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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaatctgccctatcttgattagtccacgttgtgtttgtcgtcgatgttcagacacattttgctcaattccttgttacatttaacgctgcttggtatcgtctattag

Basic information

species Zea mays
transcript GRMZM5G848768_T04
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G848768_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g57260.1 (Oryza sativa), 5'ss of exon 10
GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaatctgccctatcttgattagtccacgttgtgtttgtcgtcgatgttcagacacattttgctcaattccttgttacatttaacgctgcttggtatcgtctattag
|||| || ||||||||||| ||||||||||||||||||||||||||||  ||    || ||  ||||||| || || || |||||||||||||||||||    || | |||  |  ||||  ||  |  | ||  |||          ||    |||  | || || ||| |  | | | ||   || |    |  |      ||| | 
GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGAGGGACGTAGCGATGAAGAAGGGACTTCCTATTCTTGGTGTTTTCAGgtgctgcattttgcatttccttgtatatacagcatttggttca--------gtcttaacatgtgttcctgaatgctgtatgagat---actccctctattccaaaatataa-

upper sequence: GRMZM5G848768_T03 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA20G18980.1 (Glycine max), 5'ss of exon 10
GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaatctgccctatcttga--ttagtccacgtt-gtgtttgt-cgtcgatgttcagac--acattttgctcaattccttgttacatttaacgctgcttggtatcgtctattag
| ||||| ||||| |||||||||||||||| ||||||||| || |||||||||  ||| ||  || | || ||||| |||||||||||||| |||||||  |   || ||   |||   |   |||||||  |   || ||| |  |  ||| | || |   ||||  ||     |   |    | ||  |   |   |                
GTAATTCTAGTCAGGTGAGTGATGGTGCTGCAGCTGTTCTGCTGATGAAAAGAAGTGTTGCGTTGCAAAAGGGGCTACCCATTCTTGGTGTATTCAGgt-acttcatttgtaatatagaggctttagtccctggcagtatttatatgctgat-tccaaattgacatgctgtgtgctctatgaagaaatgaaggaccaat----------------

upper sequence: GRMZM5G848768_T03 (Zea mays), 5'ss of exon 10
lower sequence: AT1G04710.1 (Arabidopsis thaliana), 5'ss of exon 10
GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgccc----aatc--tgccctatcttgattagtccacgttgtgtttgtcgtcgatgttcagacacattttgctcaattccttgttacatttaacgctgcttggtatcgtctattag
| ||||| || ||| | ||||| ||||||||||||||||| || ||||  |||  ||| ||  || ||||||| || |||||||||||||| ||||||| | |     | |   | | |||| ||||    ||   | |   |||     |     ||    |||  || |                                            
GGAATTCTAGCCAATTAAGTGACGGTGCTGGAGCTGTTCTCCTTATGAGGAGAAATGTCGCAATGCAGAAAGGCCTTCCCATTCTTGGTGTATTCAGgtgggcttgatagttgatactctatattgacctttctttgcttcatttagtaacagcactcttggacacattacag------------------------------------------

upper sequence: GRMZM5G848768_T03 (Zea mays), 5'ss of exon 10
lower sequence: AT2G33150.1 (Arabidopsis thaliana), 5'ss of exon 10
GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaatctgccctatcttgattagtccacgttgtgtttgtcgtcgatgttcagacacattttgctcaattccttgttacattta-acgctgcttggtatcgtctattag-------------------------------------------------------
| |||||||| ||||| ||||||||||| ||||| ||||| || ||||| |||  ||| ||  || | ||||| || ||| |||||||||| ||||||| |   |   |  | ||    | |  | |   |      |      |||        || |   |  | | |||| | |||||   | | |||  |     | |   ||                                                          
GAAATTCCAGCCAAGTAAGTGATGGTGCAGGAGCGGTTCTCCTAATGAAGAGAAGTGTTGCAATGCAAAAAGGACTTCCCGTTCTTGGTGTATTCAGgtgggtaataattacttacaaagctacgactgtggaagtctgaaaaccgaaaaaactgcagaggcttgtgatttccat-ttacacagatatgctagtatacgtggaaaatacattgttctttctgtatttggctttttctaagtagcacactattggacatattgcag

upper sequence: GRMZM5G848768_T03 (Zea mays), 5'ss of exon 10
lower sequence: Vv05s0051g00720.t01 (Vitis vinifera), 5'ss of exon 10
GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaatctgccctatcttgattagtccacgtt-gtgtttgtcg-tcgatgt-tcagacacattttgctcaattccttgttacatttaacgctgcttggtatcgtctattag
| ||||| || ||||||||||||||||||||||||||||| |||||||| |||  ||| ||  ||   |||||| | || ||||||||||| |||||||     |||   || ||  |  ||  || ||  ||  ||  | | | |  |||  || |     ||| ||| |     | | ||   || |  || ||||||||          
GGAATTCTAGCCAAGTGAGTGATGGTGCTGGAGCTGTTCTCCTCATGAAGAGAAGTGTTGCAATGCGTAAAGGGTTACCTATTCTTGGTGTATTCAGgtatataaat---ccttagatgtatatgtacatatttatgaatttaggtaaatgcctctggtgtctttagctta---tatggatatggtttatact-cttggtataa--------

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|6994094|gb|AW453308.1|AW453308
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGTGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|213184067|gb|FM191388.1|FM191388
EST:     AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGTGTTGGTCCTGC
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC
EST: gi|60672291|gb|DN475055.1|DN475055
EST:     AAA-GATCTGTGGCTCTGAA-AAAGGGCTGCCCATTCTTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGA
genomic: AAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGA
EST: gi|32859848|gb|CD999529.1|CD999529
EST:     AAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTNTGGTGTTTTCAG                         GAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGT-ATGGGTGTTGGTCCTGC
genomic: AAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCT-TGGTGTTTTCAGgttgcccaat ... cgtctattagGAGCTTTGCGGCTGTTGGAGTGGATCCAGCTGTTATGGGCGTTGGTCCTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATTCCAGTCAAGTGAGTGATGGTGCTGGAGCTGTTCTTCTCATGAAAAGATCTGTGGCTCTGAAGAAAGGGCTGCCCATTCTTGGTGTTTTCAGgttgcccaatctgccctatcttgattagtccacgttgtgtttgtcgtcgatgttcagacacattttgctcaattccttgttacatttaacgctgcttggtatcgtctattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA