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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacctcagtcatgttggggcggggggttgggcttgttgctttgttatggatgttgtttgacgtacgattgatttaattacattgtttgtaatgcag

Basic information

species Zea mays
transcript GRMZM2G068755_T01
intron # 51
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068755_T01 (Zea mays), 5'ss of exon 51
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 50
GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacctcagtcatgttggggcggggggttgggcttgttgctttgttatggatgttgtttgacgtacgattgatttaattacattgtttgtaatgcag
||||||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| ||||||||||||||  |  ||| || ||  || |     |  | |  ||| || |||    ||  ||    ||  |||    |||  | |   |                 
GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatttcaatcctggaggtgtttaag-ctagttttggtgtttttaactgattggctattatcgttt--ttggctcatgcag----------------

upper sequence: GRMZM2G068755_T01 (Zea mays), 5'ss of exon 51
lower sequence: GLYMA10G35140.1 (Glycine max), 5'ss of exon 53
GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgttt-gtaacctcagtcatgttggggcgggg----ggttgggcttg----ttgctttgttatggatg-ttgtttgacgtacgattgatttaattacattgtttgtaatgcag----------------
||||| ||||||||||||||||| ||||||||||| || ||| | ||||| || |||||||| || |||||||||  || |  | | |  | ||    |  |       |||  ||||    |||  ||  ||  |  | |||   |  |||  ||||| |  |||  |   || | |||  |                 
GTTGACATATTTGCTCAGCTTCAAAATGCTAGTGAGGCATTTCGCACCTACATTAGAGATGGTCTTGCTCAGgttgagttaatttacttgtattaccacatgttcttaattgaacttgcattttgtatttctaccggcgattgggagtagtagaattgagt--atttgaccattggcaattgattttaacattttggcag

upper sequence: GRMZM2G068755_T01 (Zea mays), 5'ss of exon 51
lower sequence: GLYMA20G32430.1 (Glycine max), 5'ss of exon 52
GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgttt-gtaacctcagtcatgttggggcggggggttgggcttgttgctttgttatggatgttgtttgacg--tacgattgatttaattacattgtttgtaat--gcag----------------------
||||| ||||||||||||||||| ||||||||||| || ||| | ||||| || |||||||| || |||||||||  || |  | | |  |  |    |  |   ||    | | |  |   || || || |       ||  |  || |  |  ||||   |  ||   |||  |||                       
GTTGACATATTTGCTCAGCTTCAAAATGCTAGTGAGGCATTTCGCACCTACATTAGAGATGGTCTTGCTCAGgttgagttaatttacttgtactaacacatgttcttaa-ttggattttgcattttgtatttctaccagcgattgggagtagtagaattgagtatttgacaattggcaattgatttttgacatttttgcag

upper sequence: GRMZM2G068755_T01 (Zea mays), 5'ss of exon 51
lower sequence: AT2G35630.1 (Arabidopsis thaliana), 5'ss of exon 51
GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacctcagtcatgttggggcggggggttgggcttgttgctttgttatggatgttgtttgacgtacgattgatttaattacattgtttgtaatgcag
|||||||||||| | || ||||| |||||||||||||||||| | || || ||||||||||| || || ||||| ||||||   ||||   |                |||| || || || | | |||     |  |  |     |  |  | ||      |  ||  || ||
GTTGATATATTTTCCCAACTTCAAAATGCTAGTGAAGCGTTTCGTACTTACATCAGAGATGGTCTGGCACAGgtctgtaact--agtctcct---------------agctttttactatgatttcgataaaactcaagttttttgtcttgaagttttgcaatcggttctgtag

upper sequence: GRMZM2G068755_T01 (Zea mays), 5'ss of exon 51
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 5'ss of exon 22
GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacctcagtcatgttggggcggggggttgggcttgttgctttgttatggatgttgtttgacgtacgattgatttaatta-cattgtttgtaatgcag---
|||||||||||||| ||||| || ||||||||||| |||||| | || |||||||| |||||  |||| ||||| || |   | ||  || |       |    ||         |  ||   |||| |    ||| ||   |  ||  |||  ||  | |  ||| |  ||  |   
GTTGATATATTTGCGCAGCTCCAAAATGCTAGTGAGGCGTTTCGGACTTATATCAGGGATGGGTTAGCCCAGgtctgca--tttaga-atatccaaattgaaaattcca------ggattacaatgggtacattttaacaagcagtttcttttcttttcctcctttttgttgttgcag

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|6095379|gb|AW120046.1|AW120046
EST:     AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAG                         GTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
genomic: AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
EST: gi|93014606|gb|EB640126.1|EB640126
EST:     AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAG                         GTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
genomic: AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
EST: gi|26456806|gb|CA828389.1|CA828389
EST:     AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAG                         GTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
genomic: AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
EST: gi|20512828|gb|BQ280026.1|BQ280026
EST:     AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAG                         GTGGTATAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATC
genomic: AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGG-AGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATC
EST: gi|71444352|gb|DR825402.1|DR825402
EST:     AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAG                         GTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
genomic: AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
EST: gi|67015335|gb|CO444084.1|CO444084
EST:     AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAG                         GTGGAGAAAGA-TGCAGCAGCTGGAAGA-TGCCTTNCAGTCTTCCATTATC
genomic: AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAA-GAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATC
EST: gi|60395928|gb|DN228798.1|DN228798
EST:     AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAG                         GTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
genomic: AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
EST: gi|71444353|gb|DR825403.1|DR825403
EST:     AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAG                         GTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC
genomic: AGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacc ... tgtaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacctcagtcatgttggggcggggggttgggcttgttgctttgttatggatgttgtttgacgtacgattgatttaattacattgtttgtaatgcag

- - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA