttatcggcgt

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 5'ss of exon 2
GGAATGGGTGGTGCTGCCATGTATGAACTTGTTCGTGTCGGACATGATAACCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgca-acatggcagatcatctataataaattattcacccatgggcatgaaaagctcctttccagttgaatacacggtactaacctcgcgagtgccgtcatttgcgtgttgcag
|| ||||| || || || ||||| ||  | |||||||||||||| ||||| || || || ||||| || || |||||||| |||||||||||||| ||||||    | | || | | ||||  | | ||   ||  |  |   ||    |     | |   |   |  |  | |   |||  |   || | |||     | |              
GGCATGGGAGGAGCCGCGATGTACGAGTTGGTTCGTGTCGGACACGATAATCTGATAGGAGAAATCATTCGCCTTGAGGGTGATTCAGCTACAATTCAAGgtgcagagatattgta-atcagatttgatgtctttctttcagctgaattttcggggatgaatgttaccttgaaat--ggttgttctcttgtgaggattttgac-------------

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 2
GGAATGGGTGGTGCTGCCATGTATGAACTTGTTCGTGTCGGACATGATAACCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgcaacatggcagatcatctataataaattattcacccatgggcatgaaaagctcctttccagttgaatacacggtactaacctcgcgagtgccgtcatttgcgtgttgcag
|||||||| || || || ||||||||  | |||||||| |||||||||||  | ||||| || || || || |||||||| |||||||| || ||||||||||||| |  |           | |  ||||      |    ||    |    ||   || ||       |||  |  || |  ||     | |  | |  ||  |  | |||  
GGAATGGGAGGAGCAGCTATGTATGAGTTAGTTCGTGTGGGACATGATAAGTTGATTGGAGAGATAATTCGACTTGAGGGTGATTCAGCCACTATCCAAGgtatgcgagtt---------cttttggtaaaggg---atttgtgaaattagctag--tctgtctgagcacatatgccttattttccctctcactaac-tttttaacagggtgctt

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|18649012|gb|BM497831.1|BM497831
EST:     CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAG                         TTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA
genomic: CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgcaaca ... cgtgttgcagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA
EST: gi|32838516|gb|CD978194.1|CD978194
EST:     CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAG                         TTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA
genomic: CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgcaaca ... cgtgttgcagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA
EST: gi|32925687|gb|CF030499.1|CF030499
EST:     CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAG                         TTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA
genomic: CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgcaaca ... cgtgttgcagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA
EST: gi|32921771|gb|CF026583.1|CF026583
EST:     CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAG                         TTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA
genomic: CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgcaaca ... cgtgttgcagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA
EST: gi|32924704|gb|CF029516.1|CF029516
EST:     CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAG                         TTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA
genomic: CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgcaaca ... cgtgttgcagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA
EST: gi|32925234|gb|CF030046.1|CF030046
EST:     CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAG                         TTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA
genomic: CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgcaaca ... cgtgttgcagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA
EST: gi|18649727|gb|BM498546.1|BM498546
EST:     CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAG                         TTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA
genomic: CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgcaaca ... cgtgttgcagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA
EST: gi|32848240|gb|CD987921.1|CD987921
EST:     CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAG                         TTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA
genomic: CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgcaaca ... cgtgttgcagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA
EST: gi|32934325|gb|CF039137.1|CF039137
EST:     CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATGCAAG                         TTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA
genomic: CCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgcaaca ... cgtgttgcagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAATGGGTGGTGCTGCCATGTATGAACTTGTTCGTGTCGGACATGATAACCTCATTGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatgcaacatggcagatcatctataataaattattcacccatgggcatgaaaagctcctttccagttgaatacacggtactaacctcgcgagtgccgtcatttgcgtgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT