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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaacatcagctcgccaaggttaaatatttacttaacatggtatttgttgattccatgcgattctaattctgacatatcatcgttgtggtcttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCTAAGAACCAAGGTATTACAC

Basic information

species Physcomitrella patens
transcript PP1S34_445V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S34_445V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 2
-----tcaacatcagctcgccaaggttaaatatttacttaacatggtatttgttgattccatgcgattctaattctgacatatcatcgttgtggtcttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCTAAGAACCAAGGTATTACAC
         |||    |  ||||  ||| ||| | || |   |   |||||  |  |   ||   | | |  | || |  |||  | || ||   |||   | ||||||||||||| || || ||||| ||| | ||||| |||||||||||||||||  ||||||||||||| || || ||||| ||| |||| ||||| || |
gggtgctcccatttatttaccaat-ttatataatcacatttga--atattttgtcctgtaatcaaaatattgtgcttaactat--ttgtcgttacctttcctcagGGTTATGTGGTTTACCGTGTCCGTGTGAGGCGTGGTGGCAGGAAGAGGCCAGTGCCCAAGGGTATTGTCTACGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: PP1S34_445V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 2
--tcaacatcagctcgccaaggttaaatatttacttaacatggtatttgttgattccatgcgattctaattctg-acatatcatcgttgtggtcttg-ttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCTAAGAACCAAGGTATTACAC
   ||| ||    || |  | | |      | | | |   | | || | |||   | ||   || | |||  ||  |||| |    || ||  |||| ||| |||| |||||||| || || || |||||  | ||||| |||||||||||||||||  ||||||||||||| ||||| ||||| ||| |||| |||||||| |
agccaaaatgtattcac--atgctgctgtctgattcacttttgaatgttttggccctata--atccaaatattgtgcataactattttttgaccttgctttcagGGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCAGTGCCCAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATTACCC

upper sequence: PP1S34_445V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G084757_T02 (Zea mays), 3'ss of exon 1
-tcaacatcagctcgccaaggttaaatatttacttaacatggtatttgttgattccatgcgattctaa-ttctgacatatcatcgttgtggtcttgtt--ttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCTAAGAACCAAGGTATTACAC
  || | |   || | |   || |   ||| | |||   || |  |||   |||| |   | | ||   | |     | | | | ||||| | || ||  | |||| ||||| || || |||||||| ||| | ||||| |||||||||||||| ||  | ||||||||||| ||||| ||||| ||| |||| ||||| || |
aacagcttgtacttgtct--gtaatgcattgaattactttgct--ttgaaaattcgagtagctgctgggtgcccgggtctgaaccttgtgttatttttgttcagGGGTATGTTGTTTACCGCGTCCGTGTGAGGCGTGGTGGCAGGAAGAGGCCTGTGCCGAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: PP1S34_445V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G024354_T01 (Zea mays), 3'ss of exon 2
tcaacatcagctcgccaaggttaaatatttacttaacatggtatttg----ttgattccatgcgattctaat----tctgacatatcatcgttgtggtcttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCTAAGAACCAAGGTATTACAC
        ||   || | | |    | ||| ||| |  |   | |||    |||| |  ||  | | || ||    |||||| |    | || ||  |     || |||| ||||| || || || ||||| |||   ||||| |||||||||||||| ||  ||||||||||||| ||||| ||||| ||| |||| ||||| || |
-------tagtatgctatgttgccttgtttgcttcatcttacaattgcagtttgagtatatatg-tcctgattttgtctgacgttgtgttgtggtaattcatcttcagGGATATGTTGTCTACCGTGTCCGTGTGAAGCGTGGTGGCAGGAAGAGGCCTGTGCCCAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: PP1S34_445V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G466136_T01 (Zea mays), 3'ss of exon 1
tcaacatcagctcgccaaggttaaatattta--cttaacatggtatttgttgattccatgcgattctaat-tctgacatatcatcgttgtggtcttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCTAAGAACCAAGGTATTACAC
  |  ||      |  | | ||   || ||    |||  || | | ||   |   | |||  ||  |  | | |||  |    | || ||  | |   || |||||||||| ||||| |  ||||| ||| | ||||| ||||||||||||||  |  ||||| ||||||| ||||| ||||| ||| |||| ||||| || |
--agtat-gctatgttaggcttgtttactttattttattattgcagtttgagtacctatgtcatgattttatttgatgttatgttgtggtaatttatcttcagGGTTATGTTGTGTACCTTGTCCGTGTGAGACGTGGTGGCAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC

upper sequence: PP1S34_445V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G180724_T01 (Zea mays), 3'ss of exon 2
tcaacatcagctcgc-caaggttaaatatttacttaacatggtatttgttgattccatgcgattc--taattctgacatatcatcgttgtggtcttgtt--ttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCTAAGAACCAAGGTATTACAC
  |  | || ||||  |  |  | | || | |     ||| | | | ||| | ||       ||   || ||      | | | ||||||| | || ||  | |||| ||||| || || || ||||| ||    ||||| |||||||||||||| ||  | ||||||||||| ||||| ||||| ||| |||| ||||| || |
--atgaacaactcgtacttgtctgagtaataat---gcattgaactagttcactctgaaaatttgagtagttgctgggtctgaacgttgtgttatttttgttcagGGGTATGTTGTTTACCGTGTCCGTGTCAAGCGTGGCGGCAGGAAGAGGCCTGTGCCGAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: PP1S34_445V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv15s0021g02480.t01 (Vitis vinifera), 3'ss of exon 2
---tcaacatca-gctcgccaaggttaaatatttacttaacatggtatttgttgattccatgcgattctaattctgacatatcatcgttgtggtcttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCTAAGAACCAAGGTATTACAC
   | || || | |     |  |   |   ||||  | | |||   |   | ||||||  |   | | | ||| | |      | |  | |  |||  |||||||| |||||  | ||||| || || ||  | ||||| ||  |||||||||| ||| ||||||| ||||| |||||||||||||  ||||| ||| | || |
tgtttaaaattatgacaaactggcccattaatttgataagcatca-agacgatgattcttttt-actttgattataatgc-caaacactattttct-attttagGGGTATGTTATCTATCGTGTTCGTGTTAGACGTGGTGGTCGGAAGAGGCCTGTTCCCAAGGGCATTGTTTATGGAAAGCCTACAAACCAGGGTGTCACCC

upper sequence: PP1S34_445V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 2
tcaacatcagctcgccaaggttaaatatttacttaaca-tggtatttgttgattccatgcgattctaattctgacat-atcatcgt-----tgtggtc--ttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCTAAGAACCAAGGTATTACAC
           |  |   | ||| || ||| | |     || | | | || | ||  |||     ||||  | | || |  |||||     |||   |  |  ||| ||||||||||| | ||||| || || ||  | || || || ||||||||||||||  | ||||||||||||||||| ||||| |  ||||||||| | || |
-------tgattttct--gtttacatttttccctgctggtgctctatatttagtcactgcagcgttaatattcatattaatatcgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC

upper sequence: PP1S34_445V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ27946 (Selaginella moellendorffii), 3'ss of exon 2
tcaacatcagctcgccaaggttaaatatttacttaacatggtatttgttgattccatgcg-attctaattctgacatatcatcgttgtggtcttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCTAAGAACCAAGGTATTACAC
                                      |   |||| |   |||   | |  | |||  |||   ||    ||||  | |  |  |   |||| || || || || || ||||| ||||| || || ||| | |||||||||||  ||||||| ||||| ||||||||||| |||||||| ||||| || |
-------------------------------------gtaaaatttctcctttcttcgtgtgtgctagctctttgatcgtttcgtgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTCTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC

upper sequence: PP1S34_445V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
tcaacatcagctcgccaaggttaaatatttacttaacatggtatttgttgattccatgcg-attctaattctgacatatcatcgttgtggtcttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCTAAGAACCAAGGTATTACAC
                                      |   |||| |   |||   | |  | |||  |||   ||    ||||  | |  |  |   |||| || || || || || ||||| ||||| || || ||| | |||||||||||| ||||||| ||||| ||||||||||| |||||||| ||||| || |
-------------------------------------gtaaaatttctcctttcttcgtgtgtgctagctctttgatcgtttcgtgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC

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|208347591|gb|DC925534.1|DC925534
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|162181735|gb|FC358765.1|FC358765
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|162215478|gb|FC390543.1|FC390543
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|67575228|gb|BJ948052.1|BJ948052
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|162215477|gb|FC390542.1|FC390542
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|18370179|gb|BJ201781.1|BJ201781
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|67709455|gb|BJ965271.1|BJ965271
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|208346895|gb|DC905439.1|DC905439
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|67698687|gb|BJ958920.1|BJ958920
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|100363460|gb|BY966400.1|BY966400
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|37826795|gb|BJ584807.1|BJ584807
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|18332017|gb|BJ164029.1|BJ164029
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|18340479|gb|BJ172507.1|BJ172507
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|67723886|gb|BJ974145.1|BJ974145
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|208379859|gb|DC911744.1|DC911744
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|162268392|gb|FC444161.1|FC444161
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|208346559|gb|DC916825.1|DC916825
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTNTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|18347722|gb|BJ179769.1|BJ179769
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|162262360|gb|FC437687.1|FC437687
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|162211656|gb|FC387944.1|FC387944
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|162181734|gb|FC358764.1|FC358764
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|67709347|gb|BJ965163.1|BJ965163
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|67709809|gb|BJ965625.1|BJ965625
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|37851003|gb|BJ609011.1|BJ609011
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|208382335|gb|DC919323.1|DC919323
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|208376710|gb|DC902919.1|DC902919
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|162201995|gb|FC377201.1|FC377201
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
EST: gi|162201996|gb|FC377202.1|FC377202
EST:     GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAG                         GGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA
genomic: GCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCA

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: 32 (upstream exon), 35 (downstream exon)
Score: 25

TGTGCGCTGCTGGGAGTACAGGCAGCTCCCCGGCATCGTCCGCGTCACTCGCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttg ... cttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCTAAGAACCAAGGTATTACAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgattccatgcgattctaattctgacatatcatcgttgtggtcttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCTAAGAACCAAGGTATTACAC
                      ttctgac  putative branch site (score: 25)
                                            tcttgtttt  putative PPT
               attctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaacatcagctcgccaaggttaaatatttacttaacatggtatttgttgattccatgcgattctaattctgacatatcatcgttgtggtcttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCTAAGAACCAAGGTATTACAC

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