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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgcgccgacgtctacttacatacagttaccatagtaacatccctactgtgctatgtgactgtctgcgcag

Basic information

species Zea mays
transcript GRMZM2G062042_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgcgccgacgtctacttacatacagtta-ccatagtaacatccctactgtgctatgtgactgtctgcgcag
||| ||||| ||||| || ||| |||||||  ||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| || ||||||||||||  | ||   ||| || |||||    |      |  | |||| |||||||  |||||  ||||   ||    |  | ||               
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgt---ttccgttcatgtgtttgggactattcatttacgtacagttttccataacaacaaagcttgcttcatgtgcag------------

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgcgccgacgtctacttacatacagtta-ccatagtaacatccctactgtgctatgtgactgtctgcgcag
||| ||||| ||||| || ||| |||||||  ||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| || ||||||||||||  | ||   ||| || |||||    |      |  | ||||  ||||||  |||||  ||||   ||    |  | ||               
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgt---ttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcag------------

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgt----------agtaatttctgtccatgt----tcgcgccgacgtctacttacatacagttaccatagtaacatccctactgtgctatgtgactgtctgcgcag-------------------------------------------------------
|||||||||| | || || ||  | || ||||| ||||| ||||||||||| || ||||||||||| ||| | || ||||| ||||| ||||| |||||||||  |           ||   || | |  ||||    | | ||  |   |       | | ||     | || ||   | | |  |   | | |  || | ||                                                            
TTGCCTCTTCGTCTGTTATGATATAATACGGCCAGATGTTGCTCTTGAGCTAGCTTGGATGAACAATATGATTGATTTTGCTTTCCCATACCTCTTACAGgtatattttcccctggggtttcttttttttatgtgaaatggggctaaaagcccaaggaaaagagactaaacaggaatgacacgaggggtttctttcgctatatgtattactggatgatttttcttccttttattgataaccattttttaatatttcccccctag

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 26
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgcgccgacgtctacttacatacagttaccatagtaacatccctactgtgctatgtgactgtctgcgcag
|||||||||  | || || ||  | || ||||| ||||| ||||||||||| || ||||||||||| ||| | || ||||| ||||| ||||| |||||||||  |  |    |  |     |||| |         ||||   ||    || |     |   ||    |   |  | |   | |  |  |  ||
TTGCCTCTTTGTCTGTTATGATATAATACGGCCAGATGTTGCTCTTGAGCTAGCTTGGATGAACAATATGATTGATTTTGCTTTCCCATACCTCTTACAGgtatattttccactggggtttcgttcactatatttattact-ggatgatttttcttccttttaatgataatcattttttaatatttcccccctag

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 13
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgta---cgtagtaatttctgtccatgttcgcgccgacgtctacttacatacagttaccatagtaacatccctactgtgctatgtgactgtctgcgcag----------------
 || |||||  | || || ||| | ||||| || || || ||||| || ||||| ||||| ||||| ||| ||||||||||||||||||| ||  | |||||      |  |||         |   ||         ||| || | ||   |||   |   | |  |     || || |   |     ||| |                    
ATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatcctaaccctcaaataaactcttttgattctctgctca-atgaggttggaaccattatttgaacgctatgatgaattctcttcttcctgtcgttttttctttgcag

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 13
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgt-acgtagtaatttctgtccatgt---tcgcgccgacgtctacttacatacagttaccatagtaacatccctactgtgctatgtgactgtctgcgcag-
|||||||||  | ||||||||| | || || || ||  | |||||||| ||||| ||||| ||||| ||||| ||||||||||| || || ||||| ||||| |  |  |   ||||  || |||   || |    |     | ||  |    |  |      |  |  |  | |    || || | || | |  |    
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttcccttgtcattctcatatattaggaattttaggagggaaattagcttgcgactttcccagcctgtgggccttttttagagct

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 13
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgcgccgacgtctacttacatacagttaccatagtaacatccctactgtgctatgtgactgtctgcgcag
 ||||||||  | || |||||  | || ||||| || || |  ||||||||||||||||||||||| ||| | |||||||||||||| || || |||||||||     |   ||    || |||||     |       ||| || |  ||   |||       || ||      || |     | | | |  ||
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttgg------ctttcaaatcgtcttcat-----tttctctcaaccactgttcattttttttcatag

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 13
lower sequence: EFJ13237 (Selaginella moellendorffii), 5'ss of exon 28
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgcgccgacgtctacttacatacagttaccatagtaacatccctactgtgctatgtgactgtctgcgcag
 ||||| || |  || |||||  |||||||||| || || ||  | |||||||| ||||| ||||||||| | |||||  ||||||| ||||||||||| |||   ||   ||   || | |  ||  | |  |    ||||   ||  |  ||  |||                                    
CTGCCTGTTTACATGTTACGATTTGATCCGGCCCGACGTAGCATTGGAGCTTGCCTGGATAAACAACATGATCGACTTCTCCTTCCCTTACCTGTTACAAgta---agaccttggagttcttcctcatgacttctgacactttgctatcg--actctag------------------------------------

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|26455954|gb|CA827537.1|CA827537
EST:     TTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAG                         TTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATC
genomic: TTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagta ... gtctgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATC
EST: gi|19770178|gb|BQ034899.1|BQ034899
EST:     TTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAG                         TTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATC
genomic: TTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagta ... gtctgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATC
EST: gi|211415581|gb|FL028985.1|FL028985
EST:     TTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAG                         TTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATC
genomic: TTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagta ... gtctgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 193

TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagta ... gtctgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 70

TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagta ... gtctgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 154

TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagta ... gtctgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 102

TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagta ... gtctgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgcgccgacgtctacttacatacagttaccatagtaacatccctactgtgctatgtgactgtctgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA