Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCAGCATTCCAATGAAAGGCATGGTGGATTCGTTTAATGTATCTGTTGCAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTGgtaagtggactttcttcattttagttatcatcgtaccttaaagaagacatgataaacccaacccactattagcaaagtttatctatcatcatacggtact...

Basic information

species Zea mays
transcript GRMZM2G026869_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026869_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g40700.2 (Oryza sativa), 5'ss of exon 4
CTGCAGCATTCCAATGAAAGGCATGGTGGATTCGTTTAATGTATCTGTTGCAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTGgtaagtggactttcttcatt-ttagttatcatcgtaccttaaagaagacatgataaacccaacccactattagcaaagtttatctatcatcatacg-gtact-
||||||  |||| |||||||||||||||||||| ||||||||||||||||||||||||||||| |||||||||||||| |||||| || |||||||| | |||||||    |    ||||  || | |  ||   | |   ||||| | |    |||  ||     ||  |||     |  |  | ||  || ||   ||   
CTGCAGTGTTCCTATGAAAGGCATGGTGGATTCTTTTAATGTATCTGTTGCAGCTGGAATCCTTATGCACCATGCTGTCTGTGATCGAATTTCCCGCATCgtaagtg--tctcaagcattactactaaatataccagcaggaagaataaacaccaaattcagttt-ctgctagtgggttgaacttgtctccaaactcatatat

upper sequence: GRMZM2G026869_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA18G49880.1 (Glycine max), 5'ss of exon 4
CTGCAGCATTCCAATGAAAGGCATGGTGGATTCGTTTAATGTATCTGTTGCAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTGgtaagtggactttcttcattttagttatcatcgtaccttaaagaagacatgataaacccaacccactattagcaaagtttatctatcatcatacggtact--------
 ||||| ||||| |||  ||| |||||| | || || ||||| || ||||| || ||||||||||||||||||||||||||||||||| | || ||  |||||| ||   ||  || || |   ||||  | || |    |  | ||||    ||    || |   |||  |     ||| ||  |||      | || |        
TTGCAGTATTCCTATGGCAGGAATGGTGAAGTCTTTCAATGTTTCAGTTGCTGCAGGAATCCTCATGCACCATGCTGTTTGTGATAGAATATCTCGTATGgtaa-tgattttagtttatgtactttat-gtggtgc----agaatgacaaatcaatttgaatcgtatatctg--ggttttgtcgttcaaacattgatattgtagagat

upper sequence: GRMZM2G026869_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G26320.1 (Glycine max), 5'ss of exon 4
CTGCAGCATTCCAATGAAAGGCATGGTGGATTCGTTTAATGTATCTGTTGCAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTGgtaagtggactttcttcattttagttatcatcgtacctta-aagaagacatgataaacccaacccactattagcaaagttta--tctatcatc-atacggtact
 ||||| ||||| |||  ||| |||||||| || || ||||| || ||||| || |||||||||||||||||  |||||||||||||| | || ||  |||||| ||   ||  || || |   ||||  | || |   |  | ||  ||   | ||   || |   |||  |     | |   || | |||  |||  |||  
TTGCAGTATTCCTATGGCAGGAATGGTGGACTCTTTCAATGTTTCAGTTGCTGCGGGAATCCTCATGCACCACTCTGTTTGTGATAGAATATCTCGTATGgtaa-tgattttagtttatgtactttat-gtggtgcagaatgacaaatcaattttaattgaatcttatatctgggttttgtgattcaaacattgatattgta--

upper sequence: GRMZM2G026869_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv14s0108g01380.t01 (Vitis vinifera), 5'ss of exon 4
CTGCAGCATTCCAATGAAAGGCATGGTGGATTCGTTTAATGTATCTGTTGCAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTGgtaagtggactttcttcattttagttatcatcgtaccttaaagaagacatgataaacccaacccactattagcaaagtttatctatcatcatacggtact---
 ||||| ||||||||||||||||||||||| || || ||||| || ||||| ||||| |||||||||||||||||||||||||| |||   || ||||||||||        | ||      |  |    | | |    | ||||   ||  ||||     ||||     | ||  | ||  |  |    ||    |  |   
TTGCAGTATTCCAATGAAAGGCATGGTGGACTCCTTCAATGTTTCAGTTGCTGCTGGGATCCTCATGCACCATGCTGTTTGTGACAGAACGTCTCGCCTGgtaataatgacatttttgcacaatcttgtgttgcataggagagaatcaatc-taaattt--cccagatagatcatggattgaccttttgtattgaatgtttcc

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|6194738|gb|AW146842.1|AW146842
EST:     CAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTG                         GGCCATCACGGTGATCTCTTGCCTGAAGAAAATAGGATATTGCTTGCTGAG
genomic: CAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTGgtaagtggac ... ggtttatcagGGCCATCACGGTGATCTCTTGCCTGAAGAAAATAGGATATTGCTTGCTGAG
EST: gi|60355726|gb|DN222699.1|DN222699
EST:     GAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCTTG                         GGCCATCACGGTGATCTCTTGCCTGAAGAAAATAGGATATTGCTTGCTGAG
genomic: GAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTGgtaagtggac ... ggtttatcagGGCCATCACGGTGATCTCTTGCCTGAAGAAAATAGGATATTGCTTGCTGAG
EST: gi|78118115|gb|DV536502.1|DV536502
EST:     CAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTG                         GGCCATCACGGTGATCTCTTGCCTGAAGAAAATAGGATATTGCTTGCTGAG
genomic: CAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTGgtaagtggac ... ggtttatcagGGCCATCACGGTGATCTCTTGCCTGAAGAAAATAGGATATTGCTTGCTGAG
EST: gi|71764970|gb|DR962907.1|DR962907
EST:     CAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTG                         GGCCATCACGGTGATCTCTTGCCTGAAGAAAATAGGATATTGCTTGCTGAG
genomic: CAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTGgtaagtggac ... ggtttatcagGGCCATCACGGTGATCTCTTGCCTGAAGAAAATAGGATATTGCTTGCTGAG
EST: gi|78023024|gb|DV491411.1|DV491411
EST:     CAGCTGGAATCATCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTG                         GGCCATCACGGTGATCTCTTGCCTGAAGAAAATAGGATATTGCTTGCTGAG
genomic: CAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTGgtaagtggac ... ggtttatcagGGCCATCACGGTGATCTCTTGCCTGAAGAAAATAGGATATTGCTTGCTGAG
EST: gi|6095632|gb|AW120299.1|AW120299
EST:     CAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTG                         GGCCATCACGGTGATCTCTTGCCTGAAGAAAATAGGATATTGCTTGCTGAG
genomic: CAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTGgtaagtggac ... ggtttatcagGGCCATCACGGTGATCTCTTGCCTGAAGAAAATAGGATATTGCTTGCTGAG
EST: gi|71444034|gb|DR825084.1|DR825084
EST:     CAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTG                         GGCCATCACGGTGATCTCTTGCCTGAAGAAAATAGGATATTGCTTGCTGAG
genomic: CAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTGgtaagtggac ... ggtttatcagGGCCATCACGGTGATCTCTTGCCTGAAGAAAATAGGATATTGCTTGCTGAG
EST: gi|5847510|gb|AW000589.1|AW000589
EST:     CAGCTGGAATCCTCATGCNCCATGCTGTTTGTGATAGAGTTTCCCGCCTG                         GGCCATCNCGGTGATCTCTTGCCTGAAGAAAATAGGATATTGCTTGCTGAG
genomic: CAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTGgtaagtggac ... ggtttatcagGGCCATCACGGTGATCTCTTGCCTGAAGAAAATAGGATATTGCTTGCTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCAGCATTCCAATGAAAGGCATGGTGGATTCGTTTAATGTATCTGTTGCAGCTGGAATCCTCATGCACCATGCTGTTTGTGATAGAGTTTCCCGCCTGgtaagtggactttcttcattttagttatcatcgtaccttaaagaagacatgataaacccaacccactattagcaaagtttatctatcatcatacggtact

- - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT