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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGATgcaagtatctagtacccagtatcattactacacccttttattatctgatgttttagattttaagtacacttaccgtgctgcctttttaaaattacatccc...

Basic information

species Zea mays
transcript GRMZM2G092129_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092129_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g22640.4 (Oryza sativa), 5'ss of exon 6
CTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGATgcaagtatctagtacccagtatcattactacacccttttattatctgatgttttagatttta-agtacacttaccgtgc-tgcctttttaaaattacatccc-
||||| |||||||| ||||| ||  |  | |||||| |||||||||| || || || ||||||||||| |||||||||||||| ||||| ||||| || | |   |||||  |   |  || |||  |    |  |||   |   ||| ||||   |   | | ||||       ||| || ||    | |      ||   
CTCAAAGATCTTCAAGTCTACACCATTGTCCGTGTTGTATTTCAACTATCAGAGGAGATCCCTTGCATCTCTGCTGTTGTTGTTGCTCTTCTTGCAGAGgtatacatctacaa---aaaatgatttatctttctatttcaaaggagattttttttctaagacaatacaggagatctgcatgtctaagcagagacgagtcttg

upper sequence: GRMZM2G092129_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA03G02370.1 (Glycine max), 5'ss of exon 6
CTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGATgcaagtatctagtacccagtatcattactacacccttttattatctgatgttttagattttaagtacacttaccgtgctgcctttttaaaattacatccc-
 | |||||||| ||||| |  ||  |  | ||||| |||||||||||  ||||||| ||||| |||||||||||||||||||| ||||| |||||||| | ||   |   |      |       | ||||     ||  ||| ||| |   |  | ||    || | ||   || ||  | ||    |   | |     
TTGAAGGATCTACAGGTTTTCACCATTGTCCGTGTGATATTTCAACTTGCTGAAGAGATCCCCTGCATTTCTGCTGTTGTTGTAGCTCTGCTTGCTGAGgtaatccttgtgaggagggagaggagaatacaatgagttcatatatgaaggaatgtaatt-gcatatagttcttgttctttccttacccatcaataatatt

upper sequence: GRMZM2G092129_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA18G45720.1 (Glycine max), 5'ss of exon 6
CTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGATgcaagtatctagtacccagtatcattactacacccttttattatctgatgttttagattttaagtacacttaccgtgctgcctttttaaaattacatccc-
 | |||||||| ||||| |  ||  | || ||||||||||| |||||  |||| || || || |||||||||||||||||||| || || ||||| || | || | |  || |   |  |                         |||| |   |   |||||| |   |      |   ||         | |   || 
TTGAAGGATCTCCAGGTTTTCACCATTATCCGTGTTATATTCCAACTTGCTGACGAGATTCCCTGCATTTCTGCTGTTGTTGTTGCCCTACTTGCCGAGgtaacttttgag-atggaaaaatgaaggaggggagggggggggggggatgatgatgcacttaagttccagtgtttcacaatctcccattttgtgctctcct

upper sequence: GRMZM2G092129_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA07G09070.1 (Glycine max), 5'ss of exon 7
CTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGATgcaagtat--ctagtacccagta--tcattactacacccttttattatctgatgttt-tagattttaagtacacttaccgtgctgcctttttaaaattacatccc
 | |||||||| ||||| |  ||  |  | ||||| ||||| |||||  ||||||| |||||||||||||||||||||||||| ||||| |||||||| | ||   |  ||     |  |||  |   ||| | |   | |  |      || ||| | | ||||  || |        |  |||  ||   || ||       
TTGAAGGATCTACAGGTTTTCACCATTGTCCGTGTGATATTCCAACTTGCTGAAGAGATCCCTTGCATTTCTGCTGTTGTTGTAGCTCTGCTTGCTGAGgtaatccttgctgaaggcatgtaaatgcatacgaaaggatatagtggctctatctttattggttttttgttcctcctttttattgctattccgaagtttt-----

upper sequence: GRMZM2G092129_T02 (Zea mays), 5'ss of exon 6
lower sequence: AT3G61050.1 (Arabidopsis thaliana), 5'ss of exon 7
CTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGATgcaagtatctagtacccagtatcattactacacccttttattatctgatgttttagattttaagtacacttaccgtg-ctgcctttttaaa--attacatccc-
 | ||||||||||| || |  || ||   ||||||||| ||||||||  | || || || ||||| || |||||||||||||| ||||| |||||||| | |    | |  |    ||   ||  |  | |  | ||| |  | |    ||||| || |   ||   |||||  || |   || ||||||  ||  || ||  
TTGAAGGATCTTCAAGTTTTCACAGTTGCACGTGTTATCTTTCAACTTGCGGATGAGATTCCTTGTATATCTGCTGTTGTTGTTGCTCTACTTGCTGAGgtacacttttcctgtaaaggtccagaataagattcatttttcttatatcattttatatctcctgt---cttacaatgaccaactatttaaatgatctcaaccag

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|211220819|gb|FL457378.1|FL457378
EST:     GCTGTTGTTGTGGCTCTCCTTGCTGAT                         CCAGAGCCAAAAATTCAGTACACCCTSAAGGCCATTGGAGSAAGCCTAACT
genomic: GCTGTTGTTGTGGCTCTCCTTGCTGATgcaagtatct ... tgtgctccagCCAGAGCCAAAAATTCAGTACACCCTGAAGGCCATTGGAGGAAGCCTAACT
EST: gi|211335355|gb|FL444766.1|FL444766
EST:     CTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGAT                         CCAGAGCCAAAAATTCAGTACACCCTGAAGGCCATTGGAGGAAGCCTAACT
genomic: CTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGATgcaagtatct ... tgtgctccagCCAGAGCCAAAAATTCAGTACACCCTGAAGGCCATTGGAGGAAGCCTAACT
EST: gi|148971559|gb|EE022272.2|EE022272
EST:     TGAAGACATCCCTTGCATTTCTGCTGGGTGT-GTGGCTCTCCTTGCTGAT                         CCAGAGCCAAAAAATCAGTACACCCTGAAGGCCA
genomic: TGAAGACATCCCTTGCATTTCTGCTGT-TGTTGTGGCTCTCCTTGCTGATgcaagtatct ... tgtgctccagCCAGAGCCAAAAATTCAGTACACCCTGAAGGCCA
EST: gi|71331353|gb|DR802511.1|DR802511
EST:     CTGAAGACATCCCTTGCATTTCTGCTGTTGGTGTGGCTCTCCTTGCTGAT                         CCAGAGCCAAAAATTCAGTACACCCTGGAGGTCATTGGAGGAAAGC-TAAC
genomic: CTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGATgcaagtatct ... tgtgctccagCCAGAGCCAAAAATTCAGTACACCCTGAAGGCCATTGGAGGAA-GCCTAAC
EST: gi|211220820|gb|FL457379.1|FL457379
EST:     CTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGAT                         CCAGAGCCAAAAATTCAGTACACCCTGAAGGCCATTGGAGGAAGCCTAACT
genomic: CTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGATgcaagtatct ... tgtgctccagCCAGAGCCAAAAATTCAGTACACCCTGAAGGCCATTGGAGGAAGCCTAACT
EST: gi|111145863|gb|EE258112.1|EE258112
EST:     CTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGAT                         CCAGAGCCAAAAATTCAGTACACCCTGAAGGCCATTGGAGGAAGCCTAACT
genomic: CTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGATgcaagtatct ... tgtgctccagCCAGAGCCAAAAATTCAGTACACCCTGAAGGCCATTGGAGGAAGCCTAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGATgcaagtatctagtacccagtatcattactacacccttttattatctgatgttttagattttaagtacacttaccgtgctgcctttttaaaattacatccc

- - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT