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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACGACGGGTGCGCGAGAGTCGGCGTTCAGGAACATCAAGACGATCGCGGAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtgttgggattggggcgaggtgtgtgaggggtgggatgcatggagggaattgagtgatatggtggatagtgaatggattttgtggtggaatggaaaagaaatgggatgttgaggggattgacatagcgtggttggttgtgacag

Basic information

species Physcomitrella patens
transcript PP1S114_143V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S114_143V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G078985_T01 (Zea mays), 5'ss of exon 3
TGACGACGGGTGCGCGAGAGTCGGCGTTCAGGAACATCAAGACGATCGCGGAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtgttgggattggggcgaggtgtgtgaggggtgggatgcatggagggaattgagtgatatggtggatagtgaatggattttgtggtggaatggaaaagaaatgggatgttgaggggattgacatagcgtggttggttgtgacag
| || || |||||  | |||   || |||||||||||||| || || || |||||| | || || |||||||| ||||| |||||||| || || ||||||||  |  | |   |  |||       | | ||   | |    | |     | ||  ||| |  | || |   |  ||      | ||||    |                                                        
TCACCACTGGTGCCAGGGAGAGCGCTTTCAGGAACATCAAAACCATTGCTGAGTGCCTTGCAGATGAGTTGATCAACGCTGCCAAGGGCTCTTCCAACAGgtat-atatatcctgtctggct----atatttggttgtttttttcctatctgcgatgtgaat--tgtgctcattcatgg-caattcttgtcacag--------------------------------------------------------

upper sequence: PP1S114_143V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EDP01658 (Chlamydomonas reinhardtii), 5'ss of exon 6
TGACGACGGGTGCGCGAGAGTCGGCGTTCAGGAACATCAAGACGATCGCGGAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtgttgggattggggcgaggtgtgtgaggggtgggatgcatggagggaattgagtgatatggtggatagtgaatggattttgtggtggaatggaaaagaaatgggatgttgaggggattgacatagcgtggttggttgtgacag
  || || || || || ||| | || ||| | ||||||||||| || ||||||||| |||| |||||| || | ||||| |||||||| ||||| ||||||| ||    |   |  |    ||  | || |  |||  |||        ||||     |  |||   ||  |  ||||        |||    || ||  || | ||                                            
--ACCACTGGCGCCCGCGAGGCCGCCTTCCGCAACATCAAGACCATTGCGGAGTGCCTGGCTGACGAGCTGGTGAACGCTGCCAAGGGCTCGTCCAACAGGTggg---cgcctgcgtactagcacgatgggctaggattggaggcgccagaggccgccg--tgaggcgggcggcagtggtgccgggttggtcaggcatccaagaaaa--------------------------------------------
















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|100352574|gb|BY945340.1|BY945340
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCCATCA-GAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATC
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCC-ATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATC
EST: gi|67721494|gb|BJ971753.1|BJ971753
EST:     GTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|162230619|gb|FC406042.1|FC406042
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|162226150|gb|FC401610.1|FC401610
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|67577681|gb|BJ949848.1|BJ949848
EST:     TGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: TGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|67700555|gb|BJ960788.1|BJ960788
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|67718339|gb|BJ968598.1|BJ968598
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|37826229|gb|BJ584241.1|BJ584241
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|162273366|gb|FC449815.1|FC449815
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|67693257|gb|BJ953490.1|BJ953490
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|37846959|gb|BJ604967.1|BJ604967
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|162278768|gb|FC454878.1|FC454878
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|162268851|gb|FC445998.1|FC445998
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|162273367|gb|FC449816.1|FC449816
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|162238753|gb|FC418245.1|FC418245
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|67718322|gb|BJ968581.1|BJ968581
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|37842087|gb|BJ600095.1|BJ600095
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|162226151|gb|FC401611.1|FC401611
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|162235518|gb|FC411328.1|FC411328
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|162278767|gb|FC454877.1|FC454877
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|67721467|gb|BJ971726.1|BJ971726
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|67569987|gb|BJ942811.1|BJ942811
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|6102455|gb|AW126925.1|AW126925
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|67722587|gb|BJ972846.1|BJ972846
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|162238063|gb|FC414253.1|FC414253
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|7287019|gb|AW599506.1|AW599506
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|162230618|gb|FC406041.1|FC406041
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|37843974|gb|BJ601982.1|BJ601982
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|162229438|gb|FC405824.1|FC405824
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|208367427|gb|DC951317.1|DC951317
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|37838796|gb|BJ596804.1|BJ596804
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|67720579|gb|BJ970838.1|BJ970838
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
EST: gi|67720369|gb|BJ970628.1|BJ970628
EST:     GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAG                         CTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG
genomic: GAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCG

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: 144

TGACGACGGGTGCGCGAGAGTCGGCGTTCAGGAACATCAAGACGATCGCGGAGTGCTTGGCGGACGAGTTGATAAACGCGGCCAAGGGTTCGTCGAACAGgtaggaggtg ... gttgtgacagCTACGCCATCAAGAAGAAGGACGAGATCGAGCGTGTGGCCAAAGCCAATCGTTAAGCTAGTATCAGGATGGTGGTTGCTTCGATAAATTCTCTCCGAATT




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