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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taccttcattgcgctctctcttttgcttgtaatactgttcgtattgtattcaggctgtcattgttgtaacattaaataatactgcttgcttcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG

Basic information

species Physcomitrella patens
transcript PP1S22_40V6.2
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S22_40V6.2 (Physcomitrella patens), 3'ss of exon 17
lower sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 16
---------------------------------taccttcattgcgctctctcttttgct-tgtaatactgttcgtattgtattcaggctgtcat-tgttgtaacattaaataatactgcttgcttcatttg--cagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG
                                 |   | ||||      || || ||| |    |||  | ||| | |    ||  |     |   ||||  |  | |      | || ||| ||  |||||  |||||| ||||||||||||||||| |||||  | || |||||||| |||||||||||  | |||||||||
gtatgtttaaacattaattcccttattacttaatggttacattatttgttccctattgatgcacaattattttcctgtcaacttatgatgaacggatgtttaactaatgttctgttctactt-ctcaatttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG

upper sequence: PP1S22_40V6.2 (Physcomitrella patens), 3'ss of exon 17
lower sequence: GRMZM2G375504_T03 (Zea mays), 3'ss of exon 16
------------------------------------------------taccttcattg-cgctctctcttttgcttgtaatactgttcg----tattgtattcaggct---gtcattgttgtaacattaaataatactgc-ttgcttcatttgc---agTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG---------------------------------
                                                |   || ||    |  || | |||||   |  |   ||| |     |||| | ||  |  |    | ||  |||  || | |  | ||| | |  | || || ||||   ||||| ||||||||||||||||| ||||| || || |||||||| |||||||||||  | ||||| |||                                 
gtacgttaccagcgcctctttttttattcatttttactgtttgtgcagtcggttaataaatgtcctttgttttggccgccactgtgtacaatgttattttgtttggagttcaatgatgattgatacctgatgttatatttcacttctacaattgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCCGAGGTACGCCCTATCTTTGGAGTAAATGGGATTATT

upper sequence: PP1S22_40V6.2 (Physcomitrella patens), 3'ss of exon 17
lower sequence: GRMZM2G375504_T02 (Zea mays), 3'ss of exon 16
------------------------------------------------taccttcattg-cgctctctcttttgcttgtaatactgttcg----tattgtattcaggct---gtcattgttgtaacattaaataatactgc-ttgcttcatttgc---agTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG
                                                |   || ||    |  || | |||||   |  |   ||| |     |||| | ||  |  |    | ||  |||  || | |  | ||| | |  | || || ||||   ||||| ||||||||||||||||| ||||| || || |||||||| |||||||||||  | ||||| |||
gtacgttaccagcgcctctttttttattcatttttactgtttgtgcagtcggttaataaatgtcctttgttttggccgccactgtgtacaatgttattttgtttggagttcaatgatgattgatacctgatgttatatttcacttctacaattgcaacagTGCTGCTGTATTTCATAATGCGAGTACACGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCCGAG

upper sequence: PP1S22_40V6.2 (Physcomitrella patens), 3'ss of exon 17
lower sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 17
----------------------------------taccttcattgcgctc-tctcttttgcttgtaatactgttcg--tattgtattcaggctgtcattgttgtaac--attaaataatactgcttgcttcatt--tgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG
                                   | |||   |  ||   | |  |||| |  | ||  ||||||   |||  |||     ||   || ||  | |  |  | | |  | |  ||| || | |    |||||||||||| ||||||||||| || ||  | |||| ||||||  | ||||||||||| |||||||||
gtactgaaaccttctttccaacattcttgtggttgaactttgctatgcaagtgttatttgttactgat-ttgttcgatcattcaattgcctatgatgtttttagatctgacgacacatcattttttgtttaactgcaacagTGCCGCTGTGTTTCATAATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG

upper sequence: PP1S22_40V6.2 (Physcomitrella patens), 3'ss of exon 17
lower sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 17
taccttcattgcgctctctcttttgcttgtaatactgttcgtattgtattcaggct---gtcattgttgtaacattaaataatactgcttgcttcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG
    |  || |   ||  ||| |  |   | | ||| |   ||    ||   |  |   |||||||   | |   ||    |   | | |  |  |    |||||| |||||||| || ||||| ||||| || |||| |||||| || || |||||||||||||| |||
---ttaaatagaattcattctctcacaacttagactatgaataactcatgttgcttcatgtcattgacttgaatatatgcgacttttccttgtgtacaaacagTGCTGCTGTATTCCACAATGCAAGTACGCGGTTTTGTGATGGAGCACGCTTTGGGCTTGGTGCAGAG

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|162197988|gb|FC373691.1|FC373691
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|37835735|gb|BJ593747.1|BJ593747
EST:     GTGACCGAAAATCATATTACCGC--AGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|162154554|gb|FC330764.1|FC330764
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|208396875|gb|DC920443.1|DC920443
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|162167111|gb|FC343587.1|FC343587
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|162154553|gb|FC330763.1|FC330763
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|37839335|gb|BJ597343.1|BJ597343
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|162167110|gb|FC343586.1|FC343586
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|162276247|gb|FC452601.1|FC452601
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|37821498|gb|BJ579564.1|BJ579564
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|162197987|gb|FC373690.1|FC373690
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|162191466|gb|FC367170.1|FC367170
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|162153152|gb|FC329558.1|FC329558
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|162235435|gb|FC411570.1|FC411570
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|162210538|gb|FC386834.1|FC386834
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|162167790|gb|FC344520.1|FC344520
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|18338412|gb|BJ170436.1|BJ170436
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|162164179|gb|FC339602.1|FC339602
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
EST: gi|162235436|gb|FC411571.1|FC411571
EST:     GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAG                         TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT
genomic: GTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTT

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), 33 (downstream exon)
Score: 18

CGCGCACACGGACTGCATAGTGACCGAAAATCATATTACCGCAGAGACCTTTCTTCATCATGTGGACAGgtcttgacta ... tcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattcaggctgtcattgttgtaacattaaataatactgcttgcttcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG
                  ttgtaac  putative branch site (score: 18)
                                       cttgcttc  putative PPT
              attgttgtaacattaa  TA-rich tract