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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttggcgcattattttctgcaatcgacatcttttgttggttttcctataaaaacaaaggaatacctgtcttggacctgcagCCACATTCGCCTGACAACCGTGCTCCAGCAAGAGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATT

Basic information

species Zea mays
transcript GRMZM2G010044_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g03260.2 (Oryza sativa), 3'ss of exon 8
gtttgttggcgca-------ttattttctgcaatcgacatcttttgttggttttcctataaaaacaaaggaatacctgtcttggacctgcagCCACATTCGCCTGACAACCGTGCTCCAGCAAGAGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATT
|||||||     |       |||| || |||||||  ||||  ||  |  || | | | | |  |||||   |   | |  ||||||||||||||||||| |||||||||||||||| ||||||||| ||||||||||| ||||| ||||| |||||||| |||||||| ||||| ||||| || ||||| |
gtttgttcatatagttactgttatcttttgcaatct-catcaatt--tcattatacaaaagagtcaaagctgttattttggtggacctgcagCCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAGATTGACCGGGTCTATATCGGTTCTTGTACTGGAGGTAAAACTGAGGACT

upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 13
-------------------------------------------------gtttgttggcgcattattttctgcaatcgacatcttttgttggttttcctataaaaacaaaggaatacctgtcttggacc-tgcagCCACATTCGCCTGACAACCGTGCTCCAGCAAGAGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATT
                                                    ||||   | ||| | |  || ||   | ||  ||| |  ||||   |   || | || | |||   | |     ||| | ||||||||||| || || || ||||||   ||||||||||||||  ||||||| || ||| |||| || ||||| || ||||||||||| ||||| || ||||
gtacttttactttaacttaatcatatttttatcttcattttgccataaaaagtgttaa-gaattttgtgttgtaa--aagattctttttgagtttgattgctaatataatgcaatgtgtttgaaccaccatacagCCACATTCCCCCGATAATCGTGCTTTGGCAAGAGAATGCAACAATGTGAAAATTGACAGAGTATACATTGGATCCTGCACTGGTGGGAAGACTGAAGATT

upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 11
gtttgttggcg--cattattttctgcaatcgacatcttttgttggttttcctataaaaacaaaggaatacctgtcttggacctgcagCCACATTCGCCTGACAACCGTGCTCCAGCAAGAGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATT
||  |||  ||   |  | |||   || |       || ||    ||    |     |       |||  || | ||     | ||||| ||||| ||||||||||| |||| ||| |||||||||||||| ||||| || ||| |||| || || |||||||| |||||||| ||||| |||||||
gtgggtttacgattaccaatttaaacactgagttatttctgccacttcaggttacttattttgttaatgtctttttt-----ttcagCCTCATTCTCCTGACAACCGAGCTCTAGCTAGAGAATGCAAAGACGTGAAAATTGACAGAGTATACATCGGTTCTTGTACTGGTGGGAAGACAGAGGATT

upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 11
--------------gtttgttggcgcattattttctg-caatcgacatcttttgttggttttcctataaaaacaaaggaatacctgtcttggacctgcagCCACATTCGCCTGACAACCGTGCTCCAGCAAGAGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATT
                    || |  || |  | |    ||     ||  | ||  ||||||       || |||  | ||   |    ||   ||| |||| ||||| ||||| || ||||||   ||||||||||||||||||||||| || ||| | || |||||||| |||||||||||||| || || |||||||
aatgattattacgtaaaacatgtcaaataaactccaaataacttcaataatatgcaggtttttagtagtaatcaatagtatttgtcatatgtttctgtagCCTCATTCACCTGATAATCGTGCTTTGGCAAGAGAATGCAAAGATGTGAAAATTGACAGGGTATATATTGGATCTTGCACTGGTGGAAAAACTGAGGATT

upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 3'ss of exon 11
---------------------------------------------------------------gtttgttggcgcattattttctgcaatcgacatcttttgttggttttcctataaaaacaaaggaatacctgtcttggac--ctgcagCCACATTCGCCTGACAACCGTGCTCCAGCAAGAGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATT
                                                               || | |      |  ||    | |||  |        ||     ||  |  |  | |   |  |||| ||| | |      |||||||| ||||| ||||| ||  |||||   ||||||||||||||||| ||||| || ||| | || |||||||| ||||| |||||||| || || |||||||
gtgagtgattttatatagccttaagtgaaatcatcttaagtttttaaactgtagaccaaataggtatttcattttaaaatccatttcaagtgttgataagtggcaaattcacactttatattgaataatatctgccatatgtttctgcagCCTCATTCACCTGATAAATGTGCTTTGGCAAGAGAATGCAAAGACGTGAAAATTGACAGGGTGTATATTGGATCTTGTACTGGTGGAAAAACTGAGGATT

upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ16664 (Selaginella moellendorffii), 3'ss of exon 5
gtttgttggcgcattattttctgcaatcgacatcttttgttggttttcctataaaaacaaaggaatacctgtcttggacctgcagCCACATTCGCCTGACAACCGTGCTCCAGCAAGAGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATT
                                     |  ||   ||  | | |  ||        |      ||     ||||||| ||||| || || || || ||   ||| ||  | |||||||||||||||||||||||||| || ||||| || ||||| || || ||||| |||||  
------------------------------------gtactgtagttgttttgaccacgtgcagtcagtctctttttgtgtgcagCCGCATTCTCCGGATAAACGAGCATTAGCCAGGAACTGCAAAGATGTGAAGATCGACCGAGTGTACATTGGCTCCTGCACGGGAGGCAAGACGGAGGACG

upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ32611 (Selaginella moellendorffii), 3'ss of exon 9
gtttgttggcgcattattttctgcaatcgacatcttttgttggttttcctataaaaacaaag---gaatacctgtcttggacctgcagCCACATTCGCCTGACAACCGTGCTCCAGCAAGAGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATT
                               | || |  |||  ||  | |     ||   |   |  ||    | ||     ||||||| ||||| || || || || |    ||| || || |||||||||||||||||||||||||| || ||||| || ||||| || || ||||| ||||| |
-----------------------------gtaactgtaattgtcttgaccacttgcactcggtctgtttataatttttttgtgtgcagCCGCATTCTCCGGATAAACGAGTATTAGCCAGGGACTGCAAAGATGTGAAGATCGACCGAGTGTACATTGGCTCCTGCACGGGAGGCAAGACGGAGGACT

upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ16666 (Selaginella moellendorffii), 3'ss of exon 10
gtttgttggcgcattattttctgcaatcgacatcttttgttggttttcctataaaaacaaaggaatacctgtcttggacctgcagCCACATTCGCCTGACAACCGTGCTCCAGCAAGAGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATT
                 |  ||| ||| | | |      |||   ||  | |    | ||         | |  ||    ||||||| ||||| || || || || ||   ||| || || |||||||||||||||||||||||||| || ||||| || ||||| || || ||||| || || |
----------------gtaactgtaattgtcttgaccacttgcacttggtctgtttataat------ttttttgtgtgtgtgcagCCGCATTCTCCGGATAAACGAGCGTTAGCCAGGGACTGCAAAGATGTGAAGATCGACCGAGTGTACATTGGCTCCTGCACGGGAGGCAAGACGGAAGACT

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|91051661|gb|EB162079.1|EB162079
EST:     TTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGCCAAG                         CCACATTCGCCTGACAACCGTGCTCCAGCAAGAGAATGCAAAGATGTGAAG
genomic: TTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGCCAAGgtttgttggc ... ggacctgcagCCACATTCGCCTGACAACCGTGCTCCAGCAAGAGAATGCAAAGATGTGAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcttttgttggttttcctataaaaacaaaggaatacctgtcttggacctgcagCCACATTCGCCTGACAACCGTGCTCCAGCAAGAGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATT
             ttttcctataaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttggcgcattattttctgcaatcgacatcttttgttggttttcctataaaaacaaaggaatacctgtcttggacctgcagCCACATTCGCCTGACAACCGTGCTCCAGCAAGAGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT