Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcttttctgggagcgatcttttgcagttcctaatttgctctttgtttggtctcttcgtcttcgattttttccttttggttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGCATCTGTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCT

Basic information

species Selaginella moellendorffii
transcript EFJ35297
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ35297 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S69_31V6.1 (Physcomitrella patens), 3'ss of exon 2
------gtatggcttttctgggag--cgatc-ttttgcagttcctaatttgctctttgtttggtctcttcgtct--tcgattttttccttttggttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGCATCTGTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCT
      ||  || ||  |  | ||   | |  | ||| |||| | |    |      |||  ||  | | |  |  ||  ||  |  |  |||   || || ||| || ||||| || ||||| || || |||||||||||||| ||||| |||||||| || || ||||| ||||||||||||||||| ||  | || || |
gtgaaggtgggggttggcgcgcaggctggtagtgttggagtttcgaga--gacgacggttaagttacgttggttaatctgttcgtggcaattgcggctgca-gGTTGCGTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGCATCTGCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATAT

upper sequence: EFJ35297 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S65_161V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------------------------------------gtatggcttttctgggagcgatcttttgcagttcctaatttgctctt----tgtttggtctcttcgtcttcgattttttccttttggttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGCATCTGTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCT
                                                                                                   ||  || |  |  | | || | |  |   || |  |||     |    || |  |||  ||  |    || || ||  || ||  |  || |||| || ||||| || ||||| ||||| || || || ||||| ||||| |||||||| || || |||||||||||||| |||||||| || || || || |
gtatgttaagttggttgcgatgtaaggtatcttttgggctgggctttcgttatgttgagctttaattacgtaatcaaatgtatatcgtagggtttcagttgatttctaggttatccatttctcactactcttcttttcagtatgaaatgataagtcggtttattcaggaattctttgttatg--tgccccagGTTGCCTTCAGGACTAAGGTTTTTCACCCTAATATTAATAGTAATGGAAGCATCTGCCTGGATATTCTCAAGGAGCAATGGAGCCCTGCTTTAACCATAT
















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|169025632|gb|FE436545.1|FE436545
EST:     TCCTGGTCACTATTCATTTNNNNNNNGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169078304|gb|FE490337.1|FE490337
EST:     TCCTGGTCACTATTCATTTNNNNNNNGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169105950|gb|FE504310.1|FE504310
EST:     TCCTGGTCACTATTCATTTNNNNNNNGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169038738|gb|FE446959.1|FE446959
EST:     TCCTGGTCACTATTCATTTCCCCCCGGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|70670995|gb|DN839572.1|DN839572
EST:     TCCTGGTCACTATTCATTTNNNNNNNGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|70670805|gb|DN839382.1|DN839382
EST:     TCCTGGTCACTATTCATTTCCCCCCGGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169105396|gb|FE506420.1|FE506420
EST:     TCCTGGTCACTATTCATTTCCCCCCGGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|70670872|gb|DN839449.1|DN839449
EST:     TCCTGGTCACTATTCATTTCCCCCCGGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169022096|gb|FE429105.1|FE429105
EST:     TCCTGGTCACTATTCATTTNNNNNNNGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169112483|gb|FE512760.1|FE512760
EST:     TCCTGGTCACTATTCATTTCCCCCCGGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169039764|gb|FE449426.1|FE449426
EST:     TCCTGGTCACTATTCATTTCCCCCCGGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169079016|gb|FE488579.1|FE488579
EST:     TCCTGGTCACTATTCATTTNNNNNNNGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|70670087|gb|DN838664.1|DN838664
EST:     TCCTGGTCACTATTCATTTNNNNNNNGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169086731|gb|FE494368.1|FE494368
EST:     TCCTGGTCACTATTCATTTCCCCCCGGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169020751|gb|FE430152.1|FE430152
EST:     TCCTGGTCACTATTCATTTCCCCCCGGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169079924|gb|FE487368.1|FE487368
EST:     TCCTGGTCACTATTCATTTCCCCCCGGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169095814|gb|FE498895.1|FE498895
EST:     TCCTGGTCACTATTCATTTNNNNNNNGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169020893|gb|FE429306.1|FE429306
EST:     TCCTGGTCACTATTCATTTCCCCCCGGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169046060|gb|FE453957.1|FE453957
EST:     TCCTGGTCACTATTCATTTCCCCCCGGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169026535|gb|FE434796.1|FE434796
EST:     TCCTGGTCACTATTCATTTCCCCCCGGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169032175|gb|FE439289.1|FE439289
EST:     TCCTGGTCACTATTCATTTNNNNNNNGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169082868|gb|FE491120.1|FE491120
EST:     TCCTGGTCACTATTCATTTCCCCCCGGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169032189|gb|FE439290.1|FE439290
EST:     TCCTGGTCACTATTCATTTNNNNNNNGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169046059|gb|FE453956.1|FE453956
EST:     TCCTGGTCACTATTCATTTCCCCCCGGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169061380|gb|FE470428.1|FE470428
EST:     TCCTGGTCACTATTCATTTNNNNNNNGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|70669831|gb|DN838408.1|DN838408
EST:     TCCTGGTCACTATTCATTTNNNNNNNGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169081704|gb|FE488162.1|FE488162
EST:     TCCTGGTCACTATTCATTTNNNNNNNGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169078305|gb|FE490338.1|FE490338
EST:     TCCTGGTCACTATTCATTTNNNNNNNGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|70669414|gb|DN837991.1|DN837991
EST:     TCCTGGTCACTATTCATTTNNNNNNNGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
EST: gi|169092996|gb|FE495290.1|FE495290
EST:     TCCTGGTCACTATTCATTTCCCCCCGGATTATCCGTTCAAGCCGCCCAAG                         GTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC
genomic: TCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGC

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: 65

GCAAGCGACGATAATGGGTCCGCCCGATAGCCCCTACGCGGGCGGTGTGTTCCTGGTCACTATTCATTTCCCCCCCGATTATCCGTTCAAGCCGCCCAAGgtatggcttt ... gttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGCATCTGTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgctctttgtttggtctcttcgtcttcgattttttccttttggttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGCATCTGTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCT
 tcctaat  putative branch site (score: 65)
                 tctcttcgtcttcgat  putative PPT
                               atttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggcttttctgggagcgatcttttgcagttcctaatttgctctttgtttggtctcttcgtcttcgattttttccttttggttctccaagGTGGCATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGCATCTGTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG