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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattgtcatgttctcggagactcaaaaacaccaattttgtttttccacgttgtgcag

Basic information

species Selaginella moellendorffii
transcript EFJ38519
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ38519 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 11
CGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgta--ttgtcatgttctcggagactcaaaaacaccaattttgtttttccac---gttgtgcag------------------------------------
 ||  | ||    || ||  |||| || ||||| || || || ||||||||||| ||||||||||| || ||||||||  |||||||||| ||| | ||||||  |||  | || || |     |    ||  | ||  |  |  |   |    ||| |                                        
AGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAGgtaacttgatacgtactagtcctgtgttgaatccaaagatcatcctctgattgggttataagacatacatagtcactgtcatgtacatatccattttag

upper sequence: EFJ38519 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: LOC_Os02g31040.1 (Oryza sativa), 5'ss of exon 10
CGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattgtca--tgttctcggagac-tcaaaaacaccaattttgtttttccacgttgtgcag----------------------------
 ||  | ||    || ||  |||| || ||||| || || || ||||||||||| ||||| || ||| | ||||||||  |||||||||||||| | ||||||| | ||  |||| |     |  |  |   | | || | |  ||||   |  | ||  |                            
TGCGCTTCAAAACCAACCAATTGTTAATGCTGTCATTGATGGTGATGACATCATCTACAGGGAGTACATTGACATCAGTGTTGCTGTTGGAACTTCCAAGgtatcgccacctgtttttctttatgttgactgccctaactattattttatgcaatctgttgtaatgatgtgacatgtcatttgttttag

upper sequence: EFJ38519 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GRMZM2G079538_T01 (Zea mays), 5'ss of exon 10
CGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattgtcatgtt--ctcggagactcaaaaacaccaattttgtttttccacgttgtgcag-------------------------------------------------------------------------------
 ||  | ||    |||||  |||| || ||||| || || || ||||||||||| |||||||||||||| ||||||||  |||||||||| ||| | ||||||   |  || |  || |           ||     | |  | ||||       |  |                                                                                
TGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatattgcttacttgctactctggtgactgatgtatcatctttcttgtacctagaactagaaaagccaaaatggcctatagtttggggtggtcagagtatttactatgtatatcactaattgtaatatttttcag

upper sequence: EFJ38519 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GRMZM5G807639_T03 (Zea mays), 5'ss of exon 11
CGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattgtcatgtt--ctcggagactcaaaaacac--caattttgtttttccacgttgtgcag-----------------------------------------
 ||  | ||    |||||  |||| || ||||| || || || ||||||||||| |||||||||||||| ||| ||||  |||||||||| ||| | |||||    |  || |  |||   ||| |||||| |   |||   ||  ||    ||||| |                                            
TGCACTTCAAAACCAGCCAATTGTTAATGCTGTCATTGATGGCGATGACATCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAGgtgccatattgcttactccctgacccaaaaagaatgcaaccatgggtt---gcgttgcgtgcccgttaaactagttcacatttgatcaagtttctagtgtagt

upper sequence: EFJ38519 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: AT5G55070.1 (Arabidopsis thaliana), 5'ss of exon 13
CGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattgtcatg----ttctcggagactcaaaaacacca--attttgtttttccacgttgtgcag---------------------------------
 ||  | |||   || || || ||||| || || ||||| |||||||| |||||||||||||||||||| || ||||| || |||||||| ||  | ||||| |  |   |    |  |  || | | |   | |  |  |||| |  |||  |  | ||   |                                 
TGCCCTCCAGCACCAACCTGTAGTAAATGCAGTTATCGATGGAGATGATATCATTTACAGAGACTACGTGGATATCAGTATCGCTGTTGGTACCTCTAAGgtttgtttccgcaattcttttgacattgagtgataatatcatttgggcttttgagatagttttgattgattcctcttctctgtgtattgtatcccag

upper sequence: EFJ38519 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: Vv19s0090g00750.t01 (Vitis vinifera), 5'ss of exon 8
CGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattgtcatgttc--tcggagactcaaaaacaccaa---ttttgtttttccacgttgtgcag----------------------------------------
 |   | |||   |||||  |  | || || || || || || ||||| ||||| || ||||| ||  |  | |||||||| |||||||||||||||||||| ||||||    |   | | | ||||  | |||  |     ||| |  | || || |  | |                                        
TGGGCTTCAGAATCAGCCTATCATCAATGCGGTCATTGATGGGGATGATATCATATATAGAGATTATATAAATATCAGCATAGCTGTTGGAACTCCAAAGgt-ttgtcagcgccgacctgtggctcatta-cactgaggtccttgctcatgcatgtggccctgagctttttttttgtcccctcctaatcctatttcccaacag

upper sequence: EFJ38519 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: PP1S2_220V6.1 (Physcomitrella patens), 5'ss of exon 7
CGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattg-----tcat--------gttctcggagactca-aaaacaccaa---ttttgtttttccacgt-tgtgcag---------------------------------------------------------------------------------------------------
 ||  |  ||      || |  ||||| || || ||||| |||||||| ||||| |||||||||||| | ||||||||||||||||||||||||  |||||| |       ||||        |||     | | |   |||||||||    || || || |   |   ||||                                                                                                      
TGCACTTAAGCAATTTCCTGCAGTAAATGCGGTAATCGATGGAGATGATATCATATACAGAGACTACATTGACATCAGCATTGCTGTTGGAACTAAAAAGgtttcagaacttcataaacaatagtttatacatatttttaaaacaccagcacttatgcttatgagcacctgtgggaattttggttttgttctcagaccgttcataactttccttattacagcacgtgatggactgaactaggatatttaatgatgcgtgcatcttcttcgttcag

upper sequence: EFJ38519 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: PP1S154_6V6.2 (Physcomitrella patens), 5'ss of exon 11
CGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattgtcatgttctcggagactcaaaaacaccaatt-ttgtttttccacgttgtgcag----------------------------------------------
 ||  |  ||      || | ||| || ||||| || || |||||||||||||| ||| |||| ||||| |||||||||||||||||||| ||  | || |||   |||   |      |  |||||        |  ||||     |||||                                                     
TGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGATGGAGATGACATCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAAgtaagttcaaactt-----ggttcaaatgtgtgtttcattgtcaacacacgtaaattgatgatcctaacaagcttctatgttactaagagtatcttttcatgtag

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|169056867|gb|FE466458.1|FE466458
EST:     TCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAG                         GGCCTGGTGGTTCCCGTGGTCAGGGGTTGTGAGAAGATGAACTTTGCAGAT
genomic: TCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattgtcat ... cgttgtgcagGGCCTGGTGGTGCCCGTGGTCAGGGGTTGTGAGAAGATGAACTTTGCAGAT
EST: gi|169105894|gb|FE503552.1|FE503552
EST:     TCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAG                         GGCCTGGTGGTTCCCGTGGTCAGGGGTTGTGAGAAGATGAACTTTGCAGAT
genomic: TCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattgtcat ... cgttgtgcagGGCCTGGTGGTGCCCGTGGTCAGGGGTTGTGAGAAGATGAACTTTGCAGAT
EST: gi|169081309|gb|FE489793.1|FE489793
EST:     TCATTTACAGAGATTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAG                         GGCCTGGTGGTTCCCGTGGTCAGGGGTTGTGAGAAGATGAACTTTGCAGAT
genomic: TCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattgtcat ... cgttgtgcagGGCCTGGTGGTGCCCGTGGTCAGGGGTTGTGAGAAGATGAACTTTGCAGAT
EST: gi|169031261|gb|FE441129.1|FE441129
EST:     TCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAG                         GGCCTGGTGGTGCCCGTGGTCAGGGGTTGTGAGAAGATGAACTTTGCAGAT
genomic: TCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattgtcat ... cgttgtgcagGGCCTGGTGGTGCCCGTGGTCAGGGGTTGTGAGAAGATGAACTTTGCAGAT
EST: gi|169070985|gb|FE478923.1|FE478923
EST:     TCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAG                         GGCCTGGTGGTTCCCGTGGTCAGGGGTTGTGAGAAGATGAACTTTGCAGAT
genomic: TCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattgtcat ... cgttgtgcagGGCCTGGTGGTGCCCGTGGTCAGGGGTTGTGAGAAGATGAACTTTGCAGAT
EST: gi|169070986|gb|FE478924.1|FE478924
EST:     TCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAG                         GGCCTGGTGGTTCCCGTGGTCAGGGGTTGTGAGAAGATGAACTTTGCAGAT
genomic: TCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattgtcat ... cgttgtgcagGGCCTGGTGGTGCCCGTGGTCAGGGGTTGTGAGAAGATGAACTTTGCAGAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 32

CGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattgtcat ... cgttgtgcagGGCCTGGTGGTGCCCGTGGTCAGGGGTTGTGAGAAGATGAACTTTGCAGATGTGGAGAAAACAATTGCCAAGCTCGCGAAGAAAGCAAACGACGGAACCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattgtcatgttctcggagactcaaaaacaccaattttgtttttccacgttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT