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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctcttgacatggatcgcagctccaagcaatgtttccagaggactaaaaacgttttgttcttgtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCCGGCGGCGTGCACCTGGAGATGACCGGGCAGAACGTCACCGAGTGCATCG

Basic information

species Selaginella moellendorffii
transcript EFJ24698
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24698 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os03g27230.1 (Oryza sativa), 3'ss of exon 4
--------------------------gtaagtctcttgacatggatcgcagctccaagcaatgtttccagaggactaaaaacgttttgttcttgtccatc-cagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCCGGCGGCGTGCACCTGGAGATGACCGGGCAGAACGTCACCGAGTGCATCG
                            || | |  |    || ||  |||  ||| ||||| | ||     ||||||  | |   |  | |  || ||  ||||||||| |   ||| |||||||| || || || || ||||||||||| || || || || ||||| |||||||| ||||||||||| |||||||||||||
aactgattgtttgacatgtaccttttaaaaatgttgtattctgcatt-caggcccatgcaat-tatcagactgactaatcatgagct--tgtaatctatgacagGCCGAGGTACGAGCATTCTTCGATGTGCATGATCAAGAAGGAAGCCACCCAGGAGGTGTCCACCTCGAGATGACTGGGCAGAACGTAACCGAGTGCATCG

upper sequence: EFJ24698 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os10g41480.1 (Oryza sativa), 3'ss of exon 4
--------------gtaagtctcttgacatggatcgcagctccaagcaatg--tttccagaggactaaaaacgttt-----tgttcttgtccat--ccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCCGGCGGCGTGCACCTGGAGATGACCGGGCAGAACGTCACCGAGTGCATCG
               |   |   ||||     | |  |  |   |   |||  | |       | | | | | |||     | ||||||| |||   |||  ||||||||  ||||||||||| || || || || || |||||| | || || ||  | |||||||||||||| ||||||||||| || |||||||| |
cctgagacttcaccattcatggtttgatgaacaactgacttattacacatgaatatttgacatattgacaccatttgtgtttattcttgtacatgtgcagTGCGAGCTGAGGGCTTTCTTCGATGTCCATGAGCAAGAGGGAAGCTACCCTGGAGGGATTCACCTGGAGATGACAGGGCAGAACGTTACAGAGTGCATTG

upper sequence: EFJ24698 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G365160_T02 (Zea mays), 3'ss of exon 4
-------------------gtaagtctcttgacat---ggatcgcagctccaagcaatgt--ttccagaggactaaaaacgttttgttcttgtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCCGGCGGCGTGCACCTGGAGATGACCGGGCAGAACGTCACCGAGTGCATCG
                    |   |||    ||||   |    |     ||||   ||    ||      ||||   | | |    | | | || | | |||| ||  ||   || |||||||| || || ||||| ||||||||||| || || ||||| ||||| || ||||| |||||||| || |||||||||||||
tttcactggggcatttacacttcatctaggaacattccgttctggcctcccaactgataccatttgctgtgactctgatcatgaactccatctctaac-agGCTGAAGTGCGTGCCTTCTTCGATGTGCATGACCAAGAAGGAAGCCACCCTGGGGGCGTCCACCTTGAAATGACTGGGCAGAATGTGACCGAGTGCATCG

upper sequence: EFJ24698 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G396212_T02 (Zea mays), 3'ss of exon 3
-------------gtaagtctcttgacatggatcgcagctccaagcaatgtttccagaggactaaaaacgttttgttcttgtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCCGGCGGCGTGCACCTGGAGATGACCGGGCAGAACGTCACCGAGTGCATCG
              |   ||| | ||| | |  | |  ||| || |||| |         ||   |  | |    |   | |   | ||||||||| |    || |||||||| || |||||||| || |||||||| || || || || ||||| ||||||||||| |||||||| ||||| ||||  |
gttcttcttctttcttcttctgtcgacgtcgtactc--ctcaaaccaatatgaatgtgatacaccatgcatgc-atatatatatttacagGCCGAGGTACGGGCCTTCTTCGATGTGCACGACCAAGAGGGAAGCCAGCCTGGAGGTGTCCACCTTGAGATGACCGGTCAGAACGTGACCGAATGCACGG

upper sequence: EFJ24698 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G117707_T02 (Zea mays), 3'ss of exon 4
---------------------gtaagtctcttgacatgg-atcgcagc--tccaagcaatgtttccagaggactaaaaacgttttgttcttgtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCCGGCGGCGTGCACCTGGAGATGACCGGGCAGAACGTCACCGAGTGCATCG
                      |   |||    ||||   ||    ||  |||||   ||        |   ||  || |||    | | | || | | |||| ||  ||   || ||||||||||| || || || |||||||| || || || ||| | ||||| || ||||| ||||||||||| ||||||||||| |
atttctactggagtgtttacacttgatctaggaacattccattctggccttccaactgataccataccattgctctaatcgtgaactccatatctaac-agGCTGAAGTGCGCGCATTCTTCGACGTGCATGATCAAGAAGGAAGTCACCCAGGAGGCATCCACCTTGAAATGACTGGGCAGAACGTGACCGAGTGCATTG

upper sequence: EFJ24698 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G155813_T01 (Zea mays), 3'ss of exon 3
---------------------gtaagtctcttgacatgg-atcgcagc--tccaagcaatgtttccagaggactaaaaacgttttgttcttgtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCCGGCGGCGTGCACCTGGAGATGACCGGGCAGAACGTCACCGAGTGCATCG
                      |   |||    ||||   ||    ||  |||||  |||   |    |   ||  || ||     | | | || |   |||| ||  ||   || ||||||||||| || || || |||||||| || || || ||| | ||||| || ||||| ||||||||||| ||||||||||| |
atttctactggagtgtttacacttgatctaggaacattccattctggccttccaactaataccttaccattgctctaatcgcgaactccatatctaat-agGCTGAAGTGCGTGCATTCTTCGACGTGCATGATCAAGAAGGAAGTCACCCAGGAGGCATCCACCTTGAAATGACTGGGCAGAACGTGACCGAGTGCATTG

upper sequence: EFJ24698 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA02G37080.1 (Glycine max), 3'ss of exon 4
--------------------gtaagtct--cttgacatggat---cgcagctccaagcaatgtttccagaggactaaaaacgttttgttcttgtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCCGGCGGCGTGCACCTGGAGATGACCGGGCAGAACGTCACCGAGTGCATCG
                    || ||| |   ||  ||   ||     || |    |  | |  ||   ||    | ||       |  | ||    |  ||||||||  ||| ||| ||||||||||| ||||| || ||||||||||| || || || || || || |||||||| || ||||| || ||||||||||| |
taactaaacacatcacgaaagtgagtttactttttcaaaaatacgttcaacatttaaaagtactttttgaaaggttaatcaaacatacttttaatta--cagGCCGAAGTGAGAGCATTCTTCGACGTACACGAGCAAGAAGGAAGCCACCCAGGAGGGGTTCATCTAGAGATGACGGGTCAGAATGTGACCGAGTGCATTG

upper sequence: EFJ24698 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT1G22410.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------gtaagtctcttgacatggatcgcagctccaagcaatgtttccagaggactaaaaacgttttgttcttgtc------catccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCCGGCGGCGTGCACCTGGAGATGACCGGGCAGAACGTCACCGAGTGCATCG
                   |   |   |  ||  | |  |||    |  |   | ||     |  | |  |||   | |  | ||          ||  |||| ||  ||| ||||||||||||||| ||||| || ||||| ||||| ||||| ||  | ||||| || ||||| || |||||||| |||||||||||||
gatttgaaaaaaataatcttggattagtatactagcaaagcaaaatcg-gttgttttcttgtattattgcaaatcatctaatgttaattgaaaatatatagGCTGAAGTGAGAGCTTTCTTCGACGTGCACGAGCAAGAAGGTAGCCACCCCGGAGGAATTCACCTAGAAATGACTGGTCAGAACGTGACCGAGTGCATCG

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|169055871|gb|FE466112.1|FE466112
EST:     CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGG                         GCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCC
genomic: CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGGgtaagtctct ... gtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCC
EST: gi|169116328|gb|FE517691.1|FE517691
EST:     CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGG                         GCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCC
genomic: CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGGgtaagtctct ... gtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCC
EST: gi|169050205|gb|FE459129.1|FE459129
EST:     CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGG                         GCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCC
genomic: CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGGgtaagtctct ... gtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCC
EST: gi|169075884|gb|FE483336.1|FE483336
EST:     CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGG                         GCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCC
genomic: CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGGgtaagtctct ... gtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCC
EST: gi|169032532|gb|FE439639.1|FE439639
EST:     CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGG                         GCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCC
genomic: CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGGgtaagtctct ... gtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCC
EST: gi|169071771|gb|FE477148.1|FE477148
EST:     CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGG                         GCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCC
genomic: CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGGgtaagtctct ... gtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCC
EST: gi|169018654|gb|FE427567.1|FE427567
EST:     CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGG                         GCCGAGCTGAAAGCCTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCC
genomic: CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGGgtaagtctct ... gtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCC
EST: gi|169075885|gb|FE483337.1|FE483337
EST:     CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGG                         GCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCC
genomic: CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGGgtaagtctct ... gtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCC
EST: gi|169055872|gb|FE466113.1|FE466113
EST:     CCATCAAAACTCCGAGCGGATTGAAA-CCCGTCCTTTCGACTCGATCCGG                         GCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAG
genomic: CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGGgtaagtctct ... gtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAG
EST: gi|169032531|gb|FE439638.1|FE439638
EST:     CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGG                         GCCGAGCTGAAAGCTTTTTTCGACGTTCACGACCAGGAAGGAAGCCATCCC
genomic: CCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGGgtaagtctct ... gtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCC

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: 54

CACGGCCGGCCAGATCGTGACTTGGGTGAGCGATCCCATGCACGGGAACACCATCAAAACTCCGAGCGGATTGAAAACCCGTCCTTTCGACTCGATCCGGgtaagtctct ... gtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCCGGCGGCGTGCACCTGGAGATGACCGGGCAGAACGTCACCGAGTGCATCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagctccaagcaatgtttccagaggactaaaaacgttttgttcttgtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCCGGCGGCGTGCACCTGGAGATGACCGGGCAGAACGTCACCGAGTGCATCG
                        gactaaa  putative branch site (score: 54)
                                   ttttgttcttgtcc  putative PPT
                         actaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctcttgacatggatcgcagctccaagcaatgtttccagaggactaaaaacgttttgttcttgtccatccagGCCGAGCTGAAAGCTTTCTTCGACGTTCACGACCAGGAAGGAAGCCATCCCGGCGGCGTGCACCTGGAGATGACCGGGCAGAACGTCACCGAGTGCATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG