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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatttctcctttcttcgtgtgtgctagctctttgatcgtttcgtgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC

Basic information

species Selaginella moellendorffii
transcript EFJ36722
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 2
-------------------------------gtaaaatttct-cctttcttcgtgtgtgctagctctt----tgatcgtttcgtgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC
                                | | ||||     |||  || |||   | |  | ||    | | |  || ||  |    |   | ||||| || || || ||||||||||||||| | || || ||| | |||||||||||  ||||||| |||||||| || ||||||||| |||||||||||||||
gggtgctcccatttatttaccaatttatataatcacatttgaatattttgtcctgtaatcaaaatattgtgcttaactatttgtcgttacctttcctcagGGTTATGTGGTTTACCGTGTCCGTGTGAGGCGTGGTGGCAGGAAGAGGCCAGTGCCCAAGGGTATTGTCTACGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 2
--------------------gtaaaatttctcctttcttcgtgtgtgctagctctttgatc---gtttcgtgctcgaatc-------------ctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC
                     |    | |        || |  |||  | || || | |||    | | ||||   | |              ||  ||||| || || || |||||||| || ||  | || || ||| | |||||||||||  ||||||| ||||||||||| ||||||||| |||||||||| ||||
agccaaaatgtattcacatgctgctgtctgattcacttttgaatgttttggccctataatccaaatattgtgcataactattttttgaccttgctttcagGGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCAGTGCCCAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATTACCC

upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G024354_T01 (Zea mays), 3'ss of exon 2
-------------------------------gtaaaatttctcctttctt-cgtgtgtgctagctc--tttga--tcgtttcgtgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC
                                || |||| |   ||   |   | ||| ||   |   | |||  | || | ||| |          |||||||| |||||||||||||||||||||   || || ||| | |||||||| ||  ||||||| ||||||||||| ||||||||| |||||||||||||||
tagtatgctatgttgccttgtttgcttcatcttacaattgcagtttgagtatatatgtcctgattttgtctgacgttgtgttgtggtaattcatcttcagGGATATGTTGTCTACCGTGTCCGTGTGAAGCGTGGTGGCAGGAAGAGGCCTGTGCCCAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G084757_T02 (Zea mays), 3'ss of exon 1
-------------------------gtaaaatttctcctttct------tcgtgtg--tgctagctctttga--tcgtttcgtgctcgaatcct-cacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC
                          |  |||| ||    | |      ||| ||   |||| | |    |     |   | ||    | |  |   ||||| || ||||| ||||| ||||||||| | || || ||| | |||||||| ||  | ||||| ||||||||||| ||||||||| |||||||||||||||
aacagcttgtacttgtctgtaatgcattgaattactttgctttgaaaattcgagtagctgctgggtgcccgggtctgaaccttgtgttatttttgttcagGGGTATGTTGTTTACCGCGTCCGTGTGAGGCGTGGTGGCAGGAAGAGGCCTGTGCCGAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G180724_T01 (Zea mays), 3'ss of exon 2
---------------------------------gtaaaatttctcctttcttcgtgtgtgc-tagctctttgatcgtttcgtgctcgaatcctca--cagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC
                                  |  || |  | |  |||     | ||  ||| |  | | ||    |||  |   ||  |    ||||| || ||||| ||||||||||||||    || || ||| | |||||||| ||  | ||||| ||||||||||| ||||||||| |||||||||||||||
atgaacaactcgtacttgtctgagtaataatgcattgaactagttcactctgaaaatttgagtagttgctgggtctgaacgttgtgttatttttgttcagGGGTATGTTGTTTACCGTGTCCGTGTCAAGCGTGGCGGCAGGAAGAGGCCTGTGCCGAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G302876_T01 (Zea mays), 3'ss of exon 4
-------------------------------------gtaaaatttctcctttcttcgtgtgtgctagctctttgatcgtttcgtgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC
                                     |  || |||         |    ||   |   |   || | || | ||| |           |||| || ||| | |||| |||||||||| | |  || ||  | ||||||||  |  ||||| | ||||||||||| ||||||||| |||||||||||||||
attaggagtcttgagggtacccctaattatggtccccgacaagtttgagtacctatgtcatgattttatttgatg-ttgtgttgtggtaattcatctttagGGTTATGTTATGTACCTTGTCCGTGTGAGGCATGGTGGTAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G034794_T02 (Zea mays), 3'ss of exon 2
-gtaaaatttctc-----ctttcttcgtgtgtgctagctctttgatcgtttcgtgctcga-atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC-----------------------------
  |   | || ||       | ||| |     | |  || ||  || || ||   ||| | ||     ||||| || ||||| ||||||||||||||  | || || ||| | |||||||| ||  | || || ||||||||||| ||||| ||| |||||||||||||||                             
gattgtacttgtcagtgtaatgctttgaactagttcactattaaattgtctctgactctatatttgttcagggttatgttgtttaccgtgtccgtgttagGCGTGGTGGCAGGAAGAGGCCTGTGCCTAAAGGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCCAGCTCAAGTTCCAGAGGAACAAGAGGTCT

upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G034794_T01 (Zea mays), 3'ss of exon 2
------------------------------gtaaaatttctcctt-----tcttcgtgtgtgctagctctttgatcgtttcgtgctcga-atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC
                               |   | || ||  |      ||| |     | |  || ||  || || ||   ||| | ||     ||||| || ||||| ||||||||||||||  | || || ||| | |||||||| ||  | || || ||||||||||| ||||| ||| |||||||||||||||
gatagtttcagttttgagtagaatgaacagattgtacttgtcagtgtaatgctttgaactagttcactattaaattgtctctgactctatatttgttcagGGTTATGTTGTTTACCGTGTCCGTGTTAGGCGTGGTGGCAGGAAGAGGCCTGTGCCTAAAGGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC

upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G466136_T01 (Zea mays), 3'ss of exon 1
-------------------------------gtaaaatttctcctttctt-cgtgtgtgctagctc--tttga--tcgtttcgtgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC
                                ||  ||| |   ||   | | | |||  |   |   |||||  |  | | ||| |    |     ||||| || ||||| |||| |||||||||| | || || ||| | ||||||||  |  ||||| | ||||||||||| ||||| ||| |||||||||||||||
agtatgctatgttaggcttgtttactttattttattattgcagtttgagtacctatgtcatgattttatttgatgttatgttgtggtaatttatcttcagGGTTATGTTGTGTACCTTGTCCGTGTGAGACGTGGTGGCAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC

upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv15s0021g02480.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------gtaaaatttctcctttcttcgtgtgtgctagctctt-tgatcgtttcgtgctcgaatcctcac---agGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC
                                 | | |    ||    |   |  | |  |  || |  | ||  |  |   | | | |    |    |||| || ||| |||| ||||| |||||  | || || || || |||||||| ||| ||||||| ||||| ||||||||||| |  ||||||||| ||||||
tgtttaaaattatgacaaactggcccattaatttgataagcatcaagacgatgattctttttactttgattataatgccaaacactattttctattttagGGGTATGTTATCTATCGTGTTCGTGTTAGACGTGGTGGTCGGAAGAGGCCTGTTCCCAAGGGCATTGTTTATGGAAAGCCTACAAACCAGGGTGTCACCC

upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S134_151V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------gtaaaatttctcctttcttcgtgtgt-gctagctctttgatcgtttcgtgctcgaatcc--tcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC
                                  |  | | | ||| |      ||| | | |  ||   |  |||  |  |  | ||   |     |||||||| || ||||||||||||||||| || || || ||| | |||||||||||| ||||||| ||||| |||||||||||||||||||||||||| || |
ttatacttttcagcacccttgttgttagggtgcctggattctatccatatgatatgtttagatgtctagattttcggatgataatggacctcaactgcagGGATATGTGGTCTACCGTGTCCGTGTCCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAGGGTATTACGC

upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------gtaaaatttctcctttcttcgtgtgtgctagctctttgatcgtttcg--tgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC
                                    | ||    |   |   |  |  |        |||| | | ||  |  |  | |  |  |   |||| || ||||| || || ||||| ||||| || || ||| | |||||||||||| ||||||| ||||| |||||||||||||||||||| ||||| || |
cacgtggcgttcagtatagttattgtggattgattcagaaaggatttgtgggttatccgcttcgaagcttttaacattatgatttatggccttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAAGGTATTACGC

upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S28_15V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------gtaaaatttctccttt--cttcgtgtgtgctagctct--ttgatcgtttcgtgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC
                                   |    | |||||||    ||| |||| | ||  |     ||||  |||| ||   |  |  |  ||||| ||||| || |||||||| |||||||| || || ||| | |||||||| ||| | ||||| ||||| || |||||||| |||||||||||||| || |
ctgctgtcagtcttgagtaaaatacattctcttgcttgtttgtctccttcaatttcttgtggggtacttggagctgattatttc-tgtgtgt-ttgtatcagGGCTACGTGGTGTACCGTGTTCGTGTGCGCCGTGGAGGCAGGAAGAGGCCTGTTGCTAAGGGTATTGTGTACGGAAAGCCAAAGAACCAGGGTATTACAC

upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S7_364V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------gtaaaatttctcctttcttcgt------------gtgtgctagctctttgatcgtttcgtgctcgaatcctc------acagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC
                     | |||  || ||| ||  |            | ||  |||   | |  | ||| |        |||||       |||||| ||||| || || || ||||| || || ||||||||  | |||||||| ||| ||||||| ||||| |||||||| || ||||||||||||||||| |
ttgatgatgaaaatatggtcgatattcgtcttttgtttatcaagtatggtcagagtattagtgatgtacttgttactgaacactatcctgtgtgtgacagGGTTACGTGGTGTATCGCGTCCGCGTACGCCGCGGGGGTAGGAAGAGGCCTGTTGCCAAGGGTATTGTGTATGGAAAACCTAAGAACCAGGGTATCACAC

upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S34_445V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------gtaaaatttctcctttcttcgtgtgtgctagctctttgatcgtttcgtgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC
                                      |   |||| |   |||   | |  | |||  |||   ||    ||||  | |  |  |   |||| || || || || || ||||| ||||| || || ||| | |||||||||||| ||||||| ||||| ||||||||||| |||||||| ||||| || |
tcaacatcagctcgccaaggttaaatatttacttaacatggtatttgttgattccatgcg-attctaattctgacatatcatcgttgtggtcttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCTAAGAACCAAGGTATTACAC

upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S152_141V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------gtaaaatttctcctttcttc--gtgtgtgctagctctttgatcgt----ttcgtgctcgaatcct-cacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC
                              |  ||||  || |   |||  |||| | ||     | |  || |    || |||     ||| |    ||||||| || || ||||||||||| || || || || ||| | |||||||||||  | ||||| ||||| |||||||| || |||||||||||||| || |
gtcatgactctatctttttagggcatcatttcgaattcttcataatttcaagtgtttactcctgttctactcttgacattggtgtcattatcttgtgtagGGATATGTGGTGTACCGTGTCCGCGTTCGCCGTGGAGGCAGGAAGAGGCCAGTGGCGAAGGGTATTGTGTATGGAAAACCTAAGAACCAGGGTATTACAC

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: 44

CGTCCGCTGCTGGGAGTATCGCCAGCTCCCCGGAATCGTCCGTATCCAGCGCCCGACGCGCCCTGACAAGGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcctttcttcgtgtgtgctagctctttgatcgtttcgtgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC
                        ctttgat  putative branch site (score: 44)
                                              tcctcac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatttctcctttcttcgtgtgtgctagctctttgatcgtttcgtgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC