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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCAAGGATATTGATGATGCACTCCACTGTCACGTCCTTCCAAATGGAAACTTTGAAGTTGGAGTTCgtatcctttgtttgaggacattcattttactgatgatgcatgtgtccataggctatatgtattcaaattagcacttgtgggttactacagttggatggat...

Basic information

species Glycine max
transcript GLYMA04G39980.1
intron # 11
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39980.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os03g03710.1 (Oryza sativa), 5'ss of exon 11
GCTGCAAGGATATTGATGATGCACTCCACTGTCACGTC-CTTCCAAATGGAAACTTTGAAGTTGGAGTTCgtatcctttgtttgaggacattcattttactgatgatgcatgtgtccataggctatatgtattcaaattagcacttgtgggttactacagttggatggat----
| || | ||||||||||||||| || || || |||| | || |||||||| || |||||||||||||||||||||||||  |     |  ||   ||| | ||  || ||    |    | |||| || || ||  |   ||||||     ||   |  |||       |    
GTTGTAGGGATATTGATGATGCGCTACATTG-CACGCCACTCCCAAATGGGAATTTTGAAGTTGGAGTTCgtatcctttactgatttattttttatttgcaga--attcaaa-attggaatgcta-atttaatcttaagggcacttacactttgagatggttctcaacctgtcc

upper sequence: GLYMA04G39980.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G031859_T03 (Zea mays), 5'ss of exon 11
GCTGCAAGGATATTGATGATGCACTCCACTGTCACGTCCTTCCAAATGGAAACTTTGAAGTTGGAGTTCgtatcctt---tgtttgaggacattcattttactgatgatgcatgtgtccataggctatatgtattcaaattagcacttgtgggttactacagttggatggat
| ||    || |||||||||||||| || ||     | ||||||||||| |||||||||||||||||||||||||||      ||   |      ||| | ||| | | |      |  | | || | || |  ||   ||  |  |  |||    ||     |  ||   |
GTTGTCGAGACATTGATGATGCACTACATTGCACACTACTTCCAAATGGGAACTTTGAAGTTGGAGTTCgtatccttgaacaatttctgctgcaaattctcctgttca-gttcaaatttacaagcaa-attt-ctcgtgttttctttcttggtgacctttgagttaatatct

upper sequence: GLYMA04G39980.1 (Glycine max), 5'ss of exon 11
lower sequence: AT2G17510.1 (Arabidopsis thaliana), 5'ss of exon 11
GCTGCAAGGATATTGATGATGCACTCCACTGTCACGTC-CTTCCAAATGGAAACTTTGAAGTTGGAGTTCgtatccttt-gtttgaggacattcattttactgatgatgcatgtgtccataggctatatgtattcaaattagcacttgtgggttactacagttggatggat---
| ||||||||||||||||||||| | |||||| || || |||||||| || ||||||||| ||||||| ||||||||   ||     ||   ||||     |||   ||| |   || ||     | ||||    |    |  | ||     | | |   || ||||  ||   
GTTGCAAGGATATTGATGATGCATTGCACTGT-ACATCGCTTCCAAACGGGAACTTTGAACTTGGAGTCCgtatcctagagtcctcagattctcataaatatgactgtgctt---tcaatttaggacatgtcaatagtcaatgagttaaaaatcagt-ttgtgggatatattta

upper sequence: GLYMA04G39980.1 (Glycine max), 5'ss of exon 11
lower sequence: AT2G17510.2 (Arabidopsis thaliana), 5'ss of exon 12
GCTGCAAGGATATTGATGATGCACTCCACTGTCACGTC-CTTCCAAATGGAAACTTTGAAGTTGGAGTTCgtatccttt-gtttgaggacattcattttactgatgatgc------------atgtgtccataggctatatgtattcaaattagcacttgtgggttactacagttggatggat--------------------------
     |||||||||||||||||| | |||||| || || |||||||| || ||||||||| ||||||| ||||||||   ||     ||   ||||     |||   |||            |  |||| |||| | ||  || |  |||| ||   ||||||| ||          | | ||                          
-----AAGGATATTGATGATGCATTGCACTGT-ACATCGCTTCCAAACGGGAACTTTGAACTTGGAGTCCGTATCCTAGAGTCCTCAGATTCTCATAAATATGACTgtgctttcaatttaggacatgtcaatagtcaatgagt-taaaaatcagt--ttgtgggatatatttaaccaaagcattgaaatggctcatattaccttttagc

upper sequence: GLYMA04G39980.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv07s0031g02190.t01 (Vitis vinifera), 5'ss of exon 11
GCTGCAAGGATATTGATGATGCACTCCACTGTCACGTCCTTCCAAATGGAAACTTTGAAGTTGGAGTTCgtatcctttg-tttgaggacattcatttt-actgatgatgcatgtgtccataggctatatgtattcaaattagcacttgtgggttactacagttggatggat-
| ||||| ||||| || |||||||| || |||      ||||| |||||||| |||||||| ||||||||||||||      ||   ||   ||||||   |||  ||     | |   |    | |   | ||  | | |    || |  |  | | ||  || ||  || 
GATGCAAAGATATAGACGATGCACTGCATTGTACAACTCTTCCGAATGGAAATTTTGAAGTGGGAGTTCgtatcctccaacctgttaactggcatttttgttgaaaattttactataattgaagttttaatgtt-gactcatggtttttaaggaagttca--tgaattaatt

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCAAGGATATTGATGATGCACTCCACTGTCACGTCCTTCCAAATGGAAACTTTGAAGTTGGAGTTCgtatcctttgtttgaggacattcattttactgatgatgcatgtgtccataggctatatgtattcaaattagcacttgtgggttactacagttggatggat

- - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtggg