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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattgagcgccctctctcctttagttgccggattgaatcactggtccattgcttttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT

Basic information

species Selaginella moellendorffii
transcript EFJ31249
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os08g44380.2 (Oryza sativa), 3'ss of exon 3
----------------------------------gtaagattgagcgccctctctcctttagttgccggattgaatcactggtccattgcttttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
|| || | | |||| | | | | | | | ||| |||| || ||| |||||| |||||||| || || |||||||||||| | |||| || |||||||||||||||||||||||||| ||||||||||| || ||||||||||| ||||
ggatttttctctctgtaatatctgtctttattctgtctaatggtactgtttctccctaattttcttcctactaacatgctgcaccatggcattt--aaacagGCTGAGAAGATTGGGCTCGACTACATGGATGTTGAGGCCCTTAAGAAGATGAACAAGAACAAGAAGCTTGTGAAGAAGCTTGCCAAGAAGTACCATGCTT

upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os08g44450.1 (Oryza sativa), 3'ss of exon 2
-------------------------gtaagattgagcgccctctctcctttagttgccggattgaatcactggtcca-ttgct---------tttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
|| | | || | | | | || | | ||| | | | | | | ||||| | || ||||| |||||||| || || |||||||||||| | |||| || ||||| |||||||||||||||||||| || |||||||| || ||||||||||| ||||
ctgaaattaagaatgttcacacgttgtttg-tggatcaatttattctgtctaatga--gaatttatttatctgccaacttgctgcggattggctcgtgtgcagGCTGAGAAGATTGGGCTTGACTACATGGATGTTGAGGCTCTTAAGAAAATGAACAAGAACAAGAAGCTGGTTAAGAAGCTTGCCAAGAAGTACCATGCTT

upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os01g64090.1 (Oryza sativa), 3'ss of exon 3
--------------------------gtaagattgagcgccctctctcctttagttgccggat--tgaatcactggtccattgct----tttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
| | || || | | ||| | | | | || || | || || | | ||| ||||| ||||| || || || ||||| |||||| |||| | || |||||||||||||| ||||||||||| || |||||||| |||||||| || |||||||
cgaaaatcaggaataccttcttccatggagtgttccatgctatttgccctgcatacggatgctgatgtttcttttctctgttaccaatgctattgtgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCTCTCAAGAAGATGAACAAAAACAAGAAGCTGGTTAAGAAGCTTGCAAAGAAATATCACGCTT

upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os02g21660.1 (Oryza sativa), 3'ss of exon 3
------------------------gtaagattgagcgccctctctc----ctttagttgccggattgaatcactggtccattgcttttttg----cacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
| | || || | || || | || | | ||| | | | ||||| ||||| ||||| || || || ||||| |||||| |||| | || ||||| |||||||| ||||||||||| || |||||||| |||||||| || || ||||
tgatggcatatggaaatttgtattcttgagtgtagtgctcattcatcggactattaatgtctggctgataattctatatgctacaattttgggtctgcagGCAGAGAAAATGGGCCTAGACTATATGGATGTGGAAGCCCTCAAGAAAATGAACAAAAACAAGAAGCTAGTTAAGAAGCTTGCAAAGAAATATCATGCTT

upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G023748_T01 (Zea mays), 3'ss of exon 3
-----------------gtaagatt---gagcgccctctctcctttagttgcc---ggattgaatcactggtcc-------attgcttttttgca--cagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
| | || || | | | | || |||||| | |||| | | || | | || | || | |||| |||| || ||| | ||| | |||||| |||| | || |||||||||||||| ||||||||||| |||||||||||||||||||||||||| ||||
atatagtataactctccatgaaatcaacaagtgtcggtaatgccttggttgcctttgttttgatatatttgttctaatgatggtactatgctgtatgtagGCAGAGAGAATAGGTATAGACAATATGGATGTGGAAGCCCTCAAGAAGATGAACAAAAACAAGAAGCTAGTGAAGAAGCTGGCAAAGAAGTACCATGCTT

upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G023748_T02 (Zea mays), 3'ss of exon 3
-------------gtaagatt---gagcgccctctctcctttagttgcc---ggattgaatcactggtcc-------attgcttttttgcac--agGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT----
| | || || | | | | || |||||| | |||| | | || | | || | || | |||| |||| || ||| | ||| | |||||| |||| | || |||||||||||||| ||||||||||| |||||||||||||||||||||||||| ||||
agtataactctccatgaaatcaacaagtgtcggtaatgccttggttgcctttgttttgatatatttgttctaatgatggtactatgctgtatgtaggcagAGAGAATAGGTATAGACAATATGGATGTGGAAGCCCTCAAGAAGATGAACAAAAACAAGAAGCTAGTGAAGAAGCTGGCAAAGAAGTACCATGCTTTCCT

upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G144387_T01 (Zea mays), 3'ss of exon 3
-------------------------------gtaagattgagcgccctctctcctttagttgccggattgaatcactggtccattgcttt-tttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
||| | || | | ||| | | | | | | ||||| | | |||||||||||||| || || |||||||||||| | |||| || ||||| |||||||||||||||||||| || |||| ||| || ||||||||||| ||||
actgtatggaagtttgagagcttttgcccagataatgtcatgcactgtttctatctggatcaactcttcctcactcaaaaccattttactgcatttgcagGCCGAGAAGATGGGACTTGACTACATGGATGTTGAGGCTCTCAAGAAAATGAACAAGAACAAGAAGCTTGTTAAGAGGCTTGCCAAGAAGTACCATGCTT

upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G369991_T01 (Zea mays), 3'ss of exon 2
-------------------------------gtaagat-tgagcgccctctctcctttagttgccggattgaatcactggtccattgcttttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
|| || || ||||| || | | | | ||| | || | | | ||||| |||||||| || || |||||||||||| | |||| || ||||| |||||||||||||||||||| || |||||||| || ||||||||||| ||||
ctgcatggaagattgaaagttttgctaagatatataatgcaagtgcccttcctatctggatcaacttttccccacacaaaccattttactgcattctcagGCTGAGAAGATGGGACTTGACTACATGGATGTTGAGGCCCTCAAGAAAATGAACAAGAACAAGAAGCTTGTTAAGAAGCTTGCCAAGAAGTACCATGCTT

upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G181194_T01 (Zea mays), 3'ss of exon 3
----------------------------gtaagat----tgagcgccctctctcctttagttgccggattgaatcactggtccattgcttttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
|||||| || ||||| || | | | | ||| | || | | | ||||| |||||||| || || |||||||||||| | |||| || ||||| |||||||||||||||||||| || |||||||| || ||||||||||| ||||
tcaactgcatggaagattgaaagttttgctaagataatgcaagtgcccttcctatctggatcaacttttctccacacaaaccattttactgcattctcagGCTGAGAAGATGGGACTTGACTACATGGATGTTGAGGCCCTCAAGAAAATGAACAAGAACAAGAAGCTTGTTAAGAAGCTTGCCAAGAAGTACCATGCTT

upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G074769_T01 (Zea mays), 3'ss of exon 2
-------------------------------gtaagat-tgagcgccctctctcctttagttgccggattgaatcactggtccattgcttttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
|| || || ||||| || | | | | ||| | || | | | ||||| ||||||| || || |||||||||||| | |||| || ||||| |||||||||||||||||||| || |||||||| || ||||||||||| ||||
ctgcatggaagattgaaagttttgctaagatatataatgcaagtgcccttcctatctggatcaacttttccccacacaaaccattttactgcattctcagGCTAAGAAGATGGGACTTGACTACATGGATGTTGAGGCCCTAAAGAAAATGAACAAGAACAAGAAGCTTGTTAAGAAGCTTGCCAAGAAGTACCATGCTT

upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G170561_T01 (Zea mays), 3'ss of exon 4
----------------------------gtaagat----tgagcgccctctctcctttagttgccggattgaatcactggtccattgcttttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
|||||| || ||||| || | | | ||| | || | | | ||||| |||||||| || || |||||||||||| | |||| || ||||| |||||||||||||||||||| || |||||||| || |||| ||||| ||||
tcaactgcatggaagattgaaagttttgctaagatgatgcaagtgcccttcctatctggatcaactttcccccacacaaaccattttactgcattctcagGCTGAGAAGATGGGACTTGACTACATGGATGTTGAGGCCCTCAAGAAAATGAACAAGAACAAGAAGCTTGTTAAGAAGCTTGCCGAGAAATACCATGCTT

upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM5G862017_T01 (Zea mays), 3'ss of exon 9
----------------------------gtaagat----tgagcgccctctctcctttagttgccggattgaatcactggtccattgcttttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
|||||| || ||||| | | | | | ||| | || | | | ||||| |||||||| || || |||||||||||| | |||| || ||||| ||||||| |||||||||||| || |||||||| | ||||||||||| ||||
tcaactacatggaagattgaaagttttgctaagataatgcaagtgcccttcttatctggatcaacttttccccacacaaaccattttactgcattctcagGCTGAGAAGATGGGACTTGACTACATGGATGTTGAGGCCCTCAAGAAAATGAACAGGAACAAGAAGCTTGTTAAGAAGCTTGTCAAGAAGTACCATGCTT

upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT1G08360.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------gtaagattgagcgccctctctcctttagttgccggattgaatcactggtccattgcttttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
|| || || | | ||| || || ||| | | || ||| | ||| | |||| |||||||| || |||| |||||||| | ||| || || ||| | |||||||||||||| ||||| |||||||| |||||||| ||||| ||||
tgtagatgcatgatgttttcggaatttggtcattgtttatttaggcttcatttcttgcataattaaatatttgcttatttcatc--ttgtatcttttcgtagGCTGAGAAGATGGGGTTGGAAAACATGGATGTTGAGTCTCTAAAAAAGCTTAACAAGAACAAGAAACTCGTCAAGAAGCTTGCAAAGAAATACCATGCTT

upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv08s0007g03340.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------gtaagattgagcgccctctctcctttagttgccggattgaatcactggtccattgcttttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
|| | | | | | | | || | ||| || | | ||| | | ||| ||| |||||||| || | || ||||||||| |||| |||||||| ||| | || ||||||||||| || || |||||||| || ||||||||||| ||||
tattccccttagaatttcagagtcatcttttacagttgaagtatgagttgtatatagcttttctctttgatgtaacatttccctcgttgttaactggca--gGCAGAGAAGATAGGATTAGAGTACATGGATGTGGAAGGGCTGAAAAAGCTCAATAAGAACAAGAAACTGGTCAAGAAGCTTGCCAAGAAGTACCATGCTT

upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv06s0080g00400.t01 (Vitis vinifera), 3'ss of exon 5
----------------gtaagat--tgagcgc-cctctctcctttagttgccggattgaatcactggtccatt--gcttttttgc-----------acagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
|||||| | | | || | |||| || | ||| | | | | || | || |||| |||||| || ||||| || |||| ||||||||| |||| ||||| || ||| |||||||||||||||| || || ||||| || || ||||| ||||| || |
gtacctttattccagcttaagattttaattgagtcttatttatttattttttgcattagtttgttctttccttaaggttgtttgttaaattaaattacagGCAGAAAAGATAGGCTTGGAATACATGGATGTGGAAGGGCTAAAAAAGCTGAACAAGAACAAGAAACTGGTCAAGAAACTTGCCAAGAAATACCATGCCT

upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S427_1V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------------------------------------------------------gtaagattgagcgccctctctcctttagttgccggat--tga-atcactggtccattgcttttttg------cacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
|| | | | | |||| | || | | | ||| || || || | | ||||||| |||| ||| | || | ||||||| | ||| | ||||||||||||||||||||||||| || |||||||||||||| ||||||||||||||||
gtatgcttattctcaaattttgattctttctatttgttgatggtgccagaaattgaataaaacattgtagaattttctgctctgggtctcatctcactggcctttgtatattaaaactagaaattatcaccctttacttgataatggataattgctgatgtcgtgagtttcttttggtcgtaactcgtcacagGCGACCAAGAATGGTATCGAGTGCATGGATGTCGAGAGCTTGAAGAAGATGAACAAGAACAAGAAACTTGTGAAGAAGCTGGCTAAGAAGTACCACGCTT

upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S18_121V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------gtaagattgag-cgccctctctcctttagttgccggattgaatc--actggtccattgcttttttgc---acagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
| | ||| | | | | | | || | | |||| || | | | | | || |||| ||||||| | ||||| || |||| |||||||| | ||| | ||||||| ||||||||||||||||||||||||||||| ||||| ||||||||||||||||
gtatttcctctaactcaactaatgccacccatgttgagaagcattttgtcagcatgccacattacgcaggttgattacctcttatttattcgccccattattgcgtaacagGCCAACAAGATGGGCATGGAATACATGGACGTCGAGAGCTTGAAGAAAATGAACAAGAACAAGAAGCTCGTGAAGAAACTGGCGAAGAAGTACCACGCTT

upper sequence: EFJ31249 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S40_297V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------gtaagattgagcgccctctctcctttagttg--ccggattga------atcactggtccattgcttttttgc--acagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
| || | | || ||||| | | |||| | || || ||| | | | || | |||| | || |||||| |||| ||||||||| | ||| | ||||||||||||||||||| ||||||||||| ||||||||||| ||||||||||| ||||
gtcatattcgcacattggaataatttttgccttcatatttgtttcatttttagattatcttgattaatgtctcatttcttaaccaacgttcatctgacaatagGCAAACAAAATCGGTATGGAATACATGGATGTTGAGAGCTTGAAGAAGATGAACAAGAATAAGAAGCTCGTCAAGAAGCTGGCTAAGAAGTACCATGCTT

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: 24

GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaagattga ... ttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctctctcctttagttgccggattgaatcactggtccattgcttttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT
                                   tccattgctttttt  CT-rich tract
 tttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattgagcgccctctctcctttagttgccggattgaatcactggtccattgcttttttgcacagGCCGAGAAGATCGGTCTGGACTACATGGATCTGGAGGGGCTGAAGAAGATGAACAAGAACAAGAAGCTCGTGAAGAAGCTGGCAAAGAAGTACCACGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT