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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaatcgctgattgaatttggcagagtaactatctcttagaatccagcatatatgtcttttagatttcattaaatgcacaaatttaatgttttctgacgttattacacgtgattccttctctgcag

Basic information

species Physcomitrella patens
transcript PP1S204_49V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os02g13530.1 (Oryza sativa), 5'ss of exon 3
AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaatcgctgattgaatttggcagagtaactatctcttagaatccagcatatatgtcttttagatttcattaaatgca-caaatttaatgttttctgacgttattacacgtgattccttctctgcag
||||| || || |||||||||||||||||  | ||||| || |||||| | |||||| |  | ||||||||| | |||||||||||||| |   || |  |    |||     ||  |||     ||| |||  ||      ||||   |   | |   | | || ||| | | ||  |  |   || || || | || ||                   
AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAGgtctatatacttacc---tgacc---gccaagt-----tctattattataagagttataaaccgcattg--ctaactacatgtaactaaactgcttgcttgtgtcgattttgcag------------------

upper sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G171426_T01 (Zea mays), 5'ss of exon 4
AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgc-gtaatcgctgattgaatttggcagagtaactatctcttagaatccagcatatatgtcttttagatttcattaaatgcacaaatttaatgttttctgacgttattacacgtgattccttctctgcag
||||| || || || ||||||||||||||| | |||||||| |||||||| |||||| |  ||||||||||| | ||||| ||||||||  |   |   |    | |||   |       |     ||||||    | |||  ||||     | | || || |     |    |    | |  | | || | || || | ||    |   |  | | |||
AATGGTCTTGCTACTAAGGTTGAGAAGTCCCGCAAGCAAATGAAGGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagttatctacatacaatgatactccttacctgcagctctcttg---tgcagtttatag----tgtggactt-accgtgtcactagtgcttacatatgctaatgtaat-atacactttctgtcttttacag

upper sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G151252_T01 (Zea mays), 5'ss of exon 4
AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaatcgctgat-tgaa----tttggcagagtaactatctcttagaatccagcatatatgtcttttagatttcattaaatgcacaaatttaatgttttctgacgttattacacgtgattccttctctgcag
||||| || || || ||||||||||||||| | |||||||| || ||||| |||||| |  ||||||||||| | ||||| ||||||||  || ||    ||||  || |    | | |   |||   |||  ||||   | |  ||  | |||  |  |   || |     |  |||                                              
AATGGTCTTGCTACTAAGGTTGAGAAGTCCCGCAAGCAAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagc-tatctactgacatgcagtcctcttgtgaagtttatattacttactgtgc--cacgtgtgtaatacatgctttacgtcttttacag---------------------------------------------

upper sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G151252_T02 (Zea mays), 5'ss of exon 3
-------------AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaatcgctgat-tgaa----tttggcagagtaactatctcttagaatccagcatatatgtcttttagatttcattaaatgcacaaatttaatgttttctgacgttattacacgtgattccttctctgcag
             ||||| || || || ||||||||||||||| | |||||||| || ||||| |||||| |  ||||||||||| | ||||| ||||||||  || ||    ||||  || |    | | |   |||   |||  ||||   | |  ||  | |||  |  |   || |     |  |||                                              
TTTGTATTGCCAGAATGGTCTTGCTACTAAGGTTGAGAAGTCCCGCAAGCAAATGAAAGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAGgtgagc-tatctactgacatgcagtcctcttgtgaagtttatattacttactgtgc--cacgtgtgtaatacatgctttacgtcttttacag---------------------------------------------

upper sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G091383_T01 (Zea mays), 5'ss of exon 3
AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaatcgc--tgattgaatttggcagagtaactatctcttagaatccagcatatatgtcttt---tagatttcattaaat---gcacaaatttaatgttttctgacgttattacacgtgattccttctctgcag-----------
|| || || || |||||||| ||||||||  | ||||| || |||||| | |||||| |  | ||||||||| | ||||||||||||||||||| | | ||  | ||   | |     |  ||| |||  ||  | ||   | || |  |  |||   |   ||||  |   |     | |||  || |  ||| |  |||  | ||   | |||  ||   || |            
AACGGTCTTGCTACCAAGGTGGAGAAGTCGCGCAAGCAGATGAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGCGGTGTGAAGAAGgtatgcgcacttgcattcatctgactgttgtgtctaa-tattactgcgcatttggaatgtggggatttcattgtgtttctgtggttctgataaaaaaatagttattttttgcgt-gtaactgctaatttttttgttggattggttttgcag

upper sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv14s0030g01620.t01 (Vitis vinifera), 5'ss of exon 4
AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaatcgctgattgaatttggcagagtaactatctcttagaatccag-catatatgtcttt-tagatttcattaaatgcacaaatttaatgttttctgacgttattacacgtgattccttctctgcag
|||||| |||  |||||||| |||||||| ||||||||||| |||||| | |||||  | ||||||||| || | ||||| ||||||||| |         ||| | ||||||     ||| || | |||   | |  |  |||      ||   ||  |  ||||   |||  | |                                            
AATGGATTGGATACCAAGGTCGAGAAGTCTAGGAAGCAAATGAAGGAGAGGAAGAATAGGTCCAAGAAGGTCCGAGGTGTAAAGAAGgtaagaag------tgaataaatttgcagtggtacctttttctctcatttaactcattctcacctccctatttcccatttcttgctaacag-------------------------------------------

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|162207611|gb|FC384064.1|FC384064
EST:     AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAG                         ACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
genomic: AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaa ... ttctctgcagACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
EST: gi|162207612|gb|FC384065.1|FC384065
EST:     AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAG                         ACTAAGGCCGCTGGTGACGCTCAGAAGAAAAAGTAGATGTGACATAGTTTC
genomic: AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaa ... ttctctgcagACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
EST: gi|162264253|gb|FC441355.1|FC441355
EST:     AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAG                         ACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
genomic: AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaa ... ttctctgcagACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
EST: gi|162211993|gb|FC388455.1|FC388455
EST:     AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAG                         ACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
genomic: AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaa ... ttctctgcagACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
EST: gi|162231344|gb|FC406767.1|FC406767
EST:     AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAG                         ACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
genomic: AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaa ... ttctctgcagACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
EST: gi|162184761|gb|FC361063.1|FC361063
EST:     AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAG                         ACTAAGGCCGCTGGTGACGCTNAGAAGAAAAAGTAGATGTGACATAGTTTC
genomic: AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaa ... ttctctgcagACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
EST: gi|67722912|gb|BJ973171.1|BJ973171
EST:     AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAG                         ACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACCATAGTTT
genomic: AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaa ... ttctctgcagACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGAC-ATAGTTT
EST: gi|162184143|gb|FC358889.1|FC358889
EST:     AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAG                         ACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
genomic: AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaa ... ttctctgcagACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
EST: gi|162211994|gb|FC388456.1|FC388456
EST:     AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAG                         ACTAAGGCCGCTGGTGACGCTNAGAAGAAAAAGTAGATGTGACATAGTTTC
genomic: AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaa ... ttctctgcagACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
EST: gi|162264252|gb|FC441354.1|FC441354
EST:     AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAG                         ACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
genomic: AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaa ... ttctctgcagACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
EST: gi|7147798|gb|AW509720.1|AW509720
EST:     AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAG                         ACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
genomic: AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaa ... ttctctgcagACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
EST: gi|67728029|gb|BJ978288.1|BJ978288
EST:     AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAG                         ACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
genomic: AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaa ... ttctctgcagACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
EST: gi|100370341|gb|BY985362.1|BY985362
EST:     AGAAGATCAGGGGTGTGAAGAAG                         ACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
genomic: AGAAGATCAGGGGTGTGAAGAAGgtatgcgtaa ... ttctctgcagACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
EST: gi|162184760|gb|FC361062.1|FC361062
EST:     AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAG                         ACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
genomic: AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaa ... ttctctgcagACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
EST: gi|162252337|gb|FC427276.1|FC427276
EST:     AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAG                         ACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
genomic: AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaa ... ttctctgcagACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
EST: gi|67722063|gb|BJ972322.1|BJ972322
EST:     AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAG                         ACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC
genomic: AAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaa ... ttctctgcagACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTC

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: 35 (upstream exon), 35 (downstream exon)
Score: 202

AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaa ... ttctctgcagACTAAGGCCGCTGGTGACGCTAAGAAGAAAAAGTAGATGTGACATAGTTTCCTTCGCATGATGTAACCATGGACTCTACTCCTGCTAGGTTTTGAGATGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGGACTGGCGACCAAGGTTGAGAAGTCCAGGAAGCAAATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGTGTGAAGAAGgtatgcgtaatcgctgattgaatttggcagagtaactatctcttagaatccagcatatatgtcttttagatttcattaaatgcacaaatttaatgttttctgacgttattacacgtgattccttctctgcag

- - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG