Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactacattctatctgttgcccaagtcttatctgcattgctaaatgctgttcacgtttgctatttaaaaaactgaattttgagaatccttcatttatgtagaggttgtttttatgatgctaaactccctacatgttcgttaagcgtggcattacagttagctagttatatcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGTGTTGATCTGGGTGCCATTGAGGCAGAAGTTAGCAAGCAGTGCAACGCGC

Basic information

species Zea mays
transcript GRMZM2G058584_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g13190.1 (Oryza sativa), 3'ss of exon 10
gtactacattctatctgttgcccaagtcttatc--tgcattgc-taaatgctgttca----cgtttgctatttaaaaaactgaattttgagaatccttcatttatgtagaggttgtttttatgatgctaaactccctacatgttcgttaagcgtggcattacagttagctagttatatcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGTGTTGATCTGGGTGCCATTGAGGCAGAAGTTAGCAAGCAGTGCAACGCGC
|||     |  | |   |  ||    || ||    || | ||  ||  || | || |    | ||| || ||| |||  |   |||| |||||||       || | |     || | |  ||| |||    |   ||  | | | |      |   || ||||||      | | |  |||   |||| |||||||||||||| ||||||||||||||||||||||| ||||| ||||||||| ||||||| |||||||||||||||||||||||||||   || |
gtatcttctattcttaataccctgcttcatactggtgaaatgtgtacttgttattgaacttcctttactctttgaaatgccatattt-gagaatctgaggcataggaattacatgatgtcgtgaagct----ttgttaagtat-catattatattatataacagttgttcgttcaaaatttt---agGCGGAACATGGCCCAGACAGTCAGGTTGTTCTAGTTGTTGCGGGAGACGGTGTTGATTTGGGTGCTATTGAGGCAGAAGTTAGCAAGCAGTGCTCTGCTC

upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 10
gtactacattctatctgttgcccaagtcttatctgcattgctaaatgctgttcacgtttgctatttaaaaaactgaattttgagaatccttcatttatgtagaggttgtttttatgatgc-taaactccctacatgttcgttaagcgtggcattacagttagctagttatatcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGTGTTGATCTGGGTGCCATTGAGGCAGAAGTTAGCAAGCAGTGCAACGCGC
                                                                                |     |  ||  | ||  || |   |      ||||| | ||| ||   ||  |  | ||  |  |  |   |  |   | ||| || ||   |||  |||| || ||||| |||||||||||||||||||| ||  ||| |||||||||||| ||||||  ||| ||  |||  ||| | |||||||||||| |    |
--------------------------------------------------------------------------------tcccttttttttttctacctacacacttcgaagatgattcctaacctttttagcttcttgtacactgctgatatctatgcacctaatt-tacaattttcagGCTGAGCATGGTCCAGATAGTCAGGTTGTTCTTGTGATTGTTGGAGATGGTGTGGATCTGAATGCAATACAGGAGGAACTCAGCAAGCAGTGCGAGAGTC

upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 10
gtactacattctatctgttgcccaagtcttatctgcattgctaaatgctgttcacgtttgctatttaaaaaactgaattttgagaatccttcatttatgtagaggttgtttttatgatgc-taaactccctacatgttcgttaagcgtggcattacagttagctagttatatcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGTGTTGATCTGGGTGCCATTGAGGCAGAAGTTAGCAAGCAGTGCAACGCGC
                                                                               |||    |  ||  | ||  || |   |      ||||| | ||| ||   ||  |    ||  |  |  |   |  |   | |||||| ||   |||  ||||||| |||||||||||||||||||||||||| ||  |||||||||||||||| ||||||  ||| ||  |||  ||| | |||||||||||  ||   |
-------------------------------------------------------------------------------ttgtccctttttt-tctacctacacacttcgaagatgattcctaacctttttagcttcctgtacattgctgatatctatgcacctagtt-tacaattttcagGCAGAGCATGGCCCAGATAGTCAGGTTGTTCTTGTGATTGCTGGAGATGGTGTGGATCTGAATGCAATACAGGAGGAACTCAGCAAGCAGTGTGACAGTC

upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 12
lower sequence: PP1S15_472V6.1 (Physcomitrella patens), 3'ss of exon 11
gtactacattctatctgttgcccaagtcttatctgcattgctaaatgctgttcacgtttgctatttaaaaaactgaattttgagaatccttcatttatgtagaggttgtttttatgatgctaaactccctacatgttcgttaagcgtggcattacagttagcta-gttatatcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGTGTTGATCTGGGTGCCATTGAGGCAGAAGTTAGCAAGCAGTGCAACGCGC
                                                                              | | |  | |  |  ||| | ||   ||||  |  ||  | | | | |    | || |||| |   |  |  ||   | || | |  |||   | | ||| ||||||||||||| |||||||||||||| ||||| || |  ||  | ||||  || ||  | | ||||||  ||   || ||    |  || || |  |   
-----------------------------------------------------------------------------gtgtaatcagcgatagtttctatac--gttgaatccat--taccagattggtcatattttcgctgttctggttatgtaattttgttctgtttggtatattgcagGCAGAACATGGGCCAGATAGTCAGGTGGTTCTTGTAGCAGCAAGTGATGAAGTAGACATCGCTGCCATACAGCACGAGGTGGAGAGACAATGTAGGGATT

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|89758985|gb|DY687956.1|DY687956
EST:     CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAG                         GCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
genomic: CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAGgtactacatt ... tcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
EST: gi|71309836|gb|DR791200.1|DR791200
EST:     CCAGTTCATGTTGCTGCTGATCTGCTATCCCAG                         GCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
genomic: CCAGTTCATGTTGCTGCTGATCTGCTATCCCAGgtactacatt ... tcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
EST: gi|8516559|gb|BE123284.1|BE123284
EST:     CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAG                         GCAGAACATGGTCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
genomic: CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAGgtactacatt ... tcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
EST: gi|21331772|gb|BQ487153.1|BQ487153
EST:     CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAG                         GCAGAACATGGTCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
genomic: CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAGgtactacatt ... tcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
EST: gi|101389917|gb|EB816889.1|EB816889
EST:     TTCATGTTGCTGGTGATCTGGTATCCCAG                         GCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
genomic: TTCATGTTGCTGCTGATCTGCTATCCCAGgtactacatt ... tcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
EST: gi|23357617|gb|BU645266.1|BU645266
EST:     CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAG                         GCAGAACATGGTCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
genomic: CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAGgtactacatt ... tcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
EST: gi|38688105|gb|CK145136.1|CK145136
EST:     CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAG                         GCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
genomic: CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAGgtactacatt ... tcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
EST: gi|71432207|gb|DR813257.1|DR813257
EST:     CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAG                         GCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
genomic: CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAGgtactacatt ... tcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
EST: gi|76283948|gb|DV023516.1|DV023516
EST:     CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAG                         GCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
genomic: CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAGgtactacatt ... tcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
EST: gi|76012898|gb|DT940068.1|DT940068
EST:     CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAG                         GCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
genomic: CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAGgtactacatt ... tcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
EST: gi|76012899|gb|DT940069.1|DT940069
EST:     CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAG                         GCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
genomic: CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAGgtactacatt ... tcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
EST: gi|71774595|gb|DR972473.1|DR972473
EST:     AATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAG                         GCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
genomic: AATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAGgtactacatt ... tcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
EST: gi|211215840|gb|FL096753.1|FL096753
EST:     CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAG                         GCAGAACATGGTCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGACAGT
genomic: CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAGgtactacatt ... tcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
EST: gi|32840983|gb|CD980664.1|CD980664
EST:     CTGATAAATACGCGAACCCAGTCCATGTTGCTGCTGATCTGCTATCCCAG                         GCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGACGGT
genomic: CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAGgtactacatt ... tcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
EST: gi|38687960|gb|CK144991.1|CK144991
EST:     CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAG                         GCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT
genomic: CTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATCTGCTATCCCAGgtactacatt ... tcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccctacatgttcgttaagcgtggcattacagttagctagttatatcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGTGTTGATCTGGGTGCCATTGAGGCAGAAGTTAGCAAGCAGTGCAACGCGC
                                           tatctttt  CT-rich tract
                                     tagttatatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactacattctatctgttgcccaagtcttatctgcattgctaaatgctgttcacgtttgctatttaaaaaactgaattttgagaatccttcatttatgtagaggttgtttttatgatgctaaactccctacatgttcgttaagcgtggcattacagttagctagttatatcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGTGTTGATCTGGGTGCCATTGAGGCAGAAGTTAGCAAGCAGTGCAACGCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG