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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtttggcgcagcgttttgcctgcttgatttcttctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA

Basic information

species Selaginella moellendorffii
transcript EFJ09763
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ09763 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G030915_T07 (Zea mays), 3'ss of exon 1
-----------------------gtaagtgtttggcgcagcgttttgcctgcttgatttctt-ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA
                          |||  ||        | || |   | ||| |||||| ||||   |  ||  ||  || |   |  |  |    | |||    |  | ||   ||| ||  |   | |  |   ||| || | |||                      
gttagtttgcttgcctgttatatcccagttcttcagatctagcttgggtcgattgctttctttctttatccgttgctgatgctgttgtgtggttg---cgatacttcttttatgcagCGTCGACCCTTTCTCTAAGAAGGATTGGTATGACA---------------------

upper sequence: EFJ09763 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G030915_T05 (Zea mays), 3'ss of exon 2
gtaagtgtttggcgcagcgttttgcctgcttg-atttcttctttcct-cagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA------
                      ||| || |||  || |||||||  | ||| |||||||||||||| |||||||||||||| ||  |||||||   |||    |||| ||| ||  | ||||||||||| || ||  | || || |||||       
----------------------tgcgtggttgcgttacttcttttatgcagcgtcgaccctttctctaagaaggattggtatgacatcaaggcaccgtcggtgttcagtgtgcgcaacatcgGGAAGACTCTCGTATCCAGGACACAGGGTACCAGG

upper sequence: EFJ09763 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G030915_T08 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------gtaagtgtttggcgcagcgttttgcctgcttgatttcttctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA
                                                                    |  ||   ||  || |     ||  ||| | | ||||| | | |  || |||||||||||||| |||||||||||||| ||  |||||||   |||    |||| ||| ||  | ||||||||||| || ||  | || || ||||| 
gttagtttgcttgcctgttatatcccagttcttcagatcttacttgggtcgattgctttctttctttatccgttgctgatgcggttgcgtggttgcgttacttcttttatgc--agCGTCGACCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGT

upper sequence: EFJ09763 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G030915_T04 (Zea mays), 3'ss of exon 1
-----------------------------------------------------gtaagtgtttggcgcagcgttttgcctgcttgatttcttctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA
                                                      |  ||   ||  || |     ||  ||| | | ||||| | | |  || |||||||||||||| |||||||||||||| ||  |||||||   |||    |||| ||| ||  | ||||||||||| || ||  | || || ||||| 
ctgttatatcccagttcttcagatcttacttgggtcgattgctttctttctttatccgttgctgatgcggttgcgtggttgcgttacttcttttatgc--agCGTCGACCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGT

upper sequence: EFJ09763 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G030915_T05 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------gtaagtgtttggcgcagcgttttgcctgcttgatttcttctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA
                                                                    |  ||   ||  || |   | ||  |||  |||   |  |||   ||| |||||||||||||| |||||||||||||| ||  |||||||   |||    |||| ||| ||  | |||||                            
gttagtttgcttgcctgttatatcccagttcttcagatctagcttgggtcgattgctttctttctttatccgttgctgatgctgttgtgtggttgc--gatacttcttttatgcagCGTCGACCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGG----------------------------

upper sequence: EFJ09763 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G030915_T03 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------gtaagtgtttggcgcagcgttttgcctgcttgatttcttctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA
                                                                    |  ||   ||  || |   | ||  |||  |||   |  |||   ||| |||||||||||||| |||||||||||||| ||  |||||||   |||    |||| ||| ||  | ||||||||||| || ||  | || || ||||| 
gttagtttgcttgcctgttatatcccagttcttcagatctagcttgggtcgattgctttctttctttatccgttgctgatgctgttgtgtggttgc--gatacttcttttatgcagCGTCGACCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGT

upper sequence: EFJ09763 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G145258_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------gtaagtgtttggcgcagcgttttgcctgcttgatttcttctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA
                                                                    |  ||   ||  || |   | ||  ||| | |  || | | | |  || |||||||||||||| |||||||||||||| ||  |||||||   |||    |||| ||| ||  | ||||||||||| || ||  | || || ||||| 
gttagtttgcttgcctgttatatcccagttcttcagatcttgcttgtgtcgattgctttttttctttatccgttgctgatgcggttctgtggttgcgttacatcatttatgc--agCGTCGACCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGT

upper sequence: EFJ09763 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S80_120V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------------------------------------------gtaagtgtttggcgcagcgttttg-cctgcttgat--ttcttctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA
                                                                                ||  |||||||   |  ||  ||| |  |   ||   |      |    ||||||||| ||||||||||||||||||||||| ||  ||||||||     ||| ||||          | | |||||||| || ||||| || ||   ||| 
gtagcgctctccttctccttctctttacaggaatggctaattcgctgtcctgctgcgctggtttgagtttaggtttcgaggtttgtgtttgtttccacgcattgacgcggaggacggtgggatgtaatgcagTGTCGATCCTTTCTCGAAGAAGGATTGGTATGACATCAAGGCCCCCAACACCTTCACGCAGAAGTCGCTGGGGAAGACCCTGGTGACCAGGACCGCGGGT

upper sequence: EFJ09763 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S17_306V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------------------gtaagtgtttggcgcagcgttttgcctgcttgatttctt-----ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA
                                                          || |||  |||     |  || |||   |||||   | |        |   |||||||||||| ||||| |||||||| ||||| ||| |||||||      ||| ||||          | | |||||||| ||||| || |||||   ||| 
gtaacgtccgctggctgtctgagctctttacgacagtcgaatgtgtaatttcatttttgtgagttattga---gggtttctgctaacttgacgacgtgggagtggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACACCTTCACGCAGAAGTCGCTTGGGAAGACCCTTGTCACCAGAACCGCGGGT

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|169054227|gb|FE463168.1|FE463168
EST:     GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAAT                         TGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
genomic: GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAATgtaagtgttt ... ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
EST: gi|169098886|gb|FE502283.1|FE502283
EST:     AGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAAT                         TGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
genomic: AGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAATgtaagtgttt ... ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
EST: gi|169022541|gb|FE429425.1|FE429425
EST:     GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAAT                         TGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
genomic: GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAATgtaagtgttt ... ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
EST: gi|169020264|gb|FE430341.1|FE430341
EST:     GAAGAACAAGCGGATTTCCAAGGGAAAGAAAGGAGGCAAGAAGAAAAT                         TGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
genomic: GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAATgtaagtgttt ... ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
EST: gi|169051171|gb|FE460252.1|FE460252
EST:     GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAAT                         TGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
genomic: GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAATgtaagtgttt ... ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
EST: gi|169097436|gb|FE499022.1|FE499022
EST:     GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAAT                         TGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
genomic: GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAATgtaagtgttt ... ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
EST: gi|169104851|gb|FE508722.1|FE508722
EST:     GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAAT                         TGTCGACCCTTTCTCCAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
genomic: GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAATgtaagtgttt ... ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
EST: gi|169103249|gb|FE504821.1|FE504821
EST:     GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAAT                         TGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
genomic: GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAATgtaagtgttt ... ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
EST: gi|169055047|gb|FE462962.1|FE462962
EST:     GAAGAACAAGCGGATTTCCAAGGGAAAGAAAGGAGGCAAGAAGAAAAT                         TGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
genomic: GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAATgtaagtgttt ... ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
EST: gi|169065308|gb|FE473209.1|FE473209
EST:     GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAAT                         TGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
genomic: GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAATgtaagtgttt ... ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
EST: gi|169103251|gb|FE505629.1|FE505629
EST:     GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAAT                         TGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
genomic: GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAATgtaagtgttt ... ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
EST: gi|169033920|gb|FE441952.1|FE441952
EST:     GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAAT                         TGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
genomic: GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAATgtaagtgttt ... ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
EST: gi|169056009|gb|FE466185.1|FE466185
EST:     GGAAGAAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAAT                         TGTCGACCCTTTCTCCAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
genomic: GGAAG-AACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAATgtaagtgttt ... ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
EST: gi|169069101|gb|FE476740.1|FE476740
EST:     GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAAT                         TGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC
genomic: GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAATgtaagtgttt ... ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCAC

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), 35 (downstream exon)
Score: 59

GAAGAACAAGCGGATTTCCAAGGGAAAGAAGGGAGGCAAGAAGAAAATgtaagtgttt ... ctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtgtttggcgcagcgttttgcctgcttgatttcttctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA
                                 gcttgat  putative branch site (score: 59)
                         ttttgcctgcttgatt  CT-rich tract
                                   ttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtttggcgcagcgttttgcctgcttgatttcttctttcctcagTGTCGACCCTTTCTCGAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA