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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttcagcaatgccgctctccccttctgctctgatttgattcttccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGGGAGTTAGCAGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA

Basic information

species Selaginella moellendorffii
transcript EFJ31038
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31038 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os03g38000.1 (Oryza sativa), 3'ss of exon 1
-----------------------gttt--gttcag--caatgccgctctccccttctgctctgatttgattcttccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGGGAGTTAGCAGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA
                       ||||   |||    | || |   ||||| |         | |||  ||| |  |||||||   |||||||||||||||||| ||||| |||||| | || ||||||||| | || ||||| || ||||| |||||||||||||| || || ||||
gtacggtgcagatccctcgcagggtttcgattcgattcgattcgattctcctcgatctgatggtttttgttcatgtagTTCGTGAGCGATGGCGTGTTCTACGCGGAGCTGAACGAGATGCTGACGCGGGAGCTGGCCGAGGACGGCTACTCCGGCGTGGAGGTGCGCGTGACGCCGA

upper sequence: EFJ31038 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G074300_T04 (Zea mays), 3'ss of exon 1
---------------------gtttgttcagcaatgccgctctccccttc------tgctctgatttg-attctt----ccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGGGAGTTAGCAGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA
                     ||      | ||   |  ||| ||||| |       | |||||  ||   ||||      ||||||||  ||| ||||||||||||||||||||||| ||| | || ||||||||| | || ||||| || ||||| |||||||||||||| ||||||||||
gtacgcgagctcctcctaaacgtagcgctaccagcccttctcccccctgcgtcgatggatctgacctgtgctcttgtccgtagTTCGTCAGCGACGGCGTGTTCTACGCCGAGCTCAATGAGATGCTGACGCGGGAGCTCGCGGAGGACGGCTACTCCGGCGTGGAGGTGCGCGTCACACCGA

upper sequence: EFJ31038 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G099352_T06 (Zea mays), 3'ss of exon 1
----------gtttgttca--gcaatgccgctctccccttc-tgctctgat----ttgat------------tcttccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGGGAGTTAGCAGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA
          | ||  | |  ||| |||  | ||||||  | |||   |||     |||             | ||  ||||||||  ||| || || ||||||||||||||||| ||| | || ||||||||| | || ||||| || ||||| |||||||||||||| ||||| ||||
gtacgcgagcgcttcctaaccgcagtgctcccctcccccccgtgcgtcgatggatctgacctcggtgctcggttttgtagTTCGTCAGCGACGGTGTTTTCTACGCCGAGCTCAATGAGATGCTGACGCGGGAGCTGGCGGAGGACGGCTACTCTGGCGTGGAGGTGCGCGTCACGCCGA

upper sequence: EFJ31038 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA09G28440.1 (Glycine max), 3'ss of exon 1
---------------------------------------------gtttgttcagcaatgccgctctccccttctgctctgatttgattcttccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGGGAGTTAGCAGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA
                                              | ||||    | ||   || |    ||      || | | | | | | |||| || || ||||| ||||||| |||||| || |||||| |||| || || ||||| || ||||| || ||||| |||||||||||  | || || ||||
gtcagtggtacaatgaatctatgaatttttattttattttttctattgtgtttgaaagtgaaactgtaaa-ttgaatagtgttattaatgtgc-agTTTGTGGCGGATGGAGTGTTCTTCGCCGAACTGAACGAGGTTCTGACACGTGAGTTGGCGGAGGACGGTTACTCCGGCGTGGAGGTTAGGGTTACGCCGA

upper sequence: EFJ31038 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: EDP07493 (Chlamydomonas reinhardtii), 3'ss of exon 1
--------------------------------------------------gtttgttcagcaatgccgctc--tccccttctgctctgatttgattcttc---cagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGGGAGTTAGCAGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA
                                                    |||    |  | |  |||   ||  | | | || |   |  ||    |   |||||||||   || |||||||||||||||||||| |||||||| || || || ||| | || |||||||| ||||| || |||||||| || || || || |
gtaggccaggcttctgaatatgttgcggctgtgagcgcgggcggccggccccttgcgaggacaggtggctaagtctacgtattctattgctccatgtgccacacagTTCGTCCAGGACGGCGTGTTCTACGCCGAGCTGAACGAGCTCCTGACCCGCGAGCTGGCCGAGGATGGCTACTCCGGTGTGGAGGTCCGCGTGACCCCCA

upper sequence: EFJ31038 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S136_175V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------------------------------------gtttgttcagcaatgccgctctccccttctgctc-tgatttgattcttccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGGGAGTTAGCAGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA
                                                                              || |    ||| | ||  |    |||| || |  || |     || | ||||| || || || || || |||| ||| |||||||||||||||||||| || ||| | || || ||||| ||||| |||||||||||||||||||| || |
gtgagagaattctatttggttgggagaggagtttggagttctggtgaaatgtaagtagaatcatgcacgagctcttacttcgagatgcacttcccttactgccttgtgtttgtggtcgcgctcgtgcagTTTGTAGCAGACGGAGTTTTCTTCGCTGAGCTCAACGAGCTTCTCACCCGCGAGCTCGCTGAAGATGGTTACTCTGGCGTGGAGGTGCGTGTCACCCCCA

upper sequence: EFJ31038 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S41_146V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------------------------gtttgttcagcaatgccgctc--tccccttctgctctgatttgattcttccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGGGAGTTAGCAGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA
                                                                  ||  |||   ||   | | |  |  | || ||   || | |   |||| |||||||| || || || || |||| |||||||||||||||||||||||| |||||  | || |||||||| ||||| ||||| || ||||| || || || |
gtgaggctatctcgttttgtggaggttttccaggctcgtgttgatttgctctattctggcacggccttgcttctagaagctcacacagttgcattgtgggttggtctttgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGGGAACTTGCCGAGGATGGCTACTCCGGCGTTGAAGTGCGCGTGACCCCCA

upper sequence: EFJ31038 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S454_3V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------gtttgttcagcaatgccgctctccccttctgctc--tgatttgattcttc-----cagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGGGAGTTAGCAGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA
                             | ||   |||||           || ||||   |  | || || |||     |||||||| || ||||| || ||||  || ||||| |||||||||||||| |||||| | || || ||||| ||||| |||||||| ||||| ||||| || |
gtgtgtgtgtagccattgttccccgctcatttttgccaatgggttgggatttttttgcttattattctgttttttcatgagcagTTCGTAGCGGATGGAGTCTTCTTTGCGGAGCTGAACGAGCTTCTCACCCGGGAGCTTGCTGAAGATGGGTACTCTGGCGTGGAAGTGCGCGTCACTCCCA

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|169103364|gb|FE507341.1|FE507341
EST:     GGCATGGCGACTCAGATCAGCAAGAAGAGAAAG                         TTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGG
genomic: GGCATGGCGACTCAGATCAGCAAGAAGAGAAAGgtttgttcag ... attcttccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGG
EST: gi|169065994|gb|FE473778.1|FE473778
EST:     ACGGCTAGGGCTTTGGCGGCATGGCGACTCAGATCAGCAAGAAGAGAAAG                         TTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGG
genomic: ACGGCTAGGGCTTTGGCGGCATGGCGACTCAGATCAGCAAGAAGAGAAAGgtttgttcag ... attcttccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGG
EST: gi|169098880|gb|FE502277.1|FE502277
EST:     CTAGGGCTTTGGCGGCATGGCGACTCAGATCAGCAAGAAGAGAAAG                         TTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGG
genomic: CTAGGGCTTTGGCGGCATGGCGACTCAGATCAGCAAGAAGAGAAAGgtttgttcag ... attcttccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGG
EST: gi|169068032|gb|FE476399.1|FE476399
EST:     ATGGCGACTCAGATCAGCAAGAAGAGAAAG                         TTCGTCGCCGATGGAGTGTTCTACGCCGAGCTCAATGAGCTTCTCACGCGG
genomic: ATGGCGACTCAGATCAGCAAGAAGAGAAAGgtttgttcag ... attcttccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGG
EST: gi|169072226|gb|FE479358.1|FE479358
EST:     CTAGGGCTTTGGCGGCATGGCGACTCAGATCAGCAAGAAGAGAAAG                         TTCGTCGCCGATGGAGTGTTCTACGCCGAGCTCAATGAGCTTCTCACGCGG
genomic: CTAGGGCTTTGGCGGCATGGCGACTCAGATCAGCAAGAAGAGAAAGgtttgttcag ... attcttccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGG

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

GGCATACTGCATAATAATTTGTCAAAAGCCCTAGAAGAGCCCTAATTAGGACGGCTAGGGCTTTGGCGGCATGGCGACTCAGATCAGCAAGAAGAGAAAGgtttgttcag ... attcttccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGGGAGTTAGCAGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgttcagcaatgccgctctccccttctgctctgatttgattcttccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGGGAGTTAGCAGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA
                                                 ttcttcc  CT-rich tract
                                        atttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttcagcaatgccgctctccccttctgctctgatttgattcttccagTTCGTCGCCGATGGCGTGTTCTACGCCGAGCTCAACGAGCTTCTCACGCGGGAGTTAGCAGAGGATGGATACTCGGGCGTGGAGGTGCGTGTCACACCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG