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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatttttccagtccttggtttttgaaatgctgcttttcgattctctcttgttagaaggtactctttgttcctcatgtatcctgagacattgtgatgcagATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAG

Basic information

species Physcomitrella patens
transcript PP1S10_200V6.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os04g35700.1 (Oryza sativa), 3'ss of exon 6
gtatttttccagtccttggtttttgaaatgctgcttttcgattctctcttgttagaaggtactctttgtt----cctcatgtatcctgagacat-tgtgatgcagATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAG
      | | ||    |         | | |||    | |  || | |             ||| |  ||    |||    | || | |   |  | |||  ||||| ||  ||    |     | |  |||||||| ||||| |||||||||||||||||||||
-----ctacaagagaatatacacaatactactgtagcttgtatccccccccccccccacccctcctcttttaagcctttaatttcattacttacgtttgacacagATATCATCTTTTGCTGAAATACGCTCTTTCAAAGGAAGTCCTTACTGGATGGCTCCTGAG

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os11g10100.2 (Oryza sativa), 3'ss of exon 6
---------gtatttttccagtccttggtttttgaaatgctgcttttcgattc--tctcttgttagaaggtact-ctttgttcctcatgtatcctgagacattgtgatgcagATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAG
           ||  |   | |  |  | |  |  || | |  |  | |||    | | ||  || | | || |  ||||||    |  |||  |         | || ||||| || || ||  | | | || |||| ||||| |||||||||||||||||||| ||||||
gtaagtacaacatagtgttaattatctgataattcaaggattttaatggatctattattttcctatatgatattgttttgttgactagttattgtat-------ttatacagATATCAGCGCACACATCTATCAAGTCCTTCAAAGGAAGCCCTTACTGGATGGCGCCTGAG

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G140726_T01 (Zea mays), 3'ss of exon 6
gtatttttccagtccttggtttttgaaatgctgcttttcgattctctcttgttagaaggtactctttgttc-ctcatgtatcctgagacatt-gtgatgcagATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAG
 ||  | |    |  |  |      ||  | | |     |||| |   |  ||      |  ||| |||   | |||  ||  |  || ||| ||   |||||| ||  ||    |     | |  |||||||| ||||| |||||||||||||||||||||
-tagctcttggatggtcagcaaaacaag-gatacacactgattgtgcttgcttttgtttttttctctgtaaacccattcattttttgaaatttgttgagcagATATCATCTTTTGCTGAAATACGTTCTTTCAAAGGAAGTCCTTACTGGATGGCTCCTGAG

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 7
gtatttttccagtccttggtttttgaaatgctgcttttcgattctctcttgttagaaggtact--ctttgttcctcatgtatcctgagacattgtgatgcagATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAG
 |   |    | |       |  |   |      ||||  ||  ||    | | | | |  ||  | |  |||| ||  |||       |||  |  |||||||  | |  ||||| | ||     || ||||||||||||||||| |||||||||||||||
-tccatgcataattgccatatgatatcacatctgttttaaataatcataagattgcatgatctatcctgtttccccaaatattaacttgcat-attttgcagATAACAGGGCAATCATGTCCATTATCATTCAAGGGAAGCCCTTATTGGATGGCTCCTGAG

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA10G37730.1 (Glycine max), 3'ss of exon 8
----gtatttttccagtccttggtttttgaaatgctgcttttcgattctctcttgt-tagaaggtactctttgttcctcatgtatcctgagacattgtgatgcagATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAG
     |  |||     |  |    || | ||||| |    ||          |||  ||    || || ||||  |  | | || |||     |||    |||||||  | |  ||||| | |||   ||| |||||||||| ||||||||||||||||||||||
gcatctggtttattgattttctaattct-aaatgatttaattaatccaaaggttgcataatttgtcctgtttgccctacttataccctacataatt----tgcagATAACAGGGCAATCGTGTCTATTGTCATTCAAGGGAACCCCTTACTGGATGGCTCCTGAG

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA20G30100.2 (Glycine max), 3'ss of exon 1
gtatttttccagtcct---tggtttttgaaatgctgcttttcgattctctcttgttagaaggtactctttgttcctcatgtatcctgagacat-tgtga--tgcagATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAG
    ||||| | | ||   || |||    ||| |     ||  ||  | | |  |  |   |  ||  || | ||| |  ||  ||    | |   | |  |||||||  | |  ||||| |  |    ||| ||||||||||  |||||||||||||||||||||
----ttttctaattctaaatgatttaatgaatccaaaggttgcataatttgtcct--gcttgccctacttataccttacataaactataccttacataatttgcagATAACAGGGCAATCGTGCCCATTGTCATTCAAGGGAACACCTTACTGGATGGCTCCTGAG

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 6
gtatttttccagtccttggtttttgaaatgctgct--tttcgattctc-tcttgttagaaggtactctttgtt-cctcatgtatcctgagacattgtgatgcagATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAG
   ||  | ||   ||    |||   | |||  ||  | |  ||  || |   |||  | | |      |||| || ||  |||       |||  |  |||||||  | |  ||||| | ||     || |||||||||||||| || |||||||||||||||
---ttcctgcataactgccatttgatattgcatctggtataaataatcgtaaggttgcatgatctatcctgtttccccaaatattaatttgcat-attttgcagATAACAGGGCAATCATGTCCATTATCATTCAAGGGAAGCCCCTATTGGATGGCTCCTGAG

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 6
gtatttttccagtccttggtttttga--aatgctgcttttcgattctctcttgttagaaggtactctttgttcctcatgtatcctgagacattgtgatgcagATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAG
 || |||        | |  | |  |   |||||     |   |  |    |    |     |  |    | ||| |  |||      |||| || ||||||||  |||  || || | ||     || |||||||||||||| ||||||||||| ||||||
-tagtttcttgtgtatcgaatatcaacctatgcttgaccttagtcatgatgttcatgttaaaatccagcttacctgacatatttcattacat-gtcatgcagATCACTGGGCAGTCATGTCCTTTATCATTCAAGGGAAGCCCATACTGGATGGCACCTGAG

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|162194513|gb|FC370736.1|FC370736
EST:     TAGACACTAACGGAATGGTGAAACTTGCTGACTTCGGCATGGCTAAGCAT                         ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATG
genomic: TAGACACTAACGGAATGGTGAAACTTGCTGACTTCGGCATGGCTAAGCATgtacgtatcg ... tgtgatgcagATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATG
EST: gi|162169368|gb|FC346258.1|FC346258
EST:     TAGACACTAACGGAATGGTGAAACTTGCTGACTTCGGCATGGCTAAGCAT                         ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATG
genomic: TAGACACTAACGGAATGGTGAAACTTGCTGACTTCGGCATGGCTAAGCATgtacgtatcg ... tgtgatgcagATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATG
EST: gi|162166784|gb|FC342961.1|FC342961
EST:     TAGACACTAACGGAATGGTGAAACTTGCTGACTTCGGCATGGCTAAGCAT                         ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATG
genomic: TAGACACTAACGGAATGGTGAAACTTGCTGACTTCGGCATGGCTAAGCATgtacgtatcg ... tgtgatgcagATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATG
EST: gi|100449751|gb|CJ973917.1|CJ973917
EST:     CTAACGGAATGGTGAAACTTGCTGACTTCGGCATGGCTAAGCAT                         ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATG
genomic: CTAACGGAATGGTGAAACTTGCTGACTTCGGCATGGCTAAGCATgtacgtatcg ... tgtgatgcagATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATG

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: 33 (upstream exon), 33 (downstream exon)
Score: 5

AGATATTAAAGGAGCGAACATTCTTGTAGACACTAACGGAATGGTGAAACTTGCTGACTTCGGCATGGCTAAGCATgtacgtatcg ... tgtgatgcagATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttttccagtccttggtttttgaaatgctgcttttcgattctctcttgttagaaggtactctttgttcctcatgtatcctgagacattgtgatgcagATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAG

- - - - - - - - - - - - - - tgctgct