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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtattacacttaagtgcttctttgccgttgtcctctttgaaactctaaagaatctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG

Basic information

species Selaginella moellendorffii
transcript EFJ35508
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 2
---------------------gtacgtattacac-ttaagtgcttctttgccgttgtcc---tctttgaaactctaaagaatc-tatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
                      |   || ||| |  ||| | |   |||    || |     |  |||      || | | |  | ||  |   || |||||  | || ||||| ||  | ||||||||| | || |||||||||||||||||||||| ||| |||||| | ||||| || |||
atatttctagcaactctgataatttttactactcgctaattacgagtttattattttgtgaattattgcctaattacatacttatttctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG

upper sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os01g36950.3 (Oryza sativa), 3'ss of exon 2
---------------------gtacgtattacac-ttaagtgcttctttgccgttgtcc---tctttgaaactctaaagaatc-tatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG----------------
                      |   || ||| |  ||| | |   |||    || |     |  |||      || | | |  | ||  |   || |||||  | || ||||| ||  | ||||||||| | || |||||||||||||||||||||| ||| |||||| | ||||| || |||                
atatttctagcaactctgataatttttactactcgctaattacgagtttattattttgtgaattattgcctaattacatacttatttctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAGGTACCATTGATCTTCA

upper sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM5G860590_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------------------------------------------------------gtacgtattacacttaagtgcttctttgccgttgtcctctttgaaactctaaagaa--------------tctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
                                                                                                   | |  | |||   || | | | |  |||  |||      | | |||    || |                |||||    | ||  |||||  |||| || ||||| |||||||||||| || | || ||||||||||||||||||| ||| |||||  | ||||| ||||||
gtgaggtccaaactatacctactctactctactcttttgtgtttatcatcatcatcattattactcgatcagtcgtatgcatatgattccatcatttcagcatct-ttatctttcaat-catgcttgtggttactaaatataaaaaaagaagggggaaatttctcatcgtctatgggacgaacgcagGCTGCAAGCTTCGGAGGATCCAACATCGATCCAGCAGCTTGGGAGGACAAGAAGTGCCCCGGCGAGTCCCGCTTCCCTGCTCAG

upper sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM5G860590_T02 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------------------------------gtacgtattacacttaagtgcttctttgccgttgtcctctttgaaactctaaagaa--------------tctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
                                                                                              | |  | |||   || | | | |  |||  |||      | | |||    || |                |||||    | ||  |||||  |||| || ||||| |||||||||||| || | || ||||||||||||||||||| ||| |||||  | ||||| ||||||
gtccaaactatacctactctactctactcttttgtgtttatcatcatcatcattattactcgatcagtcgtatgcatatgattccatcatttcagcatct-ttatctttcaat-catgcttgtggttactaaatataaaaaaagaagggggaaatttctcatcgtctatgggacgaacgcagGCTGCAAGCTTCGGAGGATCCAACATCGATCCAGCAGCTTGGGAGGACAAGAAGTGCCCCGGCGAGTCCCGCTTCCCTGCTCAG

upper sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AC207342.3_FGT008 (Zea mays), 3'ss of exon 2
-----------------------gtacgtattacacttaagtgcttctttgccgttgtcctctttgaaactctaaagaatctatcaatccaatc--cagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
                       |   |       || |  ||| | ||   | |  ||  | |  |  |||| | | |||      ||| |||  |||||  | || || || ||  ||||||||||  | || |||||||||||||||||||||| ||| |||||| | ||||| || |||
gtacggtacagtacattacagtagccagccaattcctgatttgccttttcatcttcatctgcatctatgctctcatggatccggt--tccgatcaccagGCCGCCAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG

upper sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G071154_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------------------gtacgtattacact-taagtgcttctttgccgttgtcctctttgaaactctaaagaatctatcaatccaat--ccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
                                                                | | |  | | || |   ||||||||   ||||  |    || |         |  ||      ||| ||  ||||||  | || || || ||  ||||||||||  | || |||||||||||||||||||||| ||| |||||| | || || || |||
gtacagtacagcacagcacagcacagtagccactagccagttcgtggttccctttccttgcttcttcttcgttcgctgtccttgcttcttcttcgttcgctgtattcacgaggacccggttccgatcctccgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG

upper sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA20G16100.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------------------------------------------gtacgtattacacttaagtgcttctttgccgttgtcctctttgaaact--ctaaagaatctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
                                                                                                    |   | ||||  |||   |||    |    ||     |  | | | |   ||||   |   |        | |||||  ||||||||||||| ||||| || ||| |||| || |||||||||||||||||||  || || ||  | ||||| ||||||
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG

upper sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA20G16100.3 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------------------------------------------gtacgtattacacttaagtgcttctttgccgttgtcctctttgaaact--ctaaagaatctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG----------------
                                                                                                    |   | ||||  |||   |||    |    ||     |  | | | |   ||||   |   |        | |||||  ||||||||||||| ||||| || ||| |||| || |||||||||||||||||||  || || ||  | ||||| ||||||                
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGGTATATATCATCTCAT

upper sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv02s0025g01720.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------------------------gtacgtattacacttaa-gtgcttc-tttgccgttgtcctctttgaaactctaaagaatctatcaatccaat--ccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
                                                                   |  ||||| | | ||  | |  |  ||   ||| |    | || | |  ||   ||| |   | |   ||   |||||  |||| ||||||||  | ||||| ||| ||||||| |||||||||||||||||||  || || ||  | ||||| ||||||
gtttgtatttctttctaagaatcataaactctgcagtaattcatgtattcttttggggttttctcaaaaatattagattcaatattcagcacttcatgttttggattatgcaccattacctaatgttatacttgtatgttcagGCTGCAAGCTTTGGAGGAACAAACATTGATCCAACTGCTTGGGAGGACAAGAAGTGCCCTGGCGAATCACGCTTCCCTGCTCAG

upper sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S6_446V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------gtacgtattacac---ttaagtgcttctttgccgttgtcctctttgaaactctaaagaatctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
                          | |  |  ||| |   |  | ||       |  |   |  |  |  || |||   |||| |  |   ||  ||  ||||  |||| ||||||||||||||||| ||| |||| || ||||| |||||||||||||||||||| || ||||| || || |||
tgatacatgacagagcagtagttaccgcatttgctacgcgcttcgaatgtaaagaagatgaaattatgatacaatctcatgagaaacagt--gtctgatt-agGCTGCAAGCTTTGGAGGCTCCAACATAGATCCAACAGCTTGGGAAGACAAGAAGTGCCGCGGAGAATCAAGATTTCCTGCACAG

upper sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S4_323V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------gtacgtatt---acacttaagtgcttctttgccgttgtcctctttg-aaactctaaagaat----ctatcaatc--caatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
                | ||||  |   ||   |  ||| |     |   |||        | |   ||| | | ||     |  || ||   |   |||||| |||||||||||||||| ||||| ||| |||| || ||||| |||||||| || || |||||||| ||||| || || |||
caaggaggacctacttggacgtcctctgacctgtgggtggtgtcaaggacttgcttcagacgtaggttctcatgtatggtgtttacattctgtatgacagGCAGCAAGTTTTGGAGGCTCTAACATAGATCCAACCGCCTGGGAAGACAAGAAATGTCGGGGAGAGTCAAGATTTCCTGCCCAG

upper sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S168_104V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------gtacgtattacacttaagtgcttctttgccgttgtcctctttgaaactctaaagaat-ctatcaatc--caatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
                          |  | | |   |  || | |   ||    |  ||   | |||    |||| | ||    ||| ||   |   |||||| |||||||||||||||| ||||| ||  |||| || ||||| |||||||| || || ||||| |||||||| || ||||||
gagaagcaaggaagatcaatttcaacatctgtgaggttgtag-gatgtattatattcttctggtatgaggtgctaatgcatgtcgtcattctttatgacagGCAGCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG

upper sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 3
--------------------gtacgtattacacttaagtgcttctttgccgttgtcctctttgaaactctaaagaatct-atcaatcc--aatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
                      |  | | |   |  || | |   ||    |  ||   | |||    |||| | || |  ||| ||   |   |||||| |||||||||||||||| ||||| ||  |||| || ||||| |||||||| || || ||||| |||||||| || ||||||
agcaaggaagatcaatttcaacatctgtgaggttgtag-gatgtattatattcttctggtatgaggtgctaatgcatgtcgtcattctttatgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttctttgccgttgtcctctttgaaactctaaagaatctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
                           ctctaaa  putative branch site (score: 3)
                              taaagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtattacacttaagtgcttctttgccgttgtcctctttgaaactctaaagaatctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA