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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcgattcttagtaacggagaaatctcaacaatttgttgtcaagatcgttgtttcgaagtggatgtaacagtgtgaaatgtaccttttgtattgtgaacatgctctgattgtcgacattggtgtggatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAGCAATCAAAGAACTTCACTTTTAAATGCCATAGAGATAACAACGATATAT

Basic information

species Physcomitrella patens
transcript PP1S33_129V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S33_129V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA15G05740.1 (Glycine max), 3'ss of exon 6
gtgagtcgattcttagtaacggagaaatctcaacaatttgttgtcaagatcgttgtttcgaagtggatgtaacagtgtgaaatgtaccttttgtattgtgaacatgctctgattgtcgacattggtgtggatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAGCAATCAAAGAACTTCACTTTTAAATGCCATAGAGATAACAACGATATAT
                                   || |||  || ||||  ||||||    ||   | | | | ||| |  ||||  | | |  |  | ||  |       |||       || | |   |  |||||||||| ||||| || |||||||| |  || || ||  | || |||  ||||||    || ||||||||||||||||||||||||||   ||| || ||||
-----------------------------------atatgtcttccagattcttgttt----gtaattatcaaattgtaagttgtaagtctagattgattaattttgggctgttgaaactgatgatatacttgctgtagGTTGGATCAATAGAAGGAAGAGTTGGGGTGCATCATTTGGACGATAGTCAGCATGGTAAAAACTTCACTTTTAAATGCCATAGAGAGGGCAATGAAATAT

upper sequence: PP1S33_129V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA08G19260.1 (Glycine max), 3'ss of exon 6
gtgagtcgattcttagtaacggagaaatctcaacaatttgttgtcaagatcgttgtttcgaagtggatgtaacagtgtgaaatgtaccttttgtattgtgaacatgctctgattgtcgacattggtgtggatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAGCAATCAAAGAACTTCACTTTTAAATGCCATAGAGATAACAACGATATAT
                                       ||  || ||||  || ||||   ||   | | | | ||| |  ||||  | | |  |  | ||  |       |||       || | |   | |||||||| || ||||| || ||||| || |  || || ||  | ||||||  ||||||    || ||||||||||||||||||||||||||   ||| || ||||
---------------------------------------gtcttccagattcttatttcagtgtaattatcaaattgtaagttgtaagtctagattgattaattttgagctgttgaaactgatgatatactttttgtagGTCGGATCAATAGAAGGAAGGGTTGGGGTGCATCATTTGGATGATAGTCAGCAGGGTAAAAACTTCACTTTTAAATGCCATAGAGAGGGCAATGAAATAT
















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|208345666|gb|DC909597.1|DC909597
EST:     AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTT                         GTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAG
genomic: AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTTgtgagtcgat ... gatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAG
EST: gi|208383584|gb|DC903541.1|DC903541
EST:     AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTT                         GTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAG
genomic: AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTTgtgagtcgat ... gatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAG
EST: gi|208392008|gb|DC941856.1|DC941856
EST:     AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTT                         GTTGGGTCANTCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAN
genomic: AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTTgtgagtcgat ... gatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAG
EST: gi|208355495|gb|DC942615.1|DC942615
EST:     AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTT                         GTTGGGTCAATCGAGGGAA
genomic: AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTTgtgagtcgat ... gatattgtagGTTGGGTCAATCGAGGGAA
EST: gi|100434093|gb|BY978955.1|BY978955
EST:     AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTT                         GTTGGGTCAATCGAGGGAAGAGTGGGCGTTCAGCACATTGATGATGCTCAG
genomic: AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTTgtgagtcgat ... gatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAG
EST: gi|208353800|gb|DC906488.1|DC906488
EST:     AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTT                         GTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAG
genomic: AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTTgtgagtcgat ... gatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAG
EST: gi|208350426|gb|DC906128.1|DC906128
EST:     AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTT                         GTTGGGTCAATCGAGGGAAGAGTGGCCGTTCANCACATTGATGATGCTCA
genomic: AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTTgtgagtcgat ... gatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCA
EST: gi|208346265|gb|DC905240.1|DC905240
EST:     AGTATCAAACACGATGTGTGGCAACCTCCCCGGGCAAGGAGGGCTTCCTT                         GTTGGGTCANTCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAG
genomic: AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTTgtgagtcgat ... gatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAG
EST: gi|100352940|gb|BY945526.1|BY945526
EST:     AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTT                         GTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAG
genomic: AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTTgtgagtcgat ... gatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAG
EST: gi|208357300|gb|DC910683.1|DC910683
EST:     AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAANGAGGGCTTCCTT                         GTTGGGTCANTCGAGGGAAGANTGGCCGTTCAGCACATTGATGATGCTCAC
genomic: AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTTgtgagtcgat ... gatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAG
EST: gi|208358353|gb|DC934546.1|DC934546
EST:     AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTT                         GTTGGGTCANTCGAGGGAA
genomic: AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTTgtgagtcgat ... gatattgtagGTTGGGTCAATCGAGGGAA
EST: gi|162172691|gb|FC348072.1|FC348072
EST:     AGTATCANACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTT                         GGTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAG
genomic: AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTTgtgagtcgat ... gatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAG
EST: gi|100378001|gb|BY949630.1|BY949630
EST:     AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTT                         GTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAG
genomic: AGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTTgtgagtcgat ... gatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAG

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: 20 (upstream exon), 26 (downstream exon)
Score: 3

ACAGAATTTAAGCGGATACAGTCGCCATTAAAGTATCAAACACGATGTGTGGCAACCTTCCCGGGCAAGGAGGGCTTCCTTgtgagtcgat ... gatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAGCAATCAAAGAACTTCACTTTTAAATGCCATAGAGATAACAACGATATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccttttgtattgtgaacatgctctgattgtcgacattggtgtggatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAGCAATCAAAGAACTTCACTTTTAAATGCCATAGAGATAACAACGATATAT
                      ctctgat  putative branch site (score: 3)
     tttgtatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcgattcttagtaacggagaaatctcaacaatttgttgtcaagatcgttgtttcgaagtggatgtaacagtgtgaaatgtaccttttgtattgtgaacatgctctgattgtcgacattggtgtggatattgtagGTTGGGTCAATCGAGGGAAGAGTGGCCGTTCAGCACATTGATGATGCTCAGCAATCAAAGAACTTCACTTTTAAATGCCATAGAGATAACAACGATATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC