Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAGGCCAGGCCCGAGGTGGGCGACTTCACCATCTACATGGGGCTGGACAAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaattcttctcttccctaaggaattttcctggtttggatcttcccag

Basic information

species Selaginella moellendorffii
transcript EFJ06382
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06382 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os05g13440.1 (Oryza sativa), 5'ss of exon 2
TCAAGGCCAGGCCCGAGGTGGGCGACTTCACCATCTACATGGGGCTGGACAAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgta---------tggccaattcttctcttccctaagg--aattttcctggtt--tggatcttcccag---------------------------------
||||||   |||||||||  ||||||| |||||||| |||||| || ||||||  |||||||||||||||||||||||| |||||||||||||| ||||||||           |||   | ||||||||    | |  |  ||   || ||  | |||   || ||                                 
TCAAGGTGCGGCCCGAGGCCGGCGACTACACCATCTTCATGGGTCTCGACAAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttcccgcccgccgccttttctcttctgctacgctagcttgattgattgattgattgcccgaggattggtaggaggtggtcacgtggtagtattga

upper sequence: EFJ06382 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os01g54670.1 (Oryza sativa), 5'ss of exon 1
TCAAGGCCAGGCCCGAGGTGGGCGACTTCACCATCTACATGGGGCTGGACAAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatg-------gccaattcttctcttccctaaggaattttcctggtttggatcttcccag---------------------------------------
 |||||| ||||| || |  ||||||| |||||||||||||||    |||||| ||||||||||||| ||||||||||| ||| ||||||||||  ||||||| |       |   ||||| | |   | ||  | | |  |  |   | |||| || |                                         
ACAAGGCGAGGCCGGACGCCGGCGACTACACCATCTACATGGGCGCCGACAAGAACGAGAACGAGGAGCTCATCAAGTACGGCCTCCCCGAGGACGTCTGgtacgtacgtacgtgcattctccgcacacgtactgtagtagctcgtcgtcgatcctcgcgtagcggcattgcacatttgcgtttgcgcttcgcgcgcgta

upper sequence: EFJ06382 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os01g54670.2 (Oryza sativa), 5'ss of exon 1
------------------------TCAAGGCCAGGCCCGAGGTGGGCGACTTCACCATCTACATGGGGCTGGACAAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatg-------gccaattcttctcttccctaaggaattttcctggtttggatcttcccag---------------
                         |||||| ||||| || |  ||||||| |||||||||||||||    |||||| ||||||||||||| ||||||||||| ||| ||||||||||  ||||||| |       |   ||||| | |   | ||  | | |  |  |   | |||| || |                 
GGTTGTTGCTAATGGTGTTCTACTACAAGGCGAGGCCGGACGCCGGCGACTACACCATCTACATGGGCGCCGACAAGAACGAGAACGAGGAGCTCATCAAgtacggcctccccgaggacgtctggtacgtacgtacgtgcattctccgcacacgtactgtagtagctcgtcgtcgatcctcgcgtagcggcattgcacat

upper sequence: EFJ06382 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G157332_T07 (Zea mays), 5'ss of exon 1
TCAAGGCCAGGCCCGAGGTGGGCGACTTCACCATCTACATGGGGCTGGACAAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaattcttctcttccctaaggaattttcctggtttggatcttcccag----------------------------------------------
|||||||  |||||||||  |||||||  ||||||| |||||| || |||||| |||||||||||||||||||||| || |||||||||||||| ||||||||    ||  |   ||    | |  ||    | | | ||    | |   |  |                                              
TCAAGGCGCGGCCCGAGGCCGGCGACTATACCATCTTCATGGGTCTTGACAAGTACGAGAACGAGGACCTCATCAAATACGGCTTCCCCGAGGACATCTGgtaacctcatcttcccttggtcgtgtgggtgctccttagtggttaccagtcgcgtgaaatcgtttgttctctgtgttttttgctggtctgtatacttgtc

upper sequence: EFJ06382 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G055898_T01 (Zea mays), 5'ss of exon 1
TCAAGGCCAGGCCCGAGGTGGGCGACTTCACCATCTACATGGGGCTGGACAAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaattcttctcttccctaaggaattttcctggtttggatcttcccag--------------------------------------------------
|||||||  | || || |  ||||||| |||||||||||||||    |||||| ||||||||||||| |||||||| || ||| ||||||||||  ||||||| |  |        || || |||     |  | |    ||   || || |                                                    
TCAAGGCGCGTCCGGACGCCGGCGACTACACCATCTACATGGGCGCCGACAAGAACGAGAACGAGGAGCTCATCAAATACGGCCTCCCCGAGGACGTCTGgtacgtacg---tacgtcgtcgctagctgctgctacct-cttacttcctcgcgacgacgacgacgacgacgacatgccgcatgcgattcagtggtgaattgaat

upper sequence: EFJ06382 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA04G08530.3 (Glycine max), 5'ss of exon 1
TCAAGGCCAGGCCCGAGGTGGGCGACTTCACCATCTACATGGGGCTGGACAAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaattcttctcttccctaaggaattttcctggtttggatcttcccag--------------------------------------------------------------------------
|||| ||  | ||||| |  ||||| |||||||||| |||||| || |||||| ||||||||||||| |||||||| || || || ||||| || ||||||||   | |||| | |  |  || |    ||||| ||  || |  ||  |  |                                                                           
TCAAAGCGCGCCCCGAAGCCGGCGATTTCACCATCTTCATGGGCCTTGACAAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaattttcccatctccaattttatttttcttcttcgtttccgcaaactctctgctcccgacacagattattcacatgacctatgtctggaactcgatttgatttatcagttgtttgtgtag

upper sequence: EFJ06382 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA04G08530.2 (Glycine max), 5'ss of exon 1
TCAAGGCCAGGCCCGAGGTGGGCGACTTCACCATCTACATGGGGCTGGACAAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaattcttctcttccctaaggaattttcctggtttggatcttcccag-------------------------------------------------------------------------------
|||| ||  | ||||| |  ||||| |||||||||| |||||| || |||||| ||||||||||||| |||||||| || || || ||||| || ||||||||   | |||| | |  |  || |    ||||| ||  || |  ||  |  |                                                                                
TCAAAGCGCGCCCCGAAGCCGGCGATTTCACCATCTTCATGGGCCTTGACAAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaattttcccatctccaattttatttttcttcttcgtttccgcaaactctctgctcccgacacagattattcacatgacctatgtctggaactcgatttgatttatcagttgtttgtgtagcgaag

upper sequence: EFJ06382 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA04G08530.1 (Glycine max), 5'ss of exon 1
TCAAGGCCAGGCCCGAGGTGGGCGACTTCACCATCTACATGGGGCTGGACAAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaattcttctcttccctaaggaattttcctggtttggatcttcccag----------------------------------------------
|||| ||  | ||||| |  ||||| |||||||||| |||||| || |||||| ||||||||||||| |||||||| || || || ||||| || ||||||||   | |||| | |  |  || |    ||||| ||  || |  ||  |  |                                               
TCAAAGCGCGCCCCGAAGCCGGCGATTTCACCATCTTCATGGGCCTTGACAAGTACGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaattttcccatctccaattttatttttcttcttcgtttccgcaaactctctgctcccgacacagattattcacatgacctatgtctggaact

upper sequence: EFJ06382 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA06G08640.1 (Glycine max), 5'ss of exon 1
TCAAGGCCAGGCCCGAGGTGGGCGACTTCACCATCTACATGGGGCTGGACAAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaattcttctcttccctaaggaattttcctggtttggatcttcccag------------------------------------------------
|||| ||  | || || |  ||||| |||||||||| |||||| || ||||||  |||||||||||| |||||||| || || || ||||| || ||||||||   | |||  ||   ||||   |    ||||  |   ||  || | |  |                                                 
TCAAAGCGCGCCCTGAAGCCGGCGATTTCACCATCTTCATGGGCCTCGACAAGTTCGAGAACGAGGAACTCATCAAATACGGTTTTCCCGAAGACATCTGgtaaccctaatcttttaattcctccatt--tttttttcaatttaatttccgtaaattctctgctcccgacacagattattcacacgacctatgtctggaact

upper sequence: EFJ06382 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT5G11500.2 (Arabidopsis thaliana), 5'ss of exon 1
TCAAGGCCAGGCCCGAGGTGGGCGACTTCACCATCTACATGGGGCTGGACAAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaattcttctctt-ccctaaggaattttcctggtt-tggatcttcccag--------------------------------------------
|||||||| | || || |  ||||||| |||||||| ||||||||| || |||  |||||||||||| ||||||||||| |||||||| || ||| ||||||| | |   ||  ||      | |   || |||||| | |  |  ||  |    |                                            
TCAAGGCCCGTCCTGATGCTGGCGACTACACCATCTTCATGGGGCTTGATAAGTTCGAGAACGAGGAGCTCATCAAGTACGGCTTCCCTGAAGATGTCTGgtaagccgtcttaatcgagaatcttctcgatttttcccgatcatctattgtttttgtttcgtttctcgagttttctcggatcggtatcagttttgaattg

upper sequence: EFJ06382 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S24_116V6.1 (Physcomitrella patens), 5'ss of exon 1
TCAAGGCCAGGCCCGAGGTGGGCGACTTCACCATCTACATGGGGCTGGACAAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaattcttctcttccctaaggaattttcctggtttggatcttcccag----------------------------------------------
|||||||| | ||||||   || ||||    ||| |||||||| || ||||||||||||||||||||||| |||||||||||||| || |||||||||||||  |     ||  ||| ||         | |||| |||  | ||   |    |                                              
TCAAGGCCCGTCCCGAGTGCGGGGACTATGTCATATACATGGGCCTTGACAAGCACGAGAACGAGGACCTTATCAAGTATGGCTTACCGGAGGATATCTGgtgagtgttttttgtctttttgtatgttgagtttcttggcgttgacgatgattgctgttcgtggtgttgtggacgatgtttcgtgaatttagggtttggc

upper sequence: EFJ06382 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S199_23V6.1 (Physcomitrella patens), 5'ss of exon 1
TCAAGGCCAGGCCCGAGGTGGGCGACTTCACCATCTACATGGGGCTGGACAAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaattctt---ctcttcccta-aggaattttcctggtttggatcttcccag------------------------------------------
|||||||  | |||||    || ||||     || |||||||| || ||||||||||||||||||||||| |||||||||||| | || |||||||||||||  |  |  || |    |||||  | |   | ||  |  || ||  |||  |  |                                            
TCAAGGCACGTCCCGAATGCGGGGACTATGTTATTTACATGGGCCTCGACAAGCACGAGAACGAGGACCTTATCAAGTATGGCCTACCGGAGGATATCTGgtgcgttccgttttcgagctcttggcaatgagtatgattgtgcttcagattgtggcgatgtttcgtgaacttagggttcggttgtaatttgtggcattgc

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|169038818|gb|FE447494.1|FE447494
EST:     AAGCACGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGATATCTG                         GTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
genomic: AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaa ... atcttcccagGTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
EST: gi|169075487|gb|FE482497.1|FE482497
EST:     AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTG                         GTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
genomic: AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaa ... atcttcccagGTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
EST: gi|169111590|gb|FE513960.1|FE513960
EST:     AAGCACGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGATATCTG                         GTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
genomic: AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaa ... atcttcccagGTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
EST: gi|169111589|gb|FE513959.1|FE513959
EST:     GAACGAGGGCCTCATCAAGTACGGCTTCCCCGAGGATATCTG                         GTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
genomic: GAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaa ... atcttcccagGTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
EST: gi|169033678|gb|FE441918.1|FE441918
EST:     AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTG                         GTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
genomic: AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaa ... atcttcccagGTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
EST: gi|169110034|gb|FE513327.1|FE513327
EST:     AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTG                         GTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
genomic: AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaa ... atcttcccagGTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
EST: gi|169064722|gb|FE476081.1|FE476081
EST:     AAGCACGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGATATCTG                         GTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
genomic: AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaa ... atcttcccagGTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
EST: gi|169035459|gb|FE444397.1|FE444397
EST:     AAGCACGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGATATCTG                         GTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
genomic: AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaa ... atcttcccagGTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
EST: gi|169033679|gb|FE441919.1|FE441919
EST:     AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTG                         GTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
genomic: AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaa ... atcttcccagGTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
EST: gi|169069410|gb|FE479493.1|FE479493
EST:     AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTG                         GTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
genomic: AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaa ... atcttcccagGTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
EST: gi|169064721|gb|FE476080.1|FE476080
EST:     AAGCACGAGAACGAGGACCTCATCAAGTACGGTTTCCCCGAGGATATCTG                         GTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
genomic: AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaa ... atcttcccagGTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
EST: gi|169110033|gb|FE513326.1|FE513326
EST:     AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTG                         GTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
genomic: AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaa ... atcttcccagGTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
EST: gi|169035458|gb|FE444396.1|FE444396
EST:     AAGCACGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGATATCTG                         GTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTAC-TGNAGGCTCCACA
genomic: AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaa ... atcttcccagGTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTG-AGGCTCCACA
EST: gi|169069411|gb|FE479494.1|FE479494
EST:     AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTG                         GTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
genomic: AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaa ... atcttcccagGTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
EST: gi|169075488|gb|FE482498.1|FE482498
EST:     AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTG                         GTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA
genomic: AAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaa ... atcttcccagGTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAA

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: 34 (upstream exon), 35 (downstream exon)
Score: 27

TCAAGGCCAGGCCCGAGGTGGGCGACTTCACCATCTACATGGGGCTGGACAAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaa ... atcttcccagGTTTCACGTTGACAAGCTCTCCTCGGCTCATGTCTACTTGAGGCTCCACAAAGGCCAGACCATGGACAATATCAGCGCGGAGCTCCTGGAGGACTGCGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAGGCCAGGCCCGAGGTGGGCGACTTCACCATCTACATGGGGCTGGACAAGCACGAGAACGAGGACCTCATCAAGTATGGCTTCCCCGAGGATATCTGgtatggccaattcttctcttccctaaggaattttcctggtttggatcttcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT