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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaactatatctctgtttctcagtgacttagatgtagcggctgtgacttcgaagcgtgctaacttgaaattcgactcctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAGAAGAAGGTCTACGTTCTTCCGAAGCACTTGGACGAGAAGGTGGCGGCGC

Basic information

species Selaginella moellendorffii
transcript EFJ11220
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11220 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os11g26850.2 (Oryza sativa), 3'ss of exon 2
gtgaga-actat-atctctgtttctcagtgacttagatgtagcggctgtgacttcgaagcgtgctaacttga--aattcgactcctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAGAAGAAGGTCTACGTTCTTCCGAAGCACTTGGACGAGAAGGTGGCGGCGC
|| | | |  || | |  | | | |        || |  |   |  | |  ||   |       | | |  |  |||||    | | |  ||||| ||||| ||||| ||||||||||| |||| ||   | |||||||||||||||||||| ||||||||||| |||||| | |||||||||||||| || |
gtaaaatatgatgaccagtatctattgtctcactaaacatgctgagtatagctgtaagttaca-tgattgaatcaattctgtgcttgttgcagGTCATTGCTCAGCTTGAGCTGTGGAAGGAGAAGAGCACTGGCAAGTACGAGAAGAAGGTGTACGTTCTTCCCAAGCACCTCGACGAGAAGGTGGCCGCCC

upper sequence: EFJ11220 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G111909_T01 (Zea mays), 3'ss of exon 3
gtgagaac-tatatctctgtttct--cagtgacttagatgtagcggctgtgacttcgaagcgtgcta--acttgaaattcgactcctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAGAAGAAGGTCTACGTTCTTCCGAAGCACTTGGACGAGAAGGTGGCGGCGC
|| |  ||  | |||| | | | |    ||| |     |    |     | |  ||| |  ||   |  ||   ||  |  | || |    |||||  |||| ||||| ||||||||||| |||| ||| || |||||||| ||||||||||| || || || || |||||| | || ||||||||    || |
gtaaacacgcaaatctatatctttattggtgtcaccatttgtacactgattagctcgcaaggtcacattacagaaatatttattcttgatgcagGTCCTTGCCCAGCTTGAGCTGTGGAAGGAGAAGAACTCTGGCAAGTATGAGAAGAAGGTATATGTGCTCCCCAAGCACCTTGATGAGAAGGTTAATGCTC
















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|169115250|gb|FE515640.1|FE515640
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTGGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169069670|gb|FE477023.1|FE477023
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169078085|gb|FE487245.1|FE487245
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTGGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169081967|gb|FE487476.1|FE487476
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169078936|gb|FE486588.1|FE486588
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169063802|gb|FE472948.1|FE472948
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTGGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169079935|gb|FE487873.1|FE487873
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169034478|gb|FE444551.1|FE444551
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTGGAGCTGTGGAACGAGAGGAAGTCCGGGCA-GTACGA
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGG-CAAGTACGA
EST: gi|169042510|gb|FE453682.1|FE453682
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTGGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169074157|gb|FE482389.1|FE482389
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169018311|gb|FE427744.1|FE427744
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169018312|gb|FE427745.1|FE427745
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169025970|gb|FE432905.1|FE432905
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTGGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169078937|gb|FE486589.1|FE486589
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGA
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGA
EST: gi|169088085|gb|FE493350.1|FE493350
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTGGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169069331|gb|FE478829.1|FE478829
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTGGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169102873|gb|FE505238.1|FE505238
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169033066|gb|FE441400.1|FE441400
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169116227|gb|FE517174.1|FE517174
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTGGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169034477|gb|FE444550.1|FE444550
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTGGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169115249|gb|FE515639.1|FE515639
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTGGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169080950|gb|FE488693.1|FE488693
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTGGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169105777|gb|FE505124.1|FE505124
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169088084|gb|FE493349.1|FE493349
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTGGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169025971|gb|FE432906.1|FE432906
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTGGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
EST: gi|169069671|gb|FE477024.1|FE477024
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACG
EST: gi|169045948|gb|FE453104.1|FE453104
EST:     GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAG                         GTGATTGCGCAGCTGGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG
genomic: GCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAG

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), 34 (downstream exon)
Score: 47

AGGCACCGGGATCATCGTCCTTGCCGAGGGTCGTCTCATGAACTTGGGCTGCGCGACCGGGCATCCCAGCTTCGTCATGTCCTGCTCTTTCACGAACCAGgtgagaacta ... cctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAGAAGAAGGTCTACGTTCTTCCGAAGCACTTGGACGAGAAGGTGGCGGCGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtagcggctgtgacttcgaagcgtgctaacttgaaattcgactcctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAGAAGAAGGTCTACGTTCTTCCGAAGCACTTGGACGAGAAGGTGGCGGCGC
                         tgctaac  putative branch site (score: 47)
                                      ttcgactcctttccc  putative PPT
                                ttgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaactatatctctgtttctcagtgacttagatgtagcggctgtgacttcgaagcgtgctaacttgaaattcgactcctttcccagGTGATTGCGCAGCTAGAGCTGTGGAACGAGAGGAAGTCCGGCAAGTACGAGAAGAAGGTCTACGTTCTTCCGAAGCACTTGGACGAGAAGGTGGCGGCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG