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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCGGATAGGAGGATCTACCTGCCCGAGGGCCTTTTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggccccgactgtgagcatctgtggtagcatggcgttgtgggttggaggcgcattgcgtggaggtggaggggtggtaggaggcgagtgagtgagatttgaggacgagactgacaatgcggcgatgatgttgttttgcag

Basic information

species Physcomitrella patens
transcript PP1S6_313V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S6_312V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G149428_T01 (Zea mays), 5'ss of exon 2
GTCCGGATAGGAGGATCTACCTGCCCGAGGGCCTTTTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggccccgactgtgagcatctgtggtagcatggcgtt-gtgggttggaggcgcattgcgtggaggtggaggggtggtaggaggcgagtgagtgagatttgaggacgagactgacaatgcggcgatgatgttgttttgcag
|||| || ||||||||||||||||| || || || ||||        ||| | || |||||||| |||||||||||||| |||||||||||  |  | |||   |   |   |   |  | ||  || |   |||  ||      |   |    || |   | |    | |  |  || || |  |                                            
GTCCTGACAGGAGGATCTACCTGCCGGATGGGCTCTTGGACCGCTCGGAGGTACCGGAGTACCTCACCGGAGAGGTCCCTGGAGAgtaagtcacatc-actccaactttgccttccataaaggtttttgcttgtttcagaaattctagattccagttggtagtttaatgaaatcaggttagcgcta--------------------------------------------

upper sequence: PP1S6_312V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA16G33030.1 (Glycine max), 5'ss of exon 2
GTCCGGATAGGAGGATCTACCTGCCCGAGGGCCTTTTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggccccgactgtgag--catctgtggta-gcatggcgttgtgggttgg-aggcgcattgcgtggaggtggaggggtggtaggaggcgagtgagtgagatttgaggacgagactgacaatgcggcgatgatgttgttttgcag
|||| || || ||||||| | |||| ||||| || ||||        |||||||| |||||| |||||||||| |||||||||||||| ||   ||   ||   ||  ||  | | ||   |||     ||   |     |  |  |  | ||     ||    | |  | ||       |       |||||   | | |  || | |||| |                   
GTCCTGACAGAAGGATCTTCTTGCCTGAGGGTCTCTTGGACCGATCTGAGATCCCAGAGTACTTGACCGGAGAAGTCCCCGGAGAgtatgttctcctctcttatagtccacttttagttcacattaacatgcaagccattaaacaaacagtgtt----tgtgaagttttttggttcttgttttacttaatttggtaatgtg--tgtccatgcag-------------------
















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|208364400|gb|DC950701.1|DC950701
EST:     TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGA                         CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
genomic: TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggcc ... tgttttgcagCTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
EST: gi|208363096|gb|DC958009.1|DC958009
EST:     TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGA                         CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
genomic: TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggcc ... tgttttgcagCTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
EST: gi|162267721|gb|FC443711.1|FC443711
EST:     GCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGA                         CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
genomic: GCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggcc ... tgttttgcagCTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
EST: gi|162246281|gb|FC423639.1|FC423639
EST:     TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGA                         CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
genomic: TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggcc ... tgttttgcagCTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
EST: gi|208359085|gb|DC957833.1|DC957833
EST:     TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGA                         CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
genomic: TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggcc ... tgttttgcagCTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
EST: gi|162232039|gb|FC409113.1|FC409113
EST:     AAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGA                         CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
genomic: AAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggcc ... tgttttgcagCTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
EST: gi|162271665|gb|FC448590.1|FC448590
EST:     TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGA                         CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
genomic: TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggcc ... tgttttgcagCTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
EST: gi|162263794|gb|FC439659.1|FC439659
EST:     TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGA                         CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
genomic: TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggcc ... tgttttgcagCTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
EST: gi|162170792|gb|FC347406.1|FC347406
EST:     GAGAGGTCCCCGGAGA                         CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
genomic: GAGAGGTCCCCGGAGAgtaagtggcc ... tgttttgcagCTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
EST: gi|162231613|gb|FC408232.1|FC408232
EST:     TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGA                         CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
genomic: TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggcc ... tgttttgcagCTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
EST: gi|162157170|gb|FC333740.1|FC333740
EST:     AGTACCTGACCGGAGAGGTCCCCGGAGA                         CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
genomic: AGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggcc ... tgttttgcagCTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
EST: gi|162233003|gb|FC408410.1|FC408410
EST:     TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGA                         CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
genomic: TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggcc ... tgttttgcagCTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
EST: gi|208357339|gb|DC953719.1|DC953719
EST:     GAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGA                         CTATGGGTACGACCNTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
genomic: GAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggcc ... tgttttgcagCTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
EST: gi|208366912|gb|DC951399.1|DC951399
EST:     TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGA                         CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCTGAGGACTTCGACAG
genomic: TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggcc ... tgttttgcagCTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
EST: gi|162194119|gb|FC369462.1|FC369462
EST:     TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGA                         CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
genomic: TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggcc ... tgttttgcagCTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
EST: gi|208380204|gb|DC927483.1|DC927483
EST:     TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGA                         CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG
genomic: TTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggcc ... tgttttgcagCTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG

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: 1081

GTCCGGATAGGAGGATCTACCTGCCCGAGGGCCTTTTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggcc ... tgttttgcagCTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCGGATAGGAGGATCTACCTGCCCGAGGGCCTTTTGGCGAAGGACGAGATCCCCGAGTACCTGACCGGAGAGGTCCCCGGAGAgtaagtggccccgactgtgagcatctgtggtagcatggcgttgtgggttggaggcgcattgcgtggaggtggaggggtggtaggaggcgagtgagtgagatttgaggacgagactgacaatgcggcgatgatgttgttttgcag

- - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG