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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattccactgccgactttacattatgagatgaagctgaagagtatgttccatcttggtgagatatttgcagaggattacggggagaagtttgctgatgattcttcaaacattggttgcctggttatttaaacagCAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG

Basic information

species Physcomitrella patens
transcript PP1S181_117V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S181_117V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os12g13460.1 (Oryza sativa), 3'ss of exon 4
gtaattccactgccgactttacattatgagatgaagctgaagagtatgttccatcttggtgagatatttgcagaggattacggggagaagtttgctgatg-attcttcaaacattggttgcctggttatt--taaacagCAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG
                                              || |   | |||         || || |   || | |      |  | ||| || | |         ||| |  | ||   | |  ||  ||||||||||| || ||| ||||||| || |||||  |||||||||| |||||||| |||||||| || || ||||| ||||| || ||  | |||
---------------------------------------------gtgctttcttttgac------cttccaaaatgttcctgtctctgggattctgttgcactagctgcttgttgttctcatgtcaactgttatgcagCAATATCCTTTTGACATACCTACCGAGGCTTTTCCATTTGAGATCTTCAAGCAAGCTTTTGTCGCAGTACAGTCTTGCGTGGTCCATTTGCAG

upper sequence: PP1S181_117V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AC198982.3_FGT006 (Zea mays), 3'ss of exon 2
gtaattccactgccgactttacattatgagatgaagctgaagagtatgt-tccatcttggtgagatatttgca--gaggattacggggagaagtttgctgatgattcttcaaacattggttgcctggttatttaaacagCAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG
                                           ||||   |  |||||      |||||| |    ||||||  |       |||  || ||  |  |||  ||| |  ||      || |||   ||||||||||| || ||| ||||||| || |||||  | ||||| |||||||||||||||||||| || || ||||| || ||||||||  | |||
-------------------------------------------gtattccttgatcttccaagcatatttccttcaaggattg-gctatttcgttaacttattctatttctcacagttatta-----ttgttttg-cagCAATATCCTTTTGACATACCTACTGAGGCTTTTCCGTTTGAAATATTCAAGCAGGCTTTTGTTGCAGTACAGTCTTGTGTTGTTCATTTGCAG

upper sequence: PP1S181_117V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G047695_T01 (Zea mays), 3'ss of exon 4
gtaattccactgccgactttacattatgagatgaagctgaagagtatgt-tccatcttggtgagatatttgca---gaggattacggggagaagtttgctgatgattcttcaaacattggttgcctggttatttaaacagCAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG
                                           ||||   |  |||||      |||||| |     ||||||      |  | |   |||||  |  |||  |||  | ||      || |||   ||||||||||| || ||| ||||||| || |||||  | ||||| |||||||||||||||||||| || || ||||| || || |||||  | |||
-------------------------------------------gtattccttgatctttcaagcatattttctttctaggattggctatatca-tcaactgatcctctttctcacagcgattt-----ttgtttt--cagCAATATCCTTTTGACATACCTACTGAGGCTTTTCCGTTTGAAATATTCAAGCAGGCTTTTGTTGCAGTACAGTCTTGTGTGGTTCATTTGCAG

upper sequence: PP1S181_117V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G14260.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaattccactgccgactttacattatgagatgaagctgaagagtatgttccatcttggtgagatatttgcagaggattacggggagaagtttgctgatgattcttcaaacattggttgcctggttatttaaacagCAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG
                          ||    |   |  | || |  |     |  | || |  |   |  |  | ||    |  | |  |  ||    || |      |||    ||   | ||  |||   |||||||| || || ||| |||| || |||||||| ||||||||||| ||||| ||||| ||||| ||  | ||||| || || || ||  | || 
-------------------------gtgtttggctacctacgatttcggcttcttcttgtcattttaatatatggaat----gctaaacatcggcctcggactt-----acaccattttatttgtgttttg--cagCAATACCCATTTGACATACCAACTGAAGCTTTTTCATTTGAGATTTTCAAACAGGCATTTGTTGCCATTCAGTCATGTGTGGTGCATTTACAA

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|162162595|gb|FC338689.1|FC338689
EST:     AATACGAAGAACTTGACACAGTGTGGTTTATGGCGGGTTCTTTATTCAAG                         CAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAG
genomic: AATACGAAGAACTTGACACAGTGTGGTTTATGGCGGGTTCTTTATTCAAGgtaattccac ... atttaaacagCAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAG
EST: gi|162221408|gb|FC397217.1|FC397217
EST:     AATACGAAGAACTTGACACAGTGTGGTTTATGGCGGGTTCTTTATTCAAG                         CAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAG
genomic: AATACGAAGAACTTGACACAGTGTGGTTTATGGCGGGTTCTTTATTCAAGgtaattccac ... atttaaacagCAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAG
EST: gi|162233878|gb|FC409728.1|FC409728
EST:     AATACGAAGAACTTGACACAGTGTGGTTTATGGCGGGTTCTTTATTCAAG                         CAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAG
genomic: AATACGAAGAACTTGACACAGTGTGGTTTATGGCGGGTTCTTTATTCAAGgtaattccac ... atttaaacagCAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAG
EST: gi|162198877|gb|FC372904.1|FC372904
EST:     AATACGAAGAACTTGACACAGTGTGGTTTATGGCGGGTTCTTTATTCAAG                         CAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAG
genomic: AATACGAAGAACTTGACACAGTGTGGTTTATGGCGGGTTCTTTATTCAAGgtaattccac ... atttaaacagCAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAG
EST: gi|162162497|gb|FC339215.1|FC339215
EST:     AATACGAAGAACTTGACACAGTGTGGTTTATGGCGGGTTCTTTATTCAAG                         CAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAG
genomic: AATACGAAGAACTTGACACAGTGTGGTTTATGGCGGGTTCTTTATTCAAGgtaattccac ... atttaaacagCAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAG
EST: gi|162152120|gb|FC328710.1|FC328710
EST:     AATACGAAGAACTTGACACAGTGTGGTTTATGGCGGGTTCTTTATTCAAG                         CAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAG
genomic: AATACGAAGAACTTGACACAGTGTGGTTTATGGCGGGTTCTTTATTCAAGgtaattccac ... atttaaacagCAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAG
EST: gi|162158626|gb|FC335526.1|FC335526
EST:     AATACGAAGAACTTGACACAGTGTGGTTTATGGCGGGTTCTTTATTCAAG                         CAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAG
genomic: AATACGAAGAACTTGACACAGTGTGGTTTATGGCGGGTTCTTTATTCAAGgtaattccac ... atttaaacagCAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAG

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: 27 (upstream exon), 31 (downstream exon)
Score: 15

GAGGTAGTGTTAGAGAGATTGGCAGGTATCAAACGGGAATACGAAGAACTTGACACAGTGTGGTTTATGGCGGGTTCTTTATTCAAGgtaattccac ... atttaaacagCAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggggagaagtttgctgatgattcttcaaacattggttgcctggttatttaaacagCAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG
           tgctgat  putative branch site (score: 15)
                                           ttatttaaaca  TA-rich tract