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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcacttacctctattgctaatctggctgcatgaaacggtgtaaaaaacattcctttggataatagttttaattgtcgctttgtgatcaaaccttgcagGTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA

Basic information

species Zea mays
transcript GRMZM2G083344_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083344_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g15160.1 (Oryza sativa), 3'ss of exon 2
gtatgttcacttacct-----ctattgctaatctg--gctgcatgaaacggtgtaaaaaacattcctttggataatagttt--taattgtcgctttgtgatcaaaccttgcagGTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA
||||| | ||| ||||     |  ||   ||| |     |||| |  |  |     | ||  | |      ||  | ||||    |||| |  ||    ||   |  ||| |||||||||||||| || |||||||||||||| |||||||||||||||||||||||||||||||||||
gtatgcttactcacctgagcgcactttagaatttacaattgcaggtgagcgaactgagaagttgctgcctaatg-tggtttagctattgccaattcacaatatgattttgtagGTATTTTCTGAACGTGATATTTAACATCCTTAACAAGAAGATCTTCGACTACTTCCCCTATCCATA

upper sequence: GRMZM2G083344_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G32190.1 (Glycine max), 3'ss of exon 2
gtatgttcacttacctctattgctaatctggctgcatgaaacggtgtaaaaaacattcctttggataatagttttaattgtcgctttgtgatcaaaccttgcagGTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA
   |||    |  ||   |     |    | ||  || |   |  |     | |   ||    | | | | ||   ||| |  | || |  |       |||||||| ||  |||| || || || |||||||||||||||||||||| | | |||||||||||||||||
---tgtgttgtgtccatgaagaacagaaagactttattacgtgtggctgtgatcgccccgagtgttga-aattaccattttgtccttattcttttctgatgcagGTACTTCTTGAACGTGATTTTCAACATCCTCAACAAGAAGATCTACAATTACTTCCCCTATCCATA

upper sequence: GRMZM2G083344_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G24360.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------------gtatgttcacttacctctattgctaatctggctgcatgaaacggtgtaaaaaacattcctttggataatagtttt--aattgtcgctttgtgatcaaacctt------gcagGTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA
                                                                              || |||| || | ||  |    | | |    |    || |   |  |        |    | | |   ||| ||  ||||   | |||||  |    | ||      ||||||| ||  |||| || || || |||||||| ||||||||||||| | | |||||||||||||||||
gtacgtcacgtgactctgttcttattacacgcaaaaaacaacctatgattgtgtcgtgtgctcctgttctgtgtctcttacgttccctaagcttaaacttttaaccacttaacagatagacttcatgtgtggctgtgatcgttccgagtgttgaaattacggttttgtccttttccttttctgatgcagGTACTTCTTGAACGTGATTTTCAACATCCTTAACAAGAAGATCTACAATTACTTCCCCTATCCATA

upper sequence: GRMZM2G083344_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 3'ss of exon 2
-------------gtatgttcacttacctctattgctaatct----ggctgcatgaaacggtgtaaaaaacattcctttggataat----agttttaattgtcgctttgtgatcaaaccttg-cagGTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA
             || |    ||| ||  |   | | | |||      | |   ||||  ||  ||| || ||     |  | |||      || |   ||||  |     ||   || ||  ||||||||| || || || ||||| |||||||||||||||||||||| | |||||||||| ||||| ||
gtaggtcatcaccgt-taccaactaacaacatctacaattctcttcaacggtcagaaagagtcaaaataaaatggtgattcaaaatccctgtttctgggtgtctttaccaaattgtactttttcagGTATTTCCTCAACGTTATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCATATCCTTA

upper sequence: GRMZM2G083344_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ15759 (Selaginella moellendorffii), 3'ss of exon 2
gtatgttcacttacctctattgctaatctggctgcatgaaacggtgtaaaaaacattcctttggataatagttttaattgtcgctttgtgatcaaaccttgcagGTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA
                          |  |  ||| |         |    |   | | |||    | |  | |   |||    |  |   |     |||||||||||||||| ||||| || || |||||||| ||||||||||||| | | || || || ||||||||
-------------------------gtaggcatgctttttcttccttccttattttgcttttc--cacttttctctcttgcaaatgagatcttccttcttgcagGTATTTTCTCAATGTGATCTTCAACATCCTTAACAAGAAGATCTACAATTATTTTCCTTATCCATA

upper sequence: GRMZM2G083344_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ38162 (Selaginella moellendorffii), 3'ss of exon 1
gtatgttcacttacctctattgctaatctggctgcatgaaacggtgtaaaaaacattcctttggataatagttttaattgtcgctttgtgatcaaaccttgcagGTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA
||| |    |||     |  | |   | | |||        |  |||        |  || | |  |||       ||  ||  |            |||||||||||||||| ||||| || || |||||||| ||||||||||||| | | || || || ||||||||
gtaggcatgctttttcttccttccttttttgcttttc----cactgt--------tctctcttgcaaatga----gatcttcctt------------cttgcagGTATTTTCTCAATGTGATCTTCAACATCCTTAACAAGAAGATCTACAATTATTTTCCTTATCCATA

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|78105001|gb|DV523419.1|DV523419
EST:     TTTGCAGAGAGATACCCAGCTCTTGTCACAGGTTTCTTCTTCTTCTTGTG                         GTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTA
genomic: TTTGCAGAGAGATACCCAGCTCTTGTCACAGGTTTCTTCTTCTTCTTGTGgtatgttcac ... aaccttgcagGTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTA
EST: gi|50328060|gb|CO523186.1|CO523186
EST:     TTTGCAGAGAGATACCCAGCTCTTGTCACAGGTTTCTTCTTCTTCTTGTG                         GTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTA
genomic: TTTGCAGAGAGATACCCAGCTCTTGTCACAGGTTTCTTCTTCTTCTTGTGgtatgttcac ... aaccttgcagGTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTA
EST: gi|31909719|gb|CD651060.1|CD651060
EST:     TTTGCAGAGAGATACCCAGCTCTTGTCACAGGTTTCTTCTTCTTCTTGTG                         GTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTA
genomic: TTTGCAGAGAGATACCCAGCTCTTGTCACAGGTTTCTTCTTCTTCTTGTGgtatgttcac ... aaccttgcagGTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTA
EST: gi|61119701|gb|DN560662.1|DN560662
EST:     TTTGCAGAGAGATACCCAGCTCTTGTCACAGGTTTCTTCTTCTTCTTGTG                         GTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTA
genomic: TTTGCAGAGAGATACCCAGCTCTTGTCACAGGTTTCTTCTTCTTCTTGTGgtatgttcac ... aaccttgcagGTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTA
EST: gi|28931223|gb|CB334584.1|CB334584
EST:     TTTGCAGAGAGATACCCAGCTCTTGTCACAGGTTTCTTCTTCTTCTTGTG                         GTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTA
genomic: TTTGCAGAGAGATACCCAGCTCTTGTCACAGGTTTCTTCTTCTTCTTGTGgtatgttcac ... aaccttgcagGTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTA
EST: gi|94477389|gb|EB706347.1|EB706347
EST:     TTTGCAGAGAGATACCCAGCTCTTGTCACAGGTTTCTTCTTCTTCTTGTG                         GTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTA
genomic: TTTGCAGAGAGATACCCAGCTCTTGTCACAGGTTTCTTCTTCTTCTTGTGgtatgttcac ... aaccttgcagGTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTA
EST: gi|211525181|gb|FL202007.1|FL202007
EST:     TTTGCAGAGAGATACCCAGCTCTTGTCACAGGTTTCTTCTTCTTCTTGTG                         GTATYTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTA
genomic: TTTGCAGAGAGATACCCAGCTCTTGTCACAGGTTTCTTCTTCTTCTTGTGgtatgttcac ... aaccttgcagGTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTA
EST: gi|28390338|gb|CB250166.1|CB250166
EST:     TTTGCAGAGAGATACCCAGCTCTTGTCACAGGTTTCTTCTTCTTCTTGTG                         GTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTA
genomic: TTTGCAGAGAGATACCCAGCTCTTGTCACAGGTTTCTTCTTCTTCTTGTGgtatgttcac ... aaccttgcagGTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaacattcctttggataatagttttaattgtcgctttgtgatcaaaccttgcagGTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA
                      ttttaat  putative branch site (score: 3)
               ataatagttttaattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcacttacctctattgctaatctggctgcatgaaacggtgtaaaaaacattcctttggataatagttttaattgtcgctttgtgatcaaaccttgcagGTATTTTCTGAATGTAATATTTAACATCCTCAACAAGAAGATCTTCGACTACTTCCCCTATCCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG