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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTGCTCCGGCCTGGCCGTTTGGATCGAAAAATTGAAATTCCACTGCCTAATG

Basic information

species Physcomitrella patens
transcript PP1S47_46V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os06g40560.1 (Oryza sativa), 3'ss of exon 7
gtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTGCTCCGGCCTGGCCGTTTGGATCGAAAAATTGAAATTCCACTGCCTAATG
                               |  ||| |  ||  |  | |  |    ||    ||  ||||| |  || ||  |    |||  |  |||| | | |  |    ||| | |   |  |  || |||||||| ||||| ||||| |||||||| ||||||||| | || |||||  | || || ||||| || |||||  | || ||||||||||||||||| ||||
-----------------------------gatggttgtcactgattcctttaatatgatgtggaaaactgtatgt--gactcctggtattgcatg--gattgtgtgtaacagaattttcct---acttttatacagGTAAAAATGATCATGGCGACTAATCGTCCTGATGTTTTGGACCCTGCACTCCTTCGTCCTGGGCGGTTGGACAGGAAGATTGAAATTCCACTGCCAAATG

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G171604_T01 (Zea mays), 3'ss of exon 7
gtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttg--tttacatgga-atatggat----gcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTGCTCCGGCCTGGCCGTTTGGATCGAAAAATTGAAATTCCACTGCCTAATG
                                      |      ||| | |   || | | |  | |  |  ||| |||   | |||||  |    | |||| |||    ||   || ||| ||| || | ||      |||||||||||||| |||||||| ||||| ||||||||||| || |||||  | || || ||||| ||||| ||  | || ||||||||||| || || || |
--------------------------------------cacaatatttaccgtgcattttctatgattgttgcata-gaacagcttgtgtctt----gtttctgtatgagtttagtttgacaaggatattttgacctgaacagGTAAAGATGATCATGGCCACGAATCGACCTGATGTTCTGGACCCTGCGCTCCTGCGTCCTGGACGTTTAGACAGGAAGATTGAAATTCCGCTACCCAACG

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G165817_T01 (Zea mays), 3'ss of exon 7
gtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTGCTCCGGCCTGGCCGTTTGGATCGAAAAATTGAAATTCCACTGCCTAATG
                     | | || ||||        |    |||| |   | |    | ||  | |||  | ||  ||  ||   | ||  |  | |     |   |  |  ||  | |  | || |  |||||||| ||||| |||||||| ||||| ||||||||||| || || ||  | || || ||||| ||||| ||| | || ||||||||||| || || || |
------------------gtaaatttgttatttggattactcacattttttctaggtaca-acgatatagtagct-tgtgtcttgttgtttctgtctaaattcagtttgacaaggatattttggct-tgaa--cagGTAAAAATGATCATGGCCACAAATCGACCTGATGTTCTGGACCCGGCGCTCCTGCGTCCTGGACGTTTAGATAGGAAGATTGAAATTCCGCTACCCAACG

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA06G03230.1 (Glycine max), 3'ss of exon 7
gtactcttgactcttgaaaccattctggtattcat-tggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTGCTCCGGCCTGGCCGTTTGGATCGAAAAATTGAAATTCCACTGCCTAATG
                           |||||| | ||| | ||    || |     ||| |||    |||      ||||  |    | |  | |  |||||   ||  | ||  |  | |  | |   | || |||| || ||||||||||| || || || |||||||| ||||| |||||| | || || |||||  | |||||| ||||||| ||||| || ||||||||||
---------------------------gtattcttatggatatgttgattttt----tctacaaatgattgc-----tgaacaaaaaatttaatggtggattcacgatgacattactgtc-tacatttctgttgtagGTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTCCTGCGTCCTGGGAGATTGGATAGAAAAATAGAAATCCCTCTGCCTAATG

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA04G03180.1 (Glycine max), 3'ss of exon 7
gtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTGCTCCGGCCTGGCCGTTTGGATCGAAAAATTGAAATTCCACTGCCTAATG
                           ||||||      | ||| | || || |  | |  |  ||    |   |    | ||    | |  | |  ||||| | ||  |  |  |  | |  | |   | || |||| || ||||||||||| || || || |||||||| ||||| |||||| | || || |||||  | |||||| ||||||| ||||| || ||||||||||
--------------------------tgtattc-----ttatggatattttgattttttctacaaa----tgactgctgaacaaaaatttaatggtggattcatgatgacactactgtc-tccatttctgctgtagGTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTCCTGCGTCCTGGGAGATTGGATAGAAAAATAGAAATCCCTCTGCCTAATG

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|162266638|gb|FC441998.1|FC441998
EST:     CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
EST: gi|162266639|gb|FC441999.1|FC441999
EST:     CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
EST: gi|37837457|gb|BJ595465.1|BJ595465
EST:     CACTCATGGAGTTATNGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
EST: gi|37836411|gb|BJ594419.1|BJ594419
EST:     CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
EST: gi|162269526|gb|FC445082.1|FC445082
EST:     CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
EST: gi|37834916|gb|BJ592928.1|BJ592928
EST:     CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTTAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
EST: gi|208353233|gb|DC926158.1|DC926158
EST:     CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
EST: gi|37823384|gb|BJ581450.1|BJ581450
EST:     CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
EST: gi|37833453|gb|BJ591465.1|BJ591465
EST:     CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG

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), 19 (downstream exon)
Score: 3

AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTGCTCCGGCCTGGCCGTTTGGATCGAAAAATTGAAATTCCACTGCCTAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTGCTCCGGCCTGGCCGTTTGGATCGAAAAATTGAAATTCCACTGCCTAATG
                 attctttat  TA-rich tract