Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgatactgcatgaacaacaaaaaggatatgtggattttactatctagatggtgttgtcaaatgtcatcatttataggctccttc...

Basic information

species Zea mays
transcript GRMZM2G368908_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 5'ss of exon 5
AATGCTACACAGAAA-AGTCAGAAGGTATTTGTCCATGTTCCTTCAG-AAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgatactgcatgaacaacaaaaaggatatgtggattttactatctagatggtgttgtcaaatgtcatcatttataggctccttc-
|||||||| || ||| ||||| ||||| ||||| ||||||||||||| |||| ||||| || || ||||||||||| |||| | ||   | ||||| |  | |  | | || |   | | | | || ||||| | |  || |     | || |  |    | |    ||      ||  
AATGCTACTCAAAAACAGTCAAAAGGTGTTTGTTCATGTTCCTTCAGCAAATAGCTGCCCACGAGGTTGAGGAAATCGgtatgtctgtctcatctgtttttactaggaaaa-agggatgctttatgtattttgcaagttacagataatagttagcttgtttgagcggtaaatatattaa

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA11G34980.1 (Glycine max), 5'ss of exon 5
AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgatactgcatgaacaacaaaaaggatatgtggattttactatctagatggtgttgtcaaatgtcatcatttataggctccttc--------------------------------------------------------------------------
||||| || || |||||||| || || ||||| ||||| || ||||| |||||||||||||||||||||||||| ||||   | ||    ||    | || |  |||           |   |   ||||  | | ||  | || |  |  ||  |    || |  |   || |                                                                            
AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatgccattc----aatgtaaaaactggtcttttttttcttatgttttgtt-tttattttgtttgattcaaaatttctatatgaaaattcttaattttatccataccattgtgtaacctgtttctcctgttttttgtttttttttaaattcttcttacctttgtgcag

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA20G03160.1 (Glycine max), 5'ss of exon 5
----------------AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgatactgcatgaacaacaaaaaggatatgtggattttactatctagatggtgttgtcaaatgtcatcat-----ttataggctccttc---------------------------------------------------------
                ||||| || || |||||||| ||||||||| | ||||| || ||||| |||||| || ||||||||||||||||  ||| | | ||   ||   ||     ||  |            |||||    |||| ||| | | |  || |   |||| ||   ||     ||||    |   ||                                                         
TTTATTCTGTGTACATAATGCCACTCAAAAAAGTCAAAAGGTATTTATACATGTGCCATCAGAGATTGCTACTAATGAAGTTGAGGAAATATgtatgtcatgcc-attcaatgtaaaattgatgtatttcttcttatgttttgttta-tattttgtt--tgattcaaaatttctatatgaaaattatgaattttatccatacaattgtgtaaccagtttctcttgtttttttaattcttcttacctttgtgcag

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA18G03360.1 (Glycine max), 5'ss of exon 5
-AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg----ttgatctgatactg-------------catgaacaacaaaaaggatatgtggattttactatctagatggtgttgtcaaatgtcatc------att-tataggctccttc----------------------------------
 ||||| || || |||||||| ||||| ||||| ||||| || ||||| |||||||||||||||||||||||||| ||||   | ||    |  || | | ||||              |||        | |   | | ||  |   | | |||| |||    |    ||| | |||      ||| | ||  |   |||                                  
GAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAggtatttcatgccattcaatgtaaaactgatgtttttcttcttatgttttgtttatattttgtttgattcaaaatttctatatgaaaattctgaattttatccatacaattgtgtaaccagtttctcctgttttttttaattcttcttacctttgtgca

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 5
AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgta------------agacttgttgatctgat-actgcatgaac-------aacaaaaaggatatgtggatt----ttactatctagatggtgttgtcaaatgt-----catcatttataggctccttc--
|||||||| |||||||| ||||| || || || |||||  || ||||||||||||||||||||||||||||||| ||||            | |   |||  | |||| | | ||| | |       |     || || |||||  ||    ||  | |   || | | || | | |  |     | |||||  |   ||  | |  
AATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATTGCTGCTCATGAAGTTGAGGAAATCGgtatgtccaaaagggaaaacagttcttttgatgatttcatcatctcggttgagttttaaagaaatgtgttttgtgattgttctgaggaagattttctgacacttacctgcgtcattcttgttcttgtacag

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 5
AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagact--------------------tgttgatctgata-ctgcat---gaacaacaaaaaggatatgtggattttactatctagatggtgttgtcaaatgtcatcatttataggctccttc---------------------------------
|||||||| |||||||| ||  |||| ||||| || || ||| |||||||||| ||||||||||||||||||||||||| | ||                    || |  | ||||  |   ||     |  | || || |||  | | |||||  | | |  |   || |  | |      ||| |      || |||                                  
AATGCTACCCAGAAAAGCCAACAGGTTTTTGTACACGTGCCTACAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtatgtctacatggggaaacaaatcctttgatagtttgatttccttatttcagagcataagaatgatgagggaatttttttttttgta-aatgcttccgaggaaactcaatggagtccttcttgcttcgcttacgccagttggttggtcttgaacag

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 5
AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg--ttga------tctgatactgca-tgaacaacaaaaaggatatgtggattttactatctagatggtgttgtcaaatgtcatcatttataggctccttc-------------------------------------------
|||||||| |||||||| |||||||| ||||||||||| || || |||||||||||||||||||||||||||||||||| | | ||    ||      ||| ||  | |  | | |||           | |   | ||   | || || | ||       |  | |||||  ||    | | |                                            
AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtatgtcatgagccgaaaagcttcttattttcctcttagcaatgctttttccctttccgtattctgaacttgaagatgcaaattgactttatcatgaattatttacctttttgaaccttcagtaattaacttcatgtgtcacctttccctag

upper sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv02s0025g01490.t01 (Vitis vinifera), 5'ss of exon 5
AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgatactgcatgaacaacaaaaaggata--tgtggattttactatctagatggtgttgtcaaatgtca--tcatttataggctccttc---------------------------------------------
||||| || |||||||| ||||| || ||||||||  | ||||| |||||||||||||||||||||||||||||||||| | |  | |||     ||||   |   |    | |||  |   | |   |||| ||||   ||       | || |  | |  | || ||| |  |  ||                                              
AATGCCACTCAGAAAAGCCAGAAAGTTTTTGTCCACATACCTTCTGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtatgtcaagctgaaaaactacttattttcctcttagaagtgttcctttcccttttcctattctgaactcaaagacacaattgaatttatatatggattgtttaactttgaatctttaatgataaacttcctacatcacctgccaatag

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|60340869|gb|DN207842.1|DN207842
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTG
EST: gi|60355241|gb|DN222214.1|DN222214
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTG
EST: gi|108824177|gb|EC278185.1|EC278185
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTTTAAGGGATGTAAAGGACACAACCATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTG
EST: gi|110520623|gb|EE024807.1|EE024807
EST:     AAATTGCTGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTG
genomic: AAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttg ... ctgtcttcagGAGTTGAACACCTTTTAAGGGACGTAAAGGACACAACCATAAGCACACTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgatactgcatgaacaacaaaaaggatatgtggattttactatctagatggtgttgtcaaatgtcatcatttataggctccttc

- - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaaaa