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

TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttacatgacaaaattgtgcgtttgcgtgtgtgtgtggggggtgggggggggtgacagagcttcaattcttgaggttcttgaaaagtaatacagaagactgtttaatgaagtgttaattatgatgatgtttactgcattattagtattatacgtggcttagcaattaaacctttcag

Basic information

species Zea mays
transcript GRMZM2G039263_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039263_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 5'ss of exon 11
TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgc-------ttacatgacaaaattgtg----cgtt----tgcgtgtgtgtgtggggggtgggggggg-------gtgacagagcttcaattcttgaggt--tcttgaaaagtaatacagaagactgtttaatgaagtgttaattatgatgatgtttactgcattattagtattatacgtggcttagcaattaaacctttcag
||||| ||||||||||| || ||||| |||||||||||||| ||||| |||||||| ||||||||||| || |||||||||||||||||||||       ||   | |   | ||||     | ||    | | |   ||||  |  |       |          |||   |||  |    |||| | |   | || ||  | |  |  |||  ||||   |  |||  ||||  | ||| |    ||    |  || ||  | | | |   || | | | ||   || |||
TACTTCGTTGAGGCTGGAGCAATTGCTGTAAGGCGTGTGCGTAAGGAGGATTTGCGCCATGTTGCCAAGGCTACTGGTGCAACTATGgtatgcctcaccttttgtttatcgagttgtaaccacattggaatacataattgtgcagatgactaatagaattaataaatgatgaagcgacttcccttgcgatacccctgtaattttagtcttaagtttgttgcttctagtcctaatattaatgctac--accaactgtttggtgctgtcc-taatttggtagtaaa---ttgcag

upper sequence: GRMZM2G039263_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA05G29870.1 (Glycine max), 5'ss of exon 11
TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttacatgacaaaattgtgcgtttgcgtgtgtgtgtggggggtgggggggggtgacag--agcttcaattcttgaggttcttgaaaagtaat-acagaagactgtttaatgaagtgttaattatgatgatgtttactgcattattagtattatacgtggcttagcaattaaacctttcag
||||||||||||||||| || ||||| ||||| |||||||| || || ||  |||| ||||||||||| || |||||||||||  ||||| ||||           || |   ||      | |   | |    |   |   | ||||||  |   | |||  |||      | ||    | || | | | | ||                                                                             
TACTTTGTTGAGGCTGGGGCAATTGCTGTAAGACGTGTGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTGgtaggctttt---------tttttttttaataaatttaaattgcaattttagcaagttgacagtaaagctgaatatttgtcacaatggagtgttgattagatagggctc----------------------------------------------------------------------------

upper sequence: GRMZM2G039263_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G12970.1 (Glycine max), 5'ss of exon 11
TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttacatgacaaaattgtgcgtttgcgtgtgtgtgtggggggtgggggggggtgacagagcttcaattcttgaggttcttgaaaagtaat-acagaagactgtttaatgaagtgttaattatgatgatgtttactgcattattagtattatacgtggcttagcaattaaacctttcag
||||||||||||||||| || ||||| ||||| |||||||| || || ||  |||| ||||||||||| || |||||||||||  ||||| | ||   |       || ||  |||   |     ||    |   |   |  |     | | ||  |||  |||        |||   | || | | | | ||                                                                             
TACTTTGTTGAGGCTGGGGCAATTGCTGTAAGACGTGTGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTGgtaggattttgttt-----ttttgtttttaatttaaattgcaatgttagcaagttgacagtaaaactg-aatatttgtcacaacggaatgttgattagatagggct-----------------------------------------------------------------------------

upper sequence: GRMZM2G039263_T02 (Zea mays), 5'ss of exon 9
lower sequence: AT3G20050.1 (Arabidopsis thaliana), 5'ss of exon 11
TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttacatgacaaaattgtgcgtttgcgtgtgtgtgtggggggtgggggggggtgacagagcttcaattcttgaggttcttgaaaagtaatacagaagactgtttaatgaagtgttaattatgatgatgtttactgcattattagtattatacgtggcttagcaattaaacctttcag
|||||||| ||||| || || ||||| || |||||||||||||| |||||  |||| ||||||||||| || || || || ||| |||||  ||| |    | |   | |     | |   |||   ||                   |     |  || ||| |  || | |                                                                                                
TACTTTGTAGAGGCAGGAGCTATTGCTGTTAGGCGTGTGCGCAAAGAAGACATGCGTCATGTTGCCAAGGCGACAGGAGCGACTCTGgta--cttcctgcgctaggctttttcaatacccatgt---tgtcaaactaaaatttcaactaatatatttatccttta--ttttag------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G039263_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv15s0021g02230.t01 (Vitis vinifera), 5'ss of exon 11
TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttacatgacaaaattgtgcgtttgcgtgtgtgtgtggggggtgggggggggtgacagagcttcaattcttgaggttcttgaaaagtaatacagaagactgtttaatgaagtgttaattatgatgatgtttactgcattattagtattatacgtggcttagcaattaaacctttcag
|||||||| |||||||| || ||||| || |||||||| || || || ||  |||| ||||||||||| || |||||||||||||||||||| ||      |  || | ||| |     |   | |         ||| | || ||    |   |    |||||   ||    || |  ||| |   |   | |||  |                                                                      
TACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATGgtatgttt------cttaactctgcttcccaattgatatc-----accgggtgaggttgttttaatat--gctcttggaatttacaaataagaatgctttaatgtttttgttc---------------------------------------------------------------------

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|32944569|gb|CF049388.1|CF049388
EST:     TGCGCAAGGAAGATCTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|31406088|gb|CD484820.1|CD484820
EST:     TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|211163739|gb|FL337964.1|FL337964
EST:     TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|211469892|gb|FL096481.1|FL096481
EST:     TGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|32929201|gb|CF034013.1|CF034013
EST:     TGCGCAAGGAAGATCTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTTTTTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|32928649|gb|CF033461.1|CF033461
EST:     TGCGCAAGGAAGATCTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|22935598|gb|BU571873.1|BU571873
EST:     TGCGCAAGGAAGATCTGCGACATGTTGCCAAAGCCACTGG-GCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|21389952|gb|BQ528001.1|BQ528001
EST:     TGCGCAAGGAAGATCTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|32806379|gb|CD958613.1|CD958613
EST:     CGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: CGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|33094774|gb|CF054768.1|CF054768
EST:     TGCGCAAGGAAGATCTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|32929620|gb|CF034432.1|CF034432
EST:     TGCGCAAGGAAGATCTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|32806779|gb|CD959013.1|CD959013
EST:     TGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|32928302|gb|CF033114.1|CF033114
EST:     TGCGCAAGGAAGATCTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|32938970|gb|CF043789.1|CF043789
EST:     TGCGCAAGGAAGATCTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|24934261|gb|CA452479.1|CA452479
EST:     TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|32808822|gb|CD961056.1|CD961056
EST:     CGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: CGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|32938969|gb|CF043788.1|CF043788
EST:     GGAAGATCTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: GGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|211469893|gb|FL096482.1|FL096482
EST:     TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|67021395|gb|CO450144.1|CO450144
EST:     TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|7238110|gb|AW573332.1|AW573332
EST:     TGCGCAAGGAAGATCTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|60343155|gb|DN210128.1|DN210128
EST:     TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|31440979|gb|CD510410.1|CD510410
EST:     TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|32939416|gb|CF044235.1|CF044235
EST:     TGCGCAAGGAAGATCTGCGACATGTTACCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|61119168|gb|DN560129.1|DN560129
EST:     TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|67018449|gb|CO447198.1|CO447198
EST:     TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
EST: gi|87157304|gb|DY402093.1|DY402093
EST:     TGCGCAAGGAAGATCTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG                         GTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttac ... aacctttcagGTGTCTACTTTTGCGGACATGGAAGGTGAAGAAACATTCGATTCATCATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATGgtatgcttacatgacaaaattgtgcgtttgcgtgtgtgtgtggggggtgggggggggtgacagagcttcaattcttgaggttcttgaaaagtaatacagaagactgtttaatgaagtgttaattatgatgatgtttactgcattattagtattatacgtggcttagcaattaaacctttcag

- - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - GGAAGA