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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaaggtcacattgtcttagccaattcaaatggtatcgacattgaagatctgcagttggtgaacatttgcttaccaattttattttataccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAG

Basic information

species Physcomitrella patens
transcript PP1S100_124V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
agaaaggtcacattgtcttagccaattcaaatggtatcgacattgaagatctgcagttggtgaacatttgcttaccaattttattttataccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAG
      || | | | | | | || | | |        | | |  ||||   |    |   |||  |  |  |  | |  | || | ||     ||| ||| | |||||||| || ||||||||||| || || ||||| |||||||||||||||||||| |||||    | ||||||||||||||| ||  |
------gtgagactttgtcaaccgaatga--------ctaaaaagaagccatatgatgactga-tacataat--ctagctgtactctaa----ttttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG

upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
agaaaggtcacattgtcttagccaattcaaatggtatcgacattgaagatctgcagttggtgaacatttgcttaccaattttattttataccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAG
            |    ||    ||    |||| |  | | | ||   || |  ||       ||| |    | ||   || |||| ||  ||||| ||||| |||||||| || || || || || || || ||||| ||||| |||||||| ||||| |||||    |||||||||||||| ||||||||
-----------gtgaagtttcgtaacctgaatgatggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcat--cttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG

upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10
agaaaggtcacattgtcttagccaattcaaatggtatcgacattgaagatctgcagttggtgaacatttgcttaccaattttattttat-accttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAG
      || | ||| ||| | |  | | |       |  | |  |||| | |    ||| ||||||   |      ||||||||  ||| ||   || ||||| |||||||| |||||||| ||||| |||||||||||||||||||| ||||||||||| |||||    ||||||||||||||||||||  |
------gtgaaattctctcaactgaataa-------ttaaaaaggaagctat----ttgatgaacaaaagtaatgtaattttatgatatcactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG

upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 10
agaaaggtcacattgtcttagccaattcaaatggtatcgacattgaag-atctgcagttggtgaacatttgcttaccaattttattttataccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAG
      || | ||| ||||| |  ||   ||||  |  || |  |  | |||   |  || || | || || |  |      |   | | | ||||| |||||||||||| | ||||||||||| || ||||| ||||| |||||||| || || || ||||||||    | |||||||||||||||||| ||
------gtga-attttcttatc--atctgaatgagaatgaaagagccgtatcaatatctgctgta-atctgatagcg-----tgggtaacatcttttgcagCTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAG

upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
agaaaggtcacattgtcttagccaattcaaatggtatcgacattgaagatctgcag-ttggtgaacatttgcttaccaattttattttataccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAG
      || | |||  | | |   ||  || |  |     || ||||   |||| | ||  | ||    |  | ||    |   |||| |   ||   |||||||||||| | || || || || || ||||| || ||||||||||||||||| ||||| |||||   ||||||| ||||||||||||||||
------gttagattcccat-gtttatataagtaatg--agcaatgaattcctgctgctttatcaagtcatagtaactggctcattttttt---ttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG

upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
agaaaggtcacattgtcttagccaattcaaatggtatcgacattgaagatctgcag-ttggtgaacatttgcttaccaattttattttataccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAG
                 ||||          | | ||   || ||||  ||||| | ||  | ||  | |  | ||    | | |||| |   ||   |||||||||||| | || || || || || ||||| || ||||||||||||||||| ||||| |||||   ||||||| ||||||| ||||||||
----------------gttagattcccatgtttggatgagcaatgaatttctgctgctttatcaagttatagtaactggctctttttttt---ttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG

upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
-----------------agaaaggtcacattgtcttagccaatt---caaatggtatcgac-attgaagatctgcagttggtgaacatttgct-taccaattttattttataccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAG
                  ||||  |  |||  |    ||||| |   |||    |||     ||  |||     || ||  |  | | |     |   | || || | |  | |||   ||| | || ||| | || || || || || || || |||||||||||||||||||| ||||| ||||| || || |||||||||||||| |||||
gtgcgattttcttcttttgaaatctatcatc-taaaggccaaataagcaacctatataattgatctaagtgtatcattttatccataatgatggtgggacttgtactctg-atcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG

upper sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 10
----------------agaaaggtcacattgtcttagccaattcaaatggtatcgacat---tgaagatctgcagttggtgaacatttgcttaccaatt-ttat-----tttataccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAG
                |  ||| |  | || | || |    ||  | | | || ||  |   |   | | |   ||     || ||   ||    |||| ||||     |||| | |||   ||||| |||||| | || || || || ||||| |||||||| |||||||||||||| ||||| |||||    || || || |||||||| |||||
gtgatttcacttcttcatgaagcttcctttttttttggtgctttgatttgaatggagttattttgggctttattgtcaaataatatgaactatttaattattatcattatttaaatcttgatcagCTGTGTGATTTATATGAAAATGATTCTATCTTCGACAAATTTGAGTGTTGTCTGAGTGGAGATGGACTACGAGTGGCGACTGGTTCCTACAG

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|15730306|gb|BI741781.1|BI741781
EST:     AATCTGCCCCCGTGGCTACATTCAAAGTCCACGAGTATTTACGACCAAAG                         CTTTGTGATCTCTACGAGAACGACTCTATTTTCGAC
genomic: AATCTGCCCCCGTGGCTACATTCAAAGTCCACGAGTATTTACGACCAAAGgtaacctctg ... ccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGAC
EST: gi|162182432|gb|FC358031.1|FC358031
EST:     AATCTGCCCCCGTGGCTACATTCAAAGTCCACGAGTATTTACGACCAAAG                         CTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGT
genomic: AATCTGCCCCCGTGGCTACATTCAAAGTCCACGAGTATTTACGACCAAAGgtaacctctg ... ccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGT
EST: gi|67725006|gb|BJ975265.1|BJ975265
EST:     AATCTGCCCCCGTGGCTACATTCAAAGTCCACGAGTATTTACGACCAAAG                         CTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGT
genomic: AATCTGCCCCCGTGGCTACATTCAAAGTCCACGAGTATTTACGACCAAAGgtaacctctg ... ccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatctgcagttggtgaacatttgcttaccaattttattttataccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAG
                       tgcttac  putative branch site (score: 2)
                                           tacctttt  putative PPT
                               aattttattttatacc  TA-rich tract