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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatttttttctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaaatattttgagaaatcatgacttatcggctcaccgacgtgtctaataccttgtcttgttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG

Basic information

species Zea mays
transcript GRMZM5G877597_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G877597_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g50880.1 (Oryza sativa), 3'ss of exon 2
gtacatttttttctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaaatattttgagaaatcatgacttatcggctcaccgacgtgtctaataccttgtcttgttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
                   |    |  || |  | ||   || | ||  |||    | ||    |||| |  || || |||||||||||| | |  |    | ||    | |           || || |  | ||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||| |||||||| |||||||||||||| ||||| |||||||||||||
------------------gttcattttctccccacaa---ttctcatttagaatagtattatctgtgaggataacatgttgagaaatcataagtcttt---taacttttggg-----------gttttatggacagATAGATGCAGCTATTAACTCAGGAAATTCAGGTGGCCCAGCTTTTAATGACAGGGGCAAATGTGTTGGTATAGCTTTTCAATCTCTCAAACATGAAGATG

upper sequence: GRMZM5G877597_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G16820.1 (Glycine max), 3'ss of exon 2
gtacatttttttctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaaatattttgagaaatcatgacttatcggctcaccgacgtgtctaataccttgtcttgttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
                   ||  |||  ||| ||   |||  |||  |        | || || ||    |       |||   | | || |  | |      |  || | ||||    | | |  |  ||   |||||||||| || || ||||| || ||||| ||||| || ||||| ||||||| ||||||||| || || || || || ||||||||||||||||||||||
------------------gtaacataggttctaagctatcccttttcac-------ttttccatgta---tgccccgcttgtccatttat-atatgttaa---attgaagcgtct----cttcgaatcctttgcagATAGATGCTGCGATAAATTCTGGGAATTCTGGTGGACCTGCTTTCAATGATAAGGGAAAATGCGTTGGGATTGCATTCCAGTCTCTTAAACATGAAGATG

upper sequence: GRMZM5G877597_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacatttttttctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaaatattttgagaaatcatgacttatcggctcaccgacgtgtctaataccttgtcttgttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
                                              |      | |  ||  |  |||  |   |  ||     | |   || |||  ||| |    |    | |  |   || |  | ||   |||| ||||||||||||||||| || ||||| ||||| || || ||||||||||  ||||||||||| ||||| || ||||||||| | ||||| |||||||
---------------------------------------------gttggacaacacatttgacatgatatttttccttatctgactagggagttaagggcacttataaaaatgttttctgtttttgtcttttcagATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGATAAAGGAAAATGTGTTGGTATTGCATTTCAGTCTTTGAAACACGAAGATG

upper sequence: GRMZM5G877597_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv14s0066g01660.t01 (Vitis vinifera), 3'ss of exon 2
gtacatttttttctgaaattatgataacttcaaataaatctttt-tataaagatagatgtt-gcaagtgaagtaaatattttgagaaatcatgacttatcggctcaccgacgtgtctaataccttgtcttgttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
                            |||| ||   | ||   |||||| | |    || ||   |  |  |   |     | |||| ||| ||||     ||      ||   | ||   |||  ||      |||||||||| || || || || |||||||| ||||| || ||  |||||||||  || |||||||| ||||| || |||||||| ||||||||||||||||
--------------------------gtttcatatgtttgttacatataaacacactcctttgcctatctaacaggaa-----aaaaattatgtcttaaacattctt----gttgttcatgagttgctttt---gcagATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGATAAAGGCAAATGTGTGGGTATCGCATTTCAGTCCCTTAAACATGAAGATG

upper sequence: GRMZM5G877597_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g07900.t01 (Vitis vinifera), 3'ss of exon 2
gtacatttttttctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaaatattttgagaaatcatgacttatcggctcaccgacgtgtctaataccttgtcttgttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
                                           | ||   |  | || |  |   |        || ||   |    | ||      |   |  | || || ||  || | |  |  | |||  |||||||||| ||||| || || |||||||| ||||| || || || ||||| | ||| || ||||| || || || |||||||||||||||||||||||||
------------------------------------------gtcatggggtcacatttctcctttttctcttttagttattgttggcttgttgatccatttttctgatgtctcctattcttgatggtttta-cagATAGATGCTGCTATAAACTCTGGAAATTCTGGTGGGCCTGCCTTCAATGAGAAGGGCAATTGTGTGGGCATTGCATTTCAGTCTCTTAAACATGAAGATG

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|71431610|gb|DR812660.1|DR812660
EST:     TAGAAATGCTTTTATATGTTCATGGTTCTATAGAACTTCTAGGATTGCAG                         ATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGAT
genomic: TAGAAATGCTTTTATATGTTCATGGTTCTATAGAACTTCTAGGATTGCAGgtacattttt ... ttgttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGAT
EST: gi|94472958|gb|EB701916.1|EB701916
EST:     GTTCATGGTTCTATAGAACTTCTAGGATGGCAG                         ATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTCTTAATGAT
genomic: GTTCATGGTTCTATAGAACTTCTAGGATTGCAGgtacattttt ... ttgttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGAT
EST: gi|71311298|gb|DR791964.1|DR791964
EST:     TAGAAATGCTTTTATATGTTCATGGTTCTATAGAACTTCTAGGATTGCAG                         ATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGAT
genomic: TAGAAATGCTTTTATATGTTCATGGTTCTATAGAACTTCTAGGATTGCAGgtacattttt ... ttgttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGAT
EST: gi|74246237|gb|DT654151.1|DT654151
EST:     TAGAAATGCTTTTATATGTTCATGGTTCTATAGAACTTCTAGGATTGCAG                         ATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGAT
genomic: TAGAAATGCTTTTATATGTTCATGGTTCTATAGAACTTCTAGGATTGCAGgtacattttt ... ttgttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaatcatgacttatcggctcaccgacgtgtctaataccttgtcttgttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
                              gtctaat  putative branch site (score: 3)
                                      ccttgtctt  CT-rich tract
                                             ttgttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatttttttctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaaatattttgagaaatcatgacttatcggctcaccgacgtgtctaataccttgtcttgttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG