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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGCAAGTGAAGgtgaaatcatgagttttggttaaaaggaaagaatttagctcttaacatatcctttgttaacatgtggttttcttttggtaattgtag

Basic information

species Zea mays
transcript GRMZM2G006429_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006429_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g18970.1 (Oryza sativa), 5'ss of exon 4
TCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGCAAGTGAAGgtgaaatcatgagttttggttaaaaggaaagaatttagctcttaacatatcctttgtta-acatgtggttttcttttggtaattgtag
|||| ||||||||||||||||||||||||||||||| || |||||||||||||| || || ||||||||||| || |||||||||||||||||||||||||||||||  | ||  || | | ||| | ||| | |    | |    ||   |||   |    |||   ||   | | || ||||||||
TCTCAGATGCTGGCCAGGTGGATTGTGCCTTTCAAGATCGATTGGGGATACTGACGTTGGGGAGTTCATTGTGCCAATTCCACATGTCAAGCAAGTGAAGgtgaaattttaagagtttgatcaaatgcaaggagtagcttatcgcaatgaacttaactgtgtatgcttttcattctgggaaattgtag

upper sequence: GRMZM2G006429_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G39260.1 (Glycine max), 5'ss of exon 5
TCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGCAAGTGAAGgtgaa--------atcatgagttttggttaaaag-----------gaaagaatttagctcttaacatatcc-tttgttaacatgtggttttcttttggtaattgtag
||| || ||||||||||||||||||||||| || || ||||| || || || ||||| || || || ||||| || || |||||||| ||||||||||||||||         || |||  ||||| || |              | |||  ||||| |||||   | ||   |||| ||||| ||  | |   ||  | |      
TCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCCAGATCAATAGGCGACACGGATGTGGGAGAATTTATTGTGCCAATACCACATGTAAAGCAAGTGAAGgtgagctggttttattatgttttttgtttgatgacctgtttatgtggaagcttttagttcttagtttctctgcttgtaaacatttgtctattgatttctcag-----

upper sequence: GRMZM2G006429_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G41810.2 (Glycine max), 5'ss of exon 5
TCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGCAAGTGAAGgtgaa-----------atcatgagttttggttaaaag-----------gaaagaatttagctcttaacatatcctttgttaacatgtggttttcttttggtaattgtag
||| || ||||||||||||||||||||||| || || || || || || || || || || || || ||||| || || |||||||| ||||||||||||||||            || |||  ||||| ||    |           |||||  ||||| ||| |     | |  || |   |     || ||| ||| |  |   ||
TCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCTAGATCTATAGGTGACACAGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGCAAGTGAAGgtgagctggtttcattattatgttttttgtttggtggcctgtttatgtgaaagcttttagttctaagt---ttcactgctcttaaacatttgtctattgatt-tctcag

upper sequence: GRMZM2G006429_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G29060.1 (Glycine max), 5'ss of exon 5
TCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGCAAGTGAAGgtgaa--------atcatg-agttttggttaa-------aaggaaagaattt---agctcttaacatatcctttgttaacatgtggttttcttttggtaattgtag--
||| || || ||||| ||||||||||||||||| || |||||||| || || || || || || || ||||| || || ||||||||||||||||||||||| |         ||  || ||| || ||| |       | ||  |  || |   ||   |||  |     |||    ||   ||   |||| ||  |  ||      
TCTTCGCTGTTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACAGACGTGGGAGAATTTATTGTCCCAATACCACATGTCAAGCAAGTGAAGgtaagctagtttcattttgtagtcttagtttattgatcgatggccattatgtggaagtgtttagtactaaatttcagcactcctgaccttctcttattggttccccag

upper sequence: GRMZM2G006429_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA20G38270.1 (Glycine max), 5'ss of exon 5
TCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGCAAGTGAAGgtgaaatcatgagttttggttaaaaggaaagaatttagctcttaaca--tatcctt-tgttaacatgt--ggttttc--ttttggtaattgtag----------------------
||| || |||||||| ||||||||||||||||| || |||||||| || || || || || || || ||||| || || |||||||| |||||||||||||| |  |    |||||   ||  |||     | ||||  | || |     ||  || |||  | ||||   ||  |   |||  | | |  |                        
TCTTCGCTGCTGGCCTGGTGGATTGTGCCTTTCTAGATCAATTGGTGACACGGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGCAAGTGAAGgtaagct----agtttcattttgaagtctt-agtttatatattgatggtcatttttatgtggagatgtttagtactaaatttcagcactgatgaccttctcttattggttccccag

upper sequence: GRMZM2G006429_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT1G09160.2 (Arabidopsis thaliana), 5'ss of exon 5
TCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGCAAGTGAAGgtgaaatcatgagttttggttaaaaggaaagaatttagctctta-acatatcctttgttaacatgtggttttcttttggtaattgtag
 || ||||||||||| ||||| || || ||||| ||||| ||||| ||||| ||||| || || || ||||| || || ||||| || ||||||||||| || |  ||     |||   ||   |         |||  ||||| |  |  | ||  | || | ||  |||| | |  |||  |  ||
ACTACGATGCTGGCCTGGTGGTTTATGTCTTTCGAGGTCCATTGGTGATACGGATGTGGGAGAATTTATTGTCCCTATACCACACGTTAAGCAAGTGAAAgtaagctccc---tttcccttggtacatttttcattaattcttatatttgacattgatcaaaaagtatttttatct--gtacgttcag

upper sequence: GRMZM2G006429_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv14s0060g01580.t01 (Vitis vinifera), 5'ss of exon 5
TCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGCAAGTGAAGgtgaaatcatgagttttggttaaaaggaaagaatt-tagctcttaacatatcctttgttaacatg-tggttttcttttggtaattgtag-------------------------------------------
 ||||| |||||||| |||||||| || || || ||||||||||| || || ||||| || || |||||||| || || |||||||| |||||||||||||||    ||     ||| ||      ||  |  || | ||  ||    ||  |     ||   |  ||||  | ||||  | | | |                                             
ACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGCAAGTGAAGgtgtgtgcaccttattttgtactggtgatggttttattgcatttgtggtagtccaccatattgtactggtgatatttttattactttctgatggtacattctaagttcaatctcttttaattgattattaag

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|71314548|gb|DR793896.1|DR793896
EST:     CTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGCAAGTGAAG                         CTCCCAAATACTGGTGGAAGACTAATAATTGCATCAGATGGAATATGGGAC
genomic: CTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGCAAGTGAAGgtgaaatcat ... gtaattgtagCTCCCAAATACTGGTGGAAGACTAATAATTGCATCAGATGGAATATGGGAC
EST: gi|19822432|gb|BQ048456.1|BQ048456
EST:     CTGATGTCGGCGAGTTCATCGTACCGATTCCACATGTCAAGCAAGTGAAG                         CTCCCAAATACTGGTGGAAGACTAATAATTGCATCAGATGGAATATGGGAC
genomic: CTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGCAAGTGAAGgtgaaatcat ... gtaattgtagCTCCCAAATACTGGTGGAAGACTAATAATTGCATCAGATGGAATATGGGAC
EST: gi|26455794|gb|CA827377.1|CA827377
EST:     CTGATGTCGGCGAGTTCATCGTACCGATTCCACATGTCAAGCAAGTGAAG                         CTCCCAAATACTGGTGGAAGACTAATAATTGCATCAGATGGAATATGGGAC
genomic: CTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGCAAGTGAAGgtgaaatcat ... gtaattgtagCTCCCAAATACTGGTGGAAGACTAATAATTGCATCAGATGGAATATGGGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGCAAGTGAAGgtgaaatcatgagttttggttaaaaggaaagaatttagctcttaacatatcctttgttaacatgtggttttcttttggtaattgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG