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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacgtggcgttcagtatagttattgtggattgattcagaaaggatttgtgggttatccgcttcgaagcttttaacattatgatttatggccttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAAGGTATTACGC

Basic information

species Physcomitrella patens
transcript PP1S68_114V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 2
cacgtggcgttcagtatagttattgtggattgattcagaaa-ggatttgtgggttatccgcttcgaagcttttaacattatgatttat-ggcctta-ttttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAAGGTATTACGC
   |      |   |  |  |  ||  |  |||||||     | || | | ||   |    | | ||  || |  ||| |  |||| | | ||||  ||| |||||||||| || || || || |||||  | ||||| |||||||||||||||||  ||||||||||||| ||||| ||||||||| |||| |||||||| |
--agccaaaatgtattcacatgctgctgtctgattcacttttgaatgttttggccctataatccaaatattgtg-cataactattttttgaccttgctttcagGGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCAGTGCCCAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATTACCC

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 2
cacgtggcgttcagtatagttattg-tggattgattcagaaaggatttgtgggttatccgcttcgaagcttttaac--attatgatttatggccttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAAGGTATTACGC
   | |   | |  | || |||    |  ||  | ||| |   || |  |  ||  |    |   ||  || |     | |||   |  |  ||||   | |||| ||||| || || || ||||| ||| | ||||| |||||||||||||||||  ||||||||||||| || || ||||||||| |||| ||||| || |
---gggtgctcccatttatttaccaatttatataatcacatttgaatattttgtcctgtaatcaaaatattgtgcttaactatttgtcgttacctttcctcagGGTTATGTGGTTTACCGTGTCCGTGTGAGGCGTGGTGGCAGGAAGAGGCCAGTGCCCAAGGGTATTGTCTACGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G084757_T02 (Zea mays), 3'ss of exon 1
--cacgtggcgttcagtatagttattgtggattgattcaga--aaggatttgtg-ggttatccgcttcgaagcttttaacattatgatttatggccttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAAGGTATTACGC
  ||  | |   |         |    || |||  ||       |  ||| | |  | |    | | |   | | | ||| || ||  ||||    ||  || |||| |||||||| || |||||||| ||| | ||||| |||||||||||||| ||  | ||||||||||| ||||| ||||||||| |||| ||||| || |
aacagcttgtacttgtctgtaatgcattgaattactttgctttgaaaattcgagtagctgctgggtgcccgggtctgaaccttgtg--ttat---ttttgttcagGGGTATGTTGTTTACCGCGTCCGTGTGAGGCGTGGTGGCAGGAAGAGGCCTGTGCCGAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G024354_T01 (Zea mays), 3'ss of exon 2
cacgtggcgttcagtatagttattgtggattgat-tcagaaaggatttgtgggt-tatccgcttcgaagct-tttaacattatgatttatggccttat-tttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAAGGTATTACGC
    | |  | |  | | |   |  | | || || | | ||  |   | || || |||  |    ||   | | | || || || | |      | || || |||| |||||||| || || ||||| |||   ||||| |||||||||||||| ||  ||||||||||||| ||||| ||||||||| |||| ||||| || |
----tagtatgctatgttgccttgtttgcttcatcttacaattgcagtttgagtatatatgtcctgattttgtctgacgttgtgttgtggtaattcatcttcagGGATATGTTGTCTACCGTGTCCGTGTGAAGCGTGGTGGCAGGAAGAGGCCTGTGCCCAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G180724_T01 (Zea mays), 3'ss of exon 2
-----cacgtggcgttcagtatagttattgtggattgattcagaaaggatttgtgggttatccgcttcgaagcttttaacattatgatttatggccttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAAGGTATTACGC
     ||  | |   |      ||| ||  || |||||   ||       |      ||      ||    | | | ||| || ||  ||||    ||  || |||| |||||||| || || ||||| ||    ||||| |||||||||||||| ||  | ||||||||||| ||||| ||||||||| |||| ||||| || |
atgaacaactcgtacttgtctgagtaataatgcattgaactagttcactctgaaaatttgagtagttgctgggtctgaacgttgtg--ttat---ttttgttcagGGGTATGTTGTTTACCGTGTCCGTGTCAAGCGTGGCGGCAGGAAGAGGCCTGTGCCGAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G466136_T01 (Zea mays), 3'ss of exon 1
--cacgtggcgttcagtatagttattgtggattgattcagaaaggatttgtgggttatccgcttcgaagct-tttaacattatgatttatggccttat-tttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAAGGTATTACGC
   | |    |||  |  |  ||| | |   ||  |   | |    |||| |     |  |    ||   | ||| |  ||||| | |      |||| || |||| ||||||||||| |  ||||| ||| | ||||| ||||||||||||||  |  ||||| ||||||| ||||| ||||| ||| |||| ||||| || |
agtatgctatgttaggcttgtttactttattttattattgcag---tttgagtacc-tatgtcatgattttatttgatgttatgttgtggtaatttatcttcagGGTTATGTTGTGTACCTTGTCCGTGTGAGACGTGGTGGCAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 2
-cacgtggcgttcagtatagttattgtggattgattcagaaaggatttgtgggttatccgcttcgaagcttttaacattatgatttatggccttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAAGGTATTACGC
  |  |   ||| |   |  |   ||  | | | |  | |     |   ||     |     |  |   |  || | |    || |      |  ||| |||| |||||  | ||||| || || ||  | || || || ||||||||||||||  | ||||||||||||||||| |||||||  ||||||||| | || |
tgattttctgtttacatttttccctgctggt-gctctatatttagtcactgcagcgttaatattcatattaatatcgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ27946 (Selaginella moellendorffii), 3'ss of exon 2
cacgtggcgttcagtatagttattgtggattgattcagaaaggatttgtgggttatccgcttcgaagcttttaacattatgatttatggccttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAAGGTATTACGC
                                    | ||    |   |   |  |  |        |||| | | ||  |  |  | |  |  |   |||| || ||||| || || ||||| ||||| || || ||| | |||||||||||  ||||||| ||||| |||||||||||||||||||| ||||| || |
----------------------------------gtaaaatttctcctttcttcgtgtgtgctagctctttgatcgtttcg--tgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTCTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC

upper sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
cacgtggcgttcagtatagttattgtggattgattcagaaaggatttgtgggttatccgcttcgaagcttttaacattatgatttatggccttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAAGGTATTACGC
                                    | ||    |   |   |  |  |        |||| | | ||  |  |  | |  |  |   |||| || ||||| || || ||||| ||||| || || ||| | |||||||||||| ||||||| ||||| |||||||||||||||||||| ||||| || |
----------------------------------gtaaaatttctcctttcttcgtgtgtgctagctctttgatcgtttcg--tgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC

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|37836133|gb|BJ594141.1|BJ594141
EST:     GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAG                         GGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|162203237|gb|FC379334.1|FC379334
EST:     GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAG                         GGCTATGTTGTGTATCGCGTCCGCNTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|37835392|gb|BJ593404.1|BJ593404
EST:     GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAG                         GGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|67727373|gb|BJ977632.1|BJ977632
EST:     GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAG                         GGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|37832817|gb|BJ590829.1|BJ590829
EST:     GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAG                         GGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|18327613|gb|BJ159616.1|BJ159616
EST:     GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAG                         GGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|18355874|gb|BJ187933.1|BJ187933
EST:     GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAG                         GGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|67704760|gb|BJ964993.1|BJ964993
EST:     GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAG                         GGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|162203238|gb|FC379335.1|FC379335
EST:     GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAG                         GGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|162260329|gb|FC435632.1|FC435632
EST:     GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAG                         GGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|18349166|gb|BJ181215.1|BJ181215
EST:     GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAG                         GGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|37824878|gb|BJ582944.1|BJ582944
EST:     GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAG                         GGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|18353919|gb|BJ185974.1|BJ185974
EST:     GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAG                         GGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|67719044|gb|BJ969303.1|BJ969303
EST:     GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAG                         GGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|162260330|gb|FC435633.1|FC435633
EST:     GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAG                         GGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|18345767|gb|BJ177810.1|BJ177810
EST:     GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAG                         GGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|162241256|gb|FC417823.1|FC417823
EST:     GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAG                         GGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA

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: 31 (upstream exon), 34 (downstream exon)
Score: 8

TGTGCGATGCTGGGAGTACAGGCAGCTCCCAGGAATCGTCCGCGTCACTCGCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcat ... cttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAAGGTATTACGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgggttatccgcttcgaagcttttaacattatgatttatggccttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAAGGTATTACGC
                       ttttaac  putative branch site (score: 8)
                                            ccttatttt  putative PPT
                       ttttaacattatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacgtggcgttcagtatagttattgtggattgattcagaaaggatttgtgggttatccgcttcgaagcttttaacattatgatttatggccttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAAGGTATTACGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC