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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttacacaagattactaggtgtttcataggcgtcctcatattacttgaattgatatttagagctactatttctgggtacattttttttgaatgttgactaactttctattttgttaagactgaccatcaatgtatttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGCCTGTATGTATTTGCCTTCTGTTGGGTGTATGTGATCAAGATTAGAGCAG

Basic information

species Zea mays
transcript GRMZM2G068657_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068657_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
gtaagttacacaagattactaggtgtttcataggcgtcctcatattacttgaattgatatttagagctactatttctgggtacattttttttgaatgttgactaactttct----attttgttaagactgaccatcaa-tgtatttg-tgcagCGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGCCTGTATGTATTTGCCTTCTGTTGGGTGTATGTGATCAAGATTAGAGCAG
||||||  ||     || | ||  |||   ||    |||| |   ||   | |  || || | | |    | |||   | ||   ||    ||  | |     | || |||    ||    || || || | ||| ||   |||||| ||||||||||||||||||||||||| |||||||||| |||||| || || |||||||| || |||||||| ||||||||||||||  | ||||||||||||   |
gtaagtatcatgttttt-ccagcagttctgtacctatccttaccgta---ggaaagacatgt-gcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG

upper sequence: GRMZM2G068657_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G05670.2 (Glycine max), 3'ss of exon 3
gtaagttacacaagattactaggtgtttcataggcgtcctcatattacttgaattgatatttagagctactatttctgggtacattttttttgaatgttgactaactttctattttgt-taagactgaccatcaatgtatttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGCCTGTATGTATTTGCCTTCTGTTGGGTGTATGTGATCAAGATTAGAGCAG
                                           |||| ||   ||| | | |     |||| |||| |    |||||  | || ||  | | | | | |  ||| ||| |   | |  |   ||   | ||| ||||||||||||||||||||||||  |||||||| | ||| || ||  | || ||  | ||||| ||||| || || ||||| ||| |  | |  ||||  ||| 
-------------------------------------------attattttttttgttctgt----ttact-tttcagttatcatttgctatgcattattattgaatatacattatgtatcctaattgcttgcacgatttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTGTGTATATATGTTTTTGCATTTTGCTGGGTCTATATTGTAAGAATTATGGCAT

upper sequence: GRMZM2G068657_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 3
gtaagttacacaagattactaggtgtttcataggcgtcctcatattacttgaattgatatttagagctactatttctgggtacattttttttgaatgttgactaactttctattttg--ttaagactgaccatcaatgtatttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGCCTGTATGTATTTGCCTTCTGTTGGGTGTATGTGATCAAGATTAGAGCAG
                                              | | ||   || | ||     |||| ||  |   | |||||  | ||     |   | | | |  ||| ||  |    | ||       |  | ||| ||||||||||||||||||||||||  |||||||| | ||| || ||  | || ||  | ||||| ||||| || || ||||| ||  |  | |  ||||  ||| 
----------------------------------------------aatggag--gaaaattctgtttacttttcatctat-catttgctatgtgccatccttgaatatgcattatgcatcctaattgcttggataattttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGTATATATGTTTTTGCATTTTGCTGGGTCTACATTGTAAGAATTATGGCAT

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|148966165|gb|EE017106.2|EE017106
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTG                         CGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttaca ... atttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGC
EST: gi|71325398|gb|DR799378.1|DR799378
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTG                         CGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttaca ... atttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGC
EST: gi|101385920|gb|EB815008.1|EB815008
EST:     TGGAACGGGTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTG                         CGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttaca ... atttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGC
EST: gi|78115179|gb|DV533567.1|DV533567
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTG                         CGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttaca ... atttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGC
EST: gi|71325717|gb|DR799546.1|DR799546
EST:     TGGAACGGTTTGATCATCACTGTCCCTGGGTCGGCCAGTGCATAGGACTG                         CGTAATTATCGGTTCTTCTATATGTTTGTA
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttaca ... atttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTA
EST: gi|148960850|gb|EE011526.2|EE011526
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTG                         CGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttaca ... atttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgttgactaactttctattttgttaagactgaccatcaatgtatttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGCCTGTATGTATTTGCCTTCTGTTGGGTGTATGTGATCAAGATTAGAGCAG
              tttctattttgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttacacaagattactaggtgtttcataggcgtcctcatattacttgaattgatatttagagctactatttctgggtacattttttttgaatgttgactaactttctattttgttaagactgaccatcaatgtatttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGCCTGTATGTATTTGCCTTCTGTTGGGTGTATGTGATCAAGATTAGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG