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

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGCTGTATGCCGAGAAGGTGAACAACCGTGGCCTCTGCGCCATCGCTCAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttttctttcttttttggccttggtgctaagacttctctacttcgtcag

Basic information

species Selaginella moellendorffii
transcript EFJ31038
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31038 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os07g41750.1 (Oryza sativa), 5'ss of exon 3
TGGAGCTGTATGCCGAGAAGGTGAACAACCGTGGCCTCTGCGCCATCGCTCAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtt-tgatttttcttt---------cttttttggccttggtgctaagacttctctacttcgtcag------------------------------------
| ||||| || |||||||||||||||||||| ||||||||||||||||| || ||||||||  | || ||||||||||| || || || |||||| ||||||| || |   || |           |  || |   |||||       | | ||  ||||  |||                                    
TCGAGCTCTACGCCGAGAAGGTGAACAACCGCGGCCTCTGCGCCATCGCCCAGGCCGAGTCGCTCCGCTACAAGCTCCTCGGTGGCCTCGCCGTCAGAAGgttgtgctccatcctgaaactcgcgttccttagatattggtatagcagcatgtcatcttca-cagcaaccggctgcttgttcgtgccagaattgtgttcga

upper sequence: EFJ31038 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os03g38000.2 (Oryza sativa), 5'ss of exon 1
TGGAGCTGTATGCCGAGAAGGTGAACAACCGTGGCCTCTGCGCCATCGCTCAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttttctttctttt-----ttggccttggtgcta-agacttctctacttcgtcag---------------------------------------
| ||||| || |||||||||||   |||||| ||||||||||||||||| || ||||||||  | || |||||||| || ||||| || |||||||| |||| |     | |||||  ||     || || ||| ||  |  ||     |  ||  |   |                                       
TCGAGCTCTACGCCGAGAAGGTCGTCAACCGCGGCCTCTGCGCCATCGCCCAGGCCGAGTCCCTCCGCTACAAGCTTCTTGGAGGCCTCGCCGTCCGCAGgtatagcactcctttcaattgctacttcgctttgttgtcatggaggatgcatctgtgatgggatcttgtggtgcaacgtactagttgttttagttggtta

upper sequence: EFJ31038 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G093902_T02 (Zea mays), 5'ss of exon 3
TGGAGCTGTATGCCGAGAAGGTGAACAACCGTGGCCTCTGCGCCATCGCTCAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttttctttcttttttggccttggtgctaagacttctctacttcgtcag----------------------------------------------
| ||||| || || |||||||||||||||||||||||||||||||| || || ||||||||  | || |||||||| || || ||||| |||||  |||||||      || || | |   | ||       ||   |  |   ||    ||                                                 
TTGAGCTCTACGCAGAGAAGGTGAACAACCGTGGCCTCTGCGCCATTGCCCAGGCCGAGTCGCTACGCTACAAGCTTCTTGGTGGACTAGCCGTGAGAAGgttacgcacttattccctacattgcac-aacactgctatgttaatatgatgtgcatttcttagttgttgtagacttgtagtcactatcacagcaggctcgg

upper sequence: EFJ31038 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G099352_T01 (Zea mays), 5'ss of exon 2
TGGAGCTGTATGCCGAGAAGGTGAACAACCGTGGCCTCTGCGCCATCGCTCAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttttct--ttcttttttggccttggtgctaagacttctctacttcgtcag-------------------------------------------
| ||||| ||||||||||||||   ||||||||| ||||| |||||||| || ||||||||  | || ||||||||||| || || || |||||||| ||||   |  |  |     |   ||    ||    |||   | ||    | || |                                               
TTGAGCTTTATGCCGAGAAGGTCGTCAACCGTGGGCTCTGTGCCATCGCGCAGGCCGAGTCCCTCCGTTACAAGCTCCTCGGTGGCCTTGCCGTCCGCAGgtacaacatgacaagaccccgttccttctgctagctgtaatttgctaattttgatgtggttgctagttcatatatgcttgcgtttagttgcatccaggtg

upper sequence: EFJ31038 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G074300_T02 (Zea mays), 5'ss of exon 2
TGGAGCTGTATGCCGAGAAGGTGAACAACCGTGGCCTCTGCGCCATCGCTCAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt------tctttcttttttggccttggtgctaagacttctctacttcgtcag---------------------------------------
| ||||| || |||||||||||   |||||| ||||||||||||||||| || || |||||  | || ||||||||||| ||||| || |||||||| |||| | | ||        | | ||   |      | |   |  || ||    | || |                                           
TCGAGCTCTACGCCGAGAAGGTCGTCAACCGCGGCCTCTGCGCCATCGCGCAGGCTGAGTCCCTCCGCTACAAGCTCCTCGGAGGCCTTGCCGTCCGGAGgtataacttgataagaccctactccctaccagctagctgtgtgatttgctgattttgatgtgcttgctactacttataatttgtatattcttgttcgttg

upper sequence: EFJ31038 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: AT3G53870.1 (Arabidopsis thaliana), 5'ss of exon 3
TGGAGCTGTATGCCGAGAAGGTGAACAACCGTGGCCTCTGCGCCATCGCTCAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttttctttc-ttttttggccttggtgctaagacttctctacttcgtcag--------------------------------------------
| ||||| |||||||||||||| |||||| | || ||||| ||||||||||| || |||||||| || |||||||| || || || || || || || ||||  ||  ||||| |  ||  || ||  || | ||  |  |  ||   || ||                                               
TTGAGCTTTATGCCGAGAAGGTTAACAACAGAGGTCTCTGTGCCATCGCTCAGGCTGAGTCTTTACGTTACAAGCTTCTTGGTGGTCTCGCTGTTCGTAGgtacgacatttctctagttcgtttgctatgttactttgtttgatcagtttagtttatcattagagactgatttggataggttactagtgtatataagcat

upper sequence: EFJ31038 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv04s0008g01750.t01 (Vitis vinifera), 5'ss of exon 3
TGGAGCTGTATGCCGAGAAGGTGAACAACCGTGGCCTCTGCGCCATCGCTCAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttttctttcttttttggccttggtgctaagacttctctacttcgtcag---------------------------------------------
||||||| ||||| ||||| || |||||  | |||||||| ||||| ||||| || |||||  ||||||||||||| || |||||||| || || || ||||        |  || || | ||   ||  |       ||   | |       ||                                             
TGGAGCTTTATGCTGAGAAAGTTAACAATAGGGGCCTCTGTGCCATTGCTCAGGCAGAGTCACTGCGATACAAGCTTCTTGGAGGACTTGCTGTTCGGAGgtaaatcaagttcttgttatctgatgttaatttggttgctctaccatgctactagatacagtattttcaaatcggtttgaatcattaatggacctatgaa

upper sequence: EFJ31038 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: EDP07493 (Chlamydomonas reinhardtii), 5'ss of exon 3
TGGAGCTGTATGCCGAGAAGGTGAACAACCGTGGCCTCTGCGCCATCGCTCAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttttc------tttcttttttggccttggtgctaag--acttctctacttcgtcag-------------------------------------
| |||||||| || |||||||| | | ||||||| || ||||||||||| || ||||||||  |||| |||||||| ||||| || |||||||| ||  |||  |    | |          | ||  ||    ||||   ||  |     |     ||  |                                      
TTGAGCTGTACGCTGAGAAGGTCAGCGACCGTGGTCTGTGCGCCATCGCCCAGGCCGAGTCGCTGCGCTACAAGCTGCTGGGTGGCCTGGCCGTGCGCCGgtgagcagctgcgaggagagggtgttggggttgcggtgtagagggaaacggcaggaccgcgaagcgttgggggtggcaagggagggcacgaaaccgcatt

upper sequence: EFJ31038 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S29_222V6.1 (Physcomitrella patens), 5'ss of exon 3
TGGAGCTGTATGCCGAGAAGGTGAACAACCGTGGCCTCTGCGCCATCGCTCAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgat---------ttttctttcttttttggccttggtgctaagacttctctacttcgtcag-----------------------------------------------------------------------------------------
| ||| |||| || || ||||| |||||| | ||||| |||||||| ||||| |||||||||||||| |||||||| || ||||| || ||||| || ||||| |||           |  ||  | || |       ||          || | |   ||                                                                                            
TTGAGTTGTACGCGGAAAAGGTTAACAACAGGGGCCTGTGCGCCATTGCTCAGGCCGAGTCTTTGCGGTACAAGCTTCTTGGAGGGCTTGCCGTGCGCAGgttcgatgccaggacacctctttcatcttctaattcccgtagcggtggcgctgtgcaatgttcacgcgatttttacttttttgtccaataattattttcgatttcctctagtatgtttggttaatgaaattctgttttgggtggtggttacag

upper sequence: EFJ31038 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S127_74V6.1 (Physcomitrella patens), 5'ss of exon 3
TGGAGCTGTATGCCGAGAAGGTGAACAACCGTGGCCTCTGCGCCATCGCTCAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttttctttcttttttggccttggtgctaa--gacttctctacttcgtcag--------------------------------------------------------------------------------
||||| |||| |||||||||||||||||||| || || |||||||| || || || |||||  |||||||||| |||||||| || || || || || |||| ||    |  | ||| ||   | ||| || ||||    |     | |||  |||                                                                                 
TGGAGTTGTACGCCGAGAAGGTGAACAACCGGGGTCTGTGCGCCATTGCCCAGGCTGAGTCGCTGCGATACAAACTCCTGGGTGGTCTCGCTGTTCGCAGgtgtgtgcctcgtatctatt--agactttgtactaatccgcactattgcttgatcaccttgattttctacgaggttaactgcgcgttcagagctcagcgtatcgttctgatgtgctgatcttaaatctgaacgctag

upper sequence: EFJ31038 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S31_178V6.1 (Physcomitrella patens), 5'ss of exon 3
TGGAGCTGTATGCCGAGAAGGTGAACAACCGTGGCCTCTGCGCCATCGCTCAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttttctttcttttttggcct-----tggtgctaagacttctctacttcgtcag----------------------------------------------------------------------------
||||| |||| || |||||||||||||||||||| || ||||| || || ||||| |||||| | ||||||||||| || ||||| || || || || |||||||   ||     |    |   | |     |||   | | | || |  | ||     |                                                                            
TGGAGTTGTACGCTGAGAAGGTGAACAACCGTGGTCTGTGCGCTATTGCGCAAGCTGAGTCTCTTCGATACAAGCTTCTCGGAGGTCTTGCTGTACGCAGgtttgtgcttctacacaaaatatacttttaaatggcaattaaatttattcaattaaatggtaattgaatgtatgaattgttttagccaaattggaaaaaagggatactataagttcttgaacctgcggttttttag

upper sequence: EFJ31038 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S454_3V6.1 (Physcomitrella patens), 5'ss of exon 3
TGGAGCTGTATGCCGAGAAGGTGAACAACCGTGGCCTCTGCGCCATCGCTCAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgat---ttttctttcttt---tttggccttggtgctaagacttctctacttcgtcag---------------------------------------------------------------------------
| ||| ||||||||||||||||||||||| | || || |||||||| ||||| || |||||  |||| |||||||| || ||||| || || || || ||||  |||   ||  | ||| |    ||  |||   ||  | |    |  |   ||  |  |                                                                           
TTGAGTTGTATGCCGAGAAGGTGAACAACAGGGGTCTGTGCGCCATTGCTCAGGCTGAGTCGCTGCGGTACAAGCTTCTTGGAGGTCTTGCTGTGCGCAGgtgcgatgggttgccattcgtgtaattatgcccgtgtattcatcagttgcactttgatttgaatctagcttcccatgttaagtacttatcagaatcgatggtgtatgacgttttcttttttgtatgacgggtacag

upper sequence: EFJ31038 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S41_146V6.1 (Physcomitrella patens), 5'ss of exon 3
TGGAGCTGTATGCCGAGAAGGTGAACAACCGTGGCCTCTGCGCCATCGCTCAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttttcttt---cttttttggccttggtgctaagacttc---tctacttcgtcag------------------------------------------------------------------------------------------
||||| |||| || ||||||||||||||| | || || || ||||| || || ||||| || ||||||||||||||||| ||||| || || || || ||||||| |||||  ||    || ||| |  || |   || ||  |    | || ||| | |                                                                                           
TGGAGTTGTACGCTGAGAAGGTGAACAACAGGGGTCTGTGTGCCATTGCCCAGGCCGAATCCTTGCGATACAAGCTCCTCGGAGGTCTTGCGGTTCGCAGgtttgcttttttattggatttgttttgttttaggattaggatattcattttatttcttgactccagaccctttcactggtgaagtggaaaatgctcaatgctggcttagggttttttttgctgatacgtattaaaaattgtggatttacag

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|169103364|gb|FE507341.1|FE507341
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... acttcgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169065994|gb|FE473778.1|FE473778
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... acttcgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169098880|gb|FE502277.1|FE502277
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... acttcgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169068032|gb|FE476399.1|FE476399
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... acttcgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169072226|gb|FE479358.1|FE479358
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... acttcgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169098879|gb|FE502276.1|FE502276
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... acttcgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG

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: 102

TGGAGCTGTATGCCGAGAAGGTGAACAACCGTGGCCTCTGCGCCATCGCTCAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... acttcgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAGCTGTATGCCGAGAAGGTGAACAACCGTGGCCTCTGCGCCATCGCTCAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttttctttcttttttggccttggtgctaagacttctctacttcgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA