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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttgatcaaagccttctccttttctttcttacagctcgaaactaacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT

Basic information

species Selaginella moellendorffii
transcript EFJ29073
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 4
------------------------------------gtactttgatca--aagccttctccttttctttcttacagctcgaaactaacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT
                                         ||||| |    |      |  | |  ||| ||     |  ||||  |    | |  | ||||||||||||| || |||||| | ||||| |||||||||||| | |||||||||||| ||| |||||| ||||||||||||||||| ||||||||||||||
ttttaaactaatgacatgccttttgtagttagttggtcgtcttgattatctggatagtgcactgtgattcatatttgactgaactgtc--tcatctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT

upper sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 4
-------------------------------gtac-tttgatcaaagccttctcc----ttttctttcttacagctcgaaactaacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT
                               | || |||  |   ||| | | |      || | |  |||   ||      || || || |  || ||||||||||||| || |||||  | ||||| |||||||||||| | |||||||||||| ||| |||||| ||||||||||||||||| ||||||||||||||
attgttgatatatttcatgcatgatctatcagcacatttcctgtgagcttgcactgtaacttgcctatttatgactgagctgtatcacctcctcattcagGTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT

upper sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 4
--------------------------------------gtactttgatcaaagccttctccttttctttcttacagctcgaaactaacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT
                                      | || ||         |||     | | ||||| ||   |  |   || || ||    || |||||||||| || || |||||  | ||||| |||||||||||| | |||||||||||| ||| |||||| ||| ||||||||||||| ||||||||||||||
tttagaagttacatggacacacttgcttttagtgttgagcacatttcctgtgagcttgcatatctatttctgac--ttgaactgtatcacctcttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT

upper sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------gtactttgatcaaagccttctccttttctttcttacagctcgaaactaacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT
                                                           | ||||   ||||   |||| ||  | ||  |    |||   |  |  | |  |||    ||||||||||||| ||||||||| | ||||| |||||||| ||  | ||||| || ||||| || |||||||| |||||||||| ||| || ||||| |||||
gtgagaattttttttaatgagtctgaataagaaaaacttattatgtagaaaaaatattattctttccacaaaattttcttctgatgttaatgcttgct---atttctccttcaccttaccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAATAAAAAGCATAAAAAGGATATTAGCAAGGACAGCCGAGCACTTGGCAAGCT

upper sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------gtactttgatcaaagccttctccttttctttcttacagctcgaaactaacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT
                                                               || | |   |  |   || ||||||| || || |   ||   |       ||  ||  | ||||||||||||| ||||||||| | ||||| |||||||| ||  | |||||||| |||||    |||||||| |||||||||||| | || ||||| |||||
gtgagtacttttatacacatacacacaagctaatgtctgttattctatggaaatgaaattatataatctttccttaaatttttccttttgttgctaatgtctgctattctgtttcc-cctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGCAAGCT

upper sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------------gtactttgatcaaagccttctccttttctt-tcttacagctcgaaac-taacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT
                                                          || | |  |     ||   | ||  |||  | |||  ||| |  |  |  | |   ||    ||||||||||||| ||||||||| | ||||| |||||||| ||  | |||||||| |||||    |||||||| ||||||||||   | || ||||| |||||
gtgagaattttttttttttatgagtcttaataagaagaacttattatgtagaaaaatatattattctttccaccaaattctcctctgatgttaatgcttgctatgtctccttcgccttgccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAGTAGAGCACTTGGCAAGCT

upper sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------gtactttgatcaaagccttctccttttctttcttacagctcgaaactaacatctaccaatgc-agGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT
                                                || | |   || |   || || || |  | || |   || |  | |    | | ||  | | ||||||||| || ||||| ||| | ||||| |||||||| ||  | |||||||| |||||    |||||||| |||||||||||| | || |||||||||||
gtgagtacttttatacacatacacacaagagaatgaaatgaaattatatattctttccataaaattttctttctgatgctaatgtct-gctatttctgtttccccttactagGTGAGGATTTTGATCAAAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGAAAGCT

upper sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------------------------------------------------------------------gtactttgatcaaagccttctccttttc-----tttcttacagctcgaaactaacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT
                                                                                                      ||      ||  | |  || |  |  |      ||  |   | |       |   ||  | |   |||||||||||||| || || || |||||||| |||||||||||| | || |||||||||||| | ||||| |||||||||||||||  ||||||||| |||||
gtaatatacttgtgaccaggaatgaattgttttgaattgcattgtgttcaataacaaatgattgctatgccaatgcaataagctaaacatagtcaataacatgtgtcagaatggagggattgttttagtgtgatgttggtggtaaccttttgttgttatg-atctgcgcagGTGAGGACTTTGACCACAGGGTGATGGAGTACTTCATCAAGTTGATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT

upper sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------gtactttg-atcaaagccttctccttttctttcttacagctcgaaactaacatct----------accaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT
                          ||   ||  ||| |         || | ||  |   |  | |   ||||| | |          | |   |||||||||||||| || || ||  | ||||| |||||||||||| | || |||||||||||| | ||||| |||||||||||||||  ||||||||| |||||
cgatattccaagctaatcatagtcaataacatgtgtcagaatggagggattgttttagtgtgatgttggtgctaaccttttgttgttatgatctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT

upper sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 4
------------------------gtactttgatcaaagccttctccttt---------tctttcttacagctcgaaactaacatctaccaat---gcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT
                        | |     | |||    ||     |          ||  |     ||    ||||| |  |  |    |   ||||||||||| || ||||||||| | ||||| |||||||||||  | ||||||||||||||    ||||| ||||||||||||||| | ||| |||| ||| |
atagaattacggtggcaaatgggtgaaacccaaccaagtttttgcttctaaaatgatgatcaattgggaagtagaaaacttatgttcattttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT

upper sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------------------gtactttgatcaaagccttctccttttctttcttacagctcgaaactaacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT
                                                        | |  || |  | ||     |  || |  |    |  |||| |   | |  |||  |  |||||||||||| || || |||||  | ||||| ||||| |||||| | || ||||||||||||   ||||| ||||||||||||||| | |||||||| |||||
GTGAGGATTTTTTTCTCTACTGATGCTCTTTCATCTTTGCTCTTTGCACATTGAAAGAAAATTTACGAGAGGAAAGTTATTATACTGTGGAT-GCTCAAGGTTCAATTCTTTCC-TGCAGGTGAGGATTTTGACCAGAGGATTATGGAGTACTTTATCAAGTTGATTAAGAAGAAGCACGGAAAGGACATCAGCAAGGACAACAGAGCTCTTGGGAAGCT

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|169038081|gb|FE445834.1|FE445834
EST:     CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAG                         GTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
genomic: CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgtactttgat ... accaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
EST: gi|169098156|gb|FE499551.1|FE499551
EST:     CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAG                         GTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
genomic: CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgtactttgat ... accaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
EST: gi|169080680|gb|FE487188.1|FE487188
EST:     CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAG                         GTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
genomic: CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgtactttgat ... accaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
EST: gi|169115292|gb|FE517008.1|FE517008
EST:     CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAG                         GTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
genomic: CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgtactttgat ... accaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
EST: gi|169079294|gb|FE490183.1|FE490183
EST:     CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAG                         GTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
genomic: CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgtactttgat ... accaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
EST: gi|169044229|gb|FE452959.1|FE452959
EST:     GTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAG                         GTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
genomic: GTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgtactttgat ... accaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
EST: gi|169082521|gb|FE490045.1|FE490045
EST:     CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAG                         GTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
genomic: CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgtactttgat ... accaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
EST: gi|169087152|gb|FE493099.1|FE493099
EST:     CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAG                         GTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
genomic: CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgtactttgat ... accaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
EST: gi|169037137|gb|FE444422.1|FE444422
EST:     CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAG                         GTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
genomic: CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgtactttgat ... accaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
EST: gi|169034527|gb|FE444574.1|FE444574
EST:     CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAG                         GTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
genomic: CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgtactttgat ... accaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
EST: gi|169068925|gb|FE477266.1|FE477266
EST:     CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAG                         GTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA
genomic: CAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgtactttgat ... accaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGA

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: 31 (upstream exon), 31 (downstream exon)
Score: 28

GTGTTTGATCTCGGTGGTGGTACTTTCGATGTCAGTATCTTGACGATCGACAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgtactttgat ... accaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaagccttctccttttctttcttacagctcgaaactaacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT
                                  aactaac  putative branch site (score: 28)
              ttttcttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttgatcaaagccttctccttttctttcttacagctcgaaactaacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG