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

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatccttttttctggtttcttggctttcatcttgaccttcttgctcgatttctcgactgatgtgaatccttgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG

Basic information

species Selaginella moellendorffii
transcript EFJ24533
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os10g42940.1 (Oryza sativa), 3'ss of exon 2
----------------------gtaatccttttttctggtttcttggctttcatcttgacc----ttcttgctcgatttctcgac-tgatgtgaatccttgc-tagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG
                       |    |    |  | |  ||||   |||  | |||| |    | |   | | |  |  |  | | ||    ||| |     ||| || ||||||||||| || || |||||||||||||||||||| ||||||||||||||||||||||| ||  | || ||  | |||| ||||||||| | 
gtaggttcactctcatccctccctccctccgcctcatcgaatcttttattttgttttgagccaaatccaaacccaacctaacatcatcatcatcatcatcatgcagGCTTCAACGTGGAGAAAGTTCAATACAAGAATGTGGTGTTCACTGTGTGGGATGTTGGTGGCCAGGAAAAATTGAGGCCCTTATGGAGGCACTACTTCAA

upper sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os02g03610.1 (Oryza sativa), 3'ss of exon 2
---------------------gtaatccttttttctggttt-cttggctttcatcttgaccttcttgctcgatttctcgactgatgtgaatccttgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG
                      |||| | ||  | || |   |||       ||| |     || ||      | |   | |    || | |||    ||| |||||||| |||||||| ||||||||||||||||| || || |||||||||||||| || || || ||||| || ||  | ||||||   ||| | ||
aattatataattctatacctcataattcattgatgtgctcgactttttcccaatcattgatctcatgtctatatccaataataccatgtaccctctgcagGTTTTAACGTAGAGAAGGTTCAGTACAAGAATGTGGTATTTACTGTGTGGGATGTTGGCGGACAAGAAAAGCTCAGGCCATTATGGAAGATGTACCTCAG

upper sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os06g02390.1 (Oryza sativa), 3'ss of exon 2
----------------------------------------------gtaatccttttttctggtttcttggctttcatc--ttgaccttc-ttgctcgatttctcgactgatgtgaatccttgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG
                                              |  ||    |  ||   || || | | | |||     ||| | | ||  |  ||     ||       |||| |     ||| || ||||||||||||||  |||||||||| ||||  |||||||||||||| || || |||||||| |||||  |||| |||||||  || ||||| ||
gtagtgatacatcgtgttcattgtcatttatttcatcgccgaaatgggcatgacataatcca-ttcctggacctgcattgacagacatacattctttcatcctgtgaaatgaacgaattcc-atcagGGTTCAACGTGGAGAAGGTGGAGTACAAGAACGTGGCCTTCACGGTGTGGGACGTGGGAGGCCAGGACAAGCTCCGACCTCTCTGGAGACAATACTTCAG

upper sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 2
---------------------------------------------------------gtaatc-cttttttctggtttcttggctttcatc---ttgaccttcttgctcg---atttctcgactg-atgtgaatccttgc----tagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG
                                                          ||||  |  || ||    |      ||  |||    ||||       | ||     |||   ||| | |||    |  |  |    |||| || || || |||||||| || ||||||||||| |||||||| ||||||||||||||||||||||||||||| || || || |||| ||||||||| | 
gtccgattgtaccacctatctgcttgtgcatttcataacttttggtttcaaccattgctaattacagttgtccaactctgcacctgccatgcaattgattcgtccgttcatatgtttagtgacagcatgcactttatcacattgtagGTTTCAATGTTGAGAAGGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAA

upper sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G113995_T03 (Zea mays), 3'ss of exon 2
--------------gtaatccttttttctggtttcttggctttcatcttgaccttcttgctcgatt-tctcgactgatgtgaatcc-------ttgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG
              | ||  |     ||  |    |    ||  | |      | | |||    |  |||     ||| ||  ||        |  ||||| || ||||| ||||| || || |||||||||||| |||| || |||||||||||||||||||| || ||| | || ||  | |||| ||||||||| | 
ttcctgtcttaattgaaaggcagggctcctgccattacatttaaaacaaactttccctgcaaattcgtctgtgacgatatgtctctggtgctatcactagGTTTCAACGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTGTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA

upper sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G152929_T02 (Zea mays), 3'ss of exon 2
-------gtaatccttt--tttctggttt--cttggctttcatcttgaccttcttgctcgatt----tctcgactgatgtga-----atccttgct--agGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG
        |||| || |    ||||| ||  ||  |||   ||| | |  |   |   | ||      |||   | |  | |     |||| | ||  ||| ||||| || |||||||| ||||| ||||||||||  ||||| ||||||||||| ||||| || || || || ||  | || ||||||   ||| | ||
gcctaacataatgctctggcgtctggattgactctgctgcaatcctcatttctctatccaatagctacctctggtaacataatttccatccgtcctgcagGTTTTAATGTCGAGAAGGTTCAGTATAAGAATGTGGCATTCACTGTGTGGGATGTGGGTGGGCAAGAAAAACTCAGGTCACTGTGGAAGATGTACCTGAG

upper sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 2
-----------gtaatccttttttctggttt-cttggctttcatcttgaccttcttgctcgatttctcgactgatgtgaatcct----------tgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG
            |||   |||| |  || || ||     |  || ||   |||      | | |||  |  |||||  |   ||          | ||||| || || || ||||| || || |||||||||||| |||| || || ||||||||||||||||| || ||| | || ||  | |||| ||||||||| | 
ccaatatgttcttaaaggttttatgaggattactaaaaataaatgtttcactttgcctgcaaattcatgtgtgatgatatctctctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA

upper sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA12G02110.1 (Glycine max), 3'ss of exon 2
----------------------gtaatccttttttctggtttcttggctttcatcttgaccttcttgctcgatttctcgactgatgtg-aatccttgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG
                       |||   |       |      | |   | | ||  |  || ||  |  |   ||  || ||| || | | |||   ||| ||||| ||||||||||| ||||| |||||||| || |||||||| ||||||||||| || || |||||  ||||  | || |||| |||||| |||| 
caaacatgtaccagtatcacacttaagtttaacaggggaagaactagaaataacctatatgttgtttatttaaggctt-acggatttgtagtgctttgcagGTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGGATGTTGGAGGGCAAGAGAAATTAAGGGCACTTTGGAGGCACTATTTTAA

upper sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA11G09790.3 (Glycine max), 3'ss of exon 1
----------------gtaatccttttttctggtttcttggctttcatcttgacct---tcttgctcgatttc--tcgactgatgtg-aatccttgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG
                 |||   |   |   |     || |   |     | ||||   | ||| | ||||       |  ||| || | | |||   ||| ||||| ||||||||||| ||||| |||||||| || |||||||| ||||||||||| || || |||||  ||||  | || |||| |||||| |||| 
tgtaccagtatcacacttaagtttagctgaggaagaattagaagtagaaataacctatatattgtttgattaaggcttatagatttgtagtgctttgcagGTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGGATGTTGGAGGGCAAGAGAAATTAAGGGCACTTTGGAGGCACTATTTTAA

upper sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 3
-------------------gtaatccttttttctggtttcttggctttcatcttgaccttcttgctcgatttctcgact----gatgtgaat--ccttgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG
                    |    |   ||  | ||||  ||||   ||  |    || | |  |   | ||| |  |     || |  ||  |||||| ||| || || |||||||| || ||||| ||||||||  | ||||| || ||||||||||| || || ||||| ||||| || || |||| ||||||||||  
gttgaatgtctatatggtattggcgccgcttgttagttt--tggccagcaaatgagtctacataatgtttctctaggtttttaaatttatattgccttgc-agGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA

upper sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------gtaatccttttttctggtttcttggctttcatcttgaccttcttgctcgatttctcgactgatgtgaatccttgcta----gGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG
                   | |||  |  || | |||   |   |||| | |||    | | | |    |   |     || | ||    || ||    ||||| || || ||||| || ||||||||||||||| ||||||| || ||||||||||||||||| ||||| || ||||| || |||| ||| ||||| | 
ttcttgtgacattatacttttatctatgattattgttctgtcattttccttttggttgtttggattatgtctgctgacaatttaaacttatgttactcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA

upper sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------gtaatccttttttctggtttcttggctttcatcttgaccttcttgctcgatttctcgactgatgtgaatc-cttgc-tagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG
              | |  | ||||| |  ||| |  | ||||   || | |||    |  | |||   ||    | | |||  ||| |  ||| || || || ||||| || ||||||||||||||  | ||||| || ||||||||||||||||| |||||||| || ||  | |||| ||| ||||| | 
gtaggtcagattgctcaagcatttttattttttttgcgttttctcatttatcttacaacg-ggtttactgaggattttaaatttcttacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA

upper sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 2
------gtaatcct-tttttctggtttcttggctttcatcttgaccttcttgctcgatttctcgactgatgtgaatc-----cttgct----------agGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG
       | ||| | || | |  || |  |    |  || ||||  |      | ||  |   || |||| | |||       || ||          ||| || || |||||||| || ||||| ||||| ||| ||||||| ||||||||||| ||||| || ||||| || || || ||||||| ||| ||||||| 
taacagttgatcatattgtacatgtattatactatggatgttgatgtgtcgaatggagcttcagattgattttaattgatcattttctggtaatatatagGTTTCAATGTGGAGAAAGTTCAGTATAAGAACGTGATGTTCACAGTGTGGGATGTAGGTGGACAAGAGAAACTCAGGCCACTCTGGAGGCATTACTTTAA

upper sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: EDP05355 (Chlamydomonas reinhardtii), 3'ss of exon 1
----------------gtaatccttttttctggtttcttggctttcatcttgaccttcttgctcgatttctcgactgatgtgaatcct------tgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG
                 |  ||| | |  |   | |    ||    |      ||  |   | |    ||   ||  |  ||   |||       |  ||| || ||||| |||||||| || |||||||| || ||||||||||||||||| || || ||||||||||||||  | || || |||  ||| ||||| | 
cccagtatcccagcccatgctccatgtaccccttattacagcccgaacagaatcccccacacacacaatccacacacacctgcgccctgcaaaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGGACGTGGGCGGCCAGGAGAAGCTGCGGCCACTGTGGCGGCATTACTTCAA

upper sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S91_59V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------------------------------------------------gtaatccttttttctggtttcttggctt-tcatcttgaccttcttgctcgatttctcgactgatgtgaatccttgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG
                                                                                                                  |  | ||      || |   | ||||  | || ||| | ||  || ||  || ||    |   |   |||  |   ||||||||| ||||| || || || ||||||||||| | |||||| || ||||||||||| || ||||||||  |  | || || |||  ||| ||||| | 
gtaaagtgacacatgacacttgccgcaggtcttgatgattctcaaatggagtgtctcgtcgttcctagttgaaggtagttgtgttatctattgatgaacttttgcaccttaatattgtgctgagcgttgatgagtcggctggttatattggcatt--tgttcacttcctgtgttcccgc--atctct--cagGATTTAATGTGGAAAAAGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAA

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), 34 (downstream exon)
Score: 32

GTAGTGATGCTGGGGCTGGATGCCGCCGGCAAGACAACGATCCTGTTCAAGCTACACATAGGGGAAATCCTCTCCACGGTTCCAACAATTGgtaatccttt ... tccttgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggctttcatcttgaccttcttgctcgatttctcgactgatgtgaatccttgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG
                                 gactgat  putative branch site (score: 32)
                                             tccttgct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatccttttttctggtttcttggctttcatcttgaccttcttgctcgatttctcgactgatgtgaatccttgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG