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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGACCAATTCAAACAGGAGTTCTGCAAGTTATATGGCATGACTTTAGAGCCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACCgtatcctttttttaaaatgcttgcatacatataattgaaacaccccctccaccctttccaataaatcttaaaaccacttggactttccttatccttttga...

Basic information

species Glycine max
transcript GLYMA10G43910.1
intron # 5
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G43910.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os05g06760.1 (Oryza sativa), 5'ss of exon 5
TGGACCAATTCAAACAGGAGTTCTGCAAGTTATATGGCATGACTTTAGAGCCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACCgtatcctttttttaaaatgcttgcatacatataattgaaacaccccctccaccctttccaataaatc-ttaaaaccacttggactttccttatccttttga----------
||||||| || || ||||| |||||||| || ||||||||||| || ||||| ||||| || |||||| ||||||| || ||  | ||||| ||||||||||||||||    | |        |||     || ||    |  | |||  ||| |||   ||||| |  ||  |     |    ||  ||| |    ||||          
TGGACCAGTTTAAGCAGGAATTCTGCAAATTGTATGGCATGACATTGGAGCCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcgcctgat-------cat-----tattttccgcttcacctttaccatttaatataaaccactagcattgtattacattctcttttttccttgaccatcattag

upper sequence: GLYMA10G43910.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G177026_T02 (Zea mays), 5'ss of exon 5
TGGACCAATTCAAACAGGAGTTCTGCAAGTTATATGGCATGACTTTAGAGCCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACCgtatcctt-----tttttaaaatgcttgcatacata-----taattgaaacaccccctccaccctttccaataaatcttaaaaccacttggactttccttatccttttga------
| |||   ||||| || || || ||||||||||||||||||||  |||||||  |||| || || ||||||||||| |||||  | ||||||||||| |||||||||      | ||| |  | |||   |  ||      | ||||  | |   |      |   |   ||   | |||      | || | | |||||  || |||        
TTGACATTTTCAAGCAAGATTTTTGCAAGTTATATGGCATGACACTAGAGCCGCTGCTGAACATATATCTGCAAGCAGGCCTGACAGCTCTCAAGACCCCgtatcctcgcatgtgtttcacttacttttgtctatggtcttttattgctaaaatacagtttgctagtattatttttgttatggtatcctgtattgtccttgaccatttatttaaag

upper sequence: GLYMA10G43910.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv13s0067g03560.t01 (Vitis vinifera), 5'ss of exon 5
TGGACCAATTCAAACAGGAGTTCTGCAAGTTATATGGCATGACTTTAGAGCCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACCgtatcctttttttaaaatgcttgcatacatataattgaaacaccccctccaccctttccaataaatcttaaaaccacttggactttccttatccttttga---
||||||| ||||||||||| ||||| | |||||||||||||||| | ||||| ||||| ||||| ||||||||||| ||| | |||||||| || || |||||||||  ||   |  | ||   |||    |  |||     | |   | |     |    ||| |   |  ||     || | |   || |   ||||    
TGGACCAGTTCAAACAGGAATTCTGTAGGTTATATGGCATGACTCTTGAGCCTTTGCTGAATATATATCTGCAAGCAGGCTTGTCTGCTCTAAAAACTCCgtatcctcattc--atttactaatatatcgttgcttgcc-ttcacatactagttagtggcttaagtgccattacagtcaggtcatatattttgaatttgcaaa

upper sequence: GLYMA10G43910.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S101_201V6.1 (Physcomitrella patens), 5'ss of exon 7
TGGACCAATTCAAACAGGAGTTCTGCAAGTTATATGGCATGACTTTAGAGCCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACCgtatcctttttttaaaatgcttgcatacatataattgaaacaccccctccaccctttccaataaatcttaaaaccactt---ggactttccttatccttttga
   | || ||||| |||||||| || ||||||||||||||||||   |||||| ||||||||||| |||| || ||||| ||||| || ||||| || ||||||         |  || |    ||   ||   || |||       |  |     |||   | ||||         |    ||| |||  |||  |  ||  
CTCAACAGTTCAAGCAGGAGTTTTGTAAGTTATATGGCATGACTCATGAGCCCCTGCTCAATATCCATCTCCAGGCTGGACTTTCGGCGCTCAAAACGCCgtatttaacacggaccataccctaattattagtctttaaagcttttgttaaaaacatcct-cagatctcgggtttgatcttaggattttgtttaatcgatt--

upper sequence: GLYMA10G43910.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S285_18V6.1 (Physcomitrella patens), 5'ss of exon 7
TGGACCAATTCAAACAGGAGTTCTGCAAGTTATATGGCATGACTTTAGAGCCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACCgtatcctttttttaaaatgcttgcatacatataattgaaacaccccctccacccttt-ccaataaatcttaaaaccacttggactttccttatccttttga
   |  | || || |||||||| | |||||| ||||||||||||   || ||  ||||||||||  |||| || ||||| ||||||||||||||||| ||||||  |   |  |  ||   |  ||   |    || |         |  |    || |  | |  |||       | |  |   ||  | |    | |  
CTCAAGAGTTTAAGCAGGAGTTTTACAAGTTGTATGGCATGACTCATGAACCTCTGCTCAATATTCATCTCCAGGCTGGGCTTTCTGCTCTCAAGACTCCgtattttacctcaaccatatctcaattggttcttttcatggtttttttaaaagagttgctcagacttctgggtggaattcaggagtttgtgagttgtcta-

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|192319196|gb|FK006924.1|FK006924
EST:     CCTTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACC                         ATATTGTTATGAGGATGATTGCACAAAAGAGGACCCCTTATCACAG-AGGC
genomic: CCTT-GCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACCgtatcctttt ... cttgataaagATATTGTTATGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGC
EST: gi|192319197|gb|FK006925.1|FK006925
EST:     CCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACC                         ATATTGTTATGAGGATGATTGCACAAAAGAGGA
genomic: CCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACCgtatcctttt ... cttgataaagATATTGTTATGAGGATGATTGCACAAAAGAGGA
EST: gi|254334264|gb|GR849182.1|GR849182
EST:     CCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACC                         ATATTGTTATGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGC
genomic: CCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACCgtatcctttt ... cttgataaagATATTGTTATGAGGATGATTGCACAAAAGAGGACCCCTTATCACAGGAGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGACCAATTCAAACAGGAGTTCTGCAAGTTATATGGCATGACTTTAGAGCCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACCgtatcctttttttaaaatgcttgcatacatataattgaaacaccccctccaccctttccaataaatcttaaaaccacttggactttccttatccttttga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaccct