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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctccatgacgtggttgtttcatgcttttcgggacgcttgaatttttttctgttttaaaactacttttttgatatggatgtctctacttcgtgatgcagGTCTTTGTTCGTGCAGTACACGAGGCGAAGTGGATGAGTGAGATGGAAATCAGCATATATGACTCGTGGTTTAATCCAGTTGTGTCAGAGCTTCCCGGAT

Basic information

species Physcomitrella patens
transcript PP1S70_117V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S70_117V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os05g35520.2 (Oryza sativa), 3'ss of exon 3
------gtaagctccatg-acgtggttgtttcatgctttt-cgggacgcttgaatttttttctgttttaaaactactt---ttttgatatggatg--tctctacttcgtgatgca---gGTCTTTGTTCGTGCAGTACACGAGGCGAAGTGGATGAGTGAGATGGAAATCAGCATATATGACTCGTGGTTTAATCCAGTTGTGTCAGAGCTTCCCGGAT
       ||   | | || |  |  | |||      ||   | | || ||  | |||  ||||| |  ||   |  ||    |||  | ||  |       |  ||| | |||||   ||| ||||||||||| || || || || || ||||||| ||||||||| |||||||| || ||||| |||||| |||| |||||||||  |||||| ||  
gtgagtttatcgtacttgcaaatactagttcagcaattgaacagaacactgtagtttccttctggtgcaattttttttcctcttttgtgtgactaaactattctttcattatgcactagGTATTTGTTCGTGCTGTTCATGAAGCTAACTGGATGAATGAGATGGAGATCAGCATTTACGACTCATGGTTTGATCCTGTTGTGTCATCGCTTCCAGGTC

upper sequence: PP1S70_117V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os01g65350.2 (Oryza sativa), 3'ss of exon 2
-----------------gtaagctccatgacgtggttgtttcatgcttttcgggacgcttg-aatttttttctgttttaaaactacttttttgatatggatg----tctctacttcg---tgatgcagGTCTTTGTTCGTGCAGTACACGAGGCGAAGTGGATGAGTGAGATGGAAATCAGCATATATGACTCGTGGTTTAATCCAGTTGTGTCAGAGCTTCCCGGAT
                   ||  |||     |    ||  ||  |   || |  ||| ||| | | ||| | | |   |    || ||| ||    | | |     | || |  |     |  || |||| ||||||||||| || || || || || |||||||  |||||||| |||||||| |||||||| |||||| | ||||| ||||||   || || ||| 
gtaggtaaatctttccgtcaaagtccgcttggattgtgaatctagagctttgatacgattgcagtctttatatttcccattgttattttcttctcctagttaaaattttcaaagttaaatttttgaagGTTTTTGTTCGTGCTGTCCATGAAGCCAACTGGATGAACGAGATGGAGATCAGCATCTATGACTCCTGGTTTGACCCAGTGGTGTCATCACTCCCAGGAC

upper sequence: PP1S70_117V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G091845_T03 (Zea mays), 3'ss of exon 2
-----------------------------------------gtaagctccatgacgtggtt-gtttcatgcttttcgggacgcttgaatttttttctgttttaaaactacttttttgatatggatgtctctacttcgtgatg-cagGTCTTTGTTCGTGCAGTACACGAGGCGAAGTGGATGAGTGAGATGGAAATCAGCATATATGACTCGTGGTTTAATCCAGTTGTGTCAGAGCTTCCCGGAT
                                          | ||  |  |||  |  || |  |    | ||| ||     |||  ||||||||  |||     || | | ||| |     | || | |  ||  |  |  ||||| ||||||||||| || || || || || |||||||  ||||||||||||||||| |||||||| |||||| | ||||||||||||   || || ||  
gtaggtttaccttttgttgtaaaaactaccttggtgatggattgagtgctttgatataatttgaatttcaccttttggtctatttgtttttttttcaatttct---cttcctattttaagca-acgttttttgttgatattttcagGTTTTTGTTCGTGCTGTGCATGAAGCAAACTGGATGAACGAGATGGAAATCAGCATTTATGACTCTTGGTTTGACCCAGTTGTGTCATCACTCCCAGGTC

upper sequence: PP1S70_117V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G147213_T01 (Zea mays), 3'ss of exon 2
----gtaagc--tccatgacgtggttgtttcatgcttttcggg-acgcttgaatttttttctgttttaa-----aactacttttttgatatggatgtctctact-tcgtgatgcagGTCTTTGTTCGTGCAGTACACGAGGCGAAGTGGATGAGTGAGATGGAAATCAGCATATATGACTCGTGGTTTAATCCAGTTGTGTCAGAGCTTCCCGGAT
    || |    | | |      | | ||||| |   |       |  || |  |   ||||| |   |     || |||  |  |   |  |||   |||| | | |||   ||||| || || ||||| || ||||| || || ||||||| ||||||||| |||||||| ||||| || |||||| ||||||||||||||   || || ||  
gtaggtcaatcattctttcaaatgctatttcaggaactgaacatgcatttcagctgccttctgatacgattatcaagtaccatcatccaactgattgttctattcttgtgtaccagGTATTCGTCCGTGCTGTTCACGAAGCTAATTGGATGAATGAGATGGAGATCAGCATCTATGATTCCTGGTTTGATCCAGTTGTGTCATCACTCCCAGGTC

upper sequence: PP1S70_117V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ08351 (Selaginella moellendorffii), 3'ss of exon 1
------------------------------------------------------------------------------gtaagctccatgacgtggttgtttcatgcttttcgggacgcttg--aatttttttctgttttaaaactacttttttgatatggatgtctctacttcgtgatgcagGTCTTTGTTCGTGCAGTACACGAGGCGAAGTGGATGAGTGAGATGGAAATCAGCATATATGACTCGTGGTTTAATCCAGTTGTGTCAGAGCTTCCCGGAT
                                                                               | ||     | ||| |  | |||  | ||||||   ||   ||  ||   ||||  ||||      |  | |  | |  |       | |    | || | ||||| ||||| ||||| || ||||| || ||||||||||| |||||||| |||||||| || |||||||||||  | || || ||  | ||||||||||| |
gtaagctctcaagttttgtttgagctctcttgcattgcttggtttctagttcgtagtttttcttctggactgattgaaatgagtgtttttacgagact-ttttgttcttttcttcacttctgccaagagtttttcgtttcttcg-tgatgtagtaacttacgctggtatgtcgcttgct-cagGTGTTTGTGCGTGCCGTGCACGAAGCAAAGTGGATGAGCGAGATGGAGATCAGCATCTACGACTCGTGGTTCGACCCGGTGGTAGCCGAGCTTCCCGGTT

upper sequence: PP1S70_117V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ15275 (Selaginella moellendorffii), 3'ss of exon 2
----------------------------------------------------------------gtaagctccatgacgtgg--ttgtttcatgcttttcgggacgcttgaatttttttctg---ttttaaaactacttttt----------tgatatgg------atgtctctacttcg-tgatgcagGTCTTTGTTCGTGCAGTACACGAGGCGAAGTGGATGAGTGAGATGGAAATCAGCATATATGACTCGTGGTTTAATCCAGTTGTGTCAGAGCTTCCCGGAT
                                                                 |   ||   |||   ||  |  |||| || |||   |   | ||   ||||| |||    || |   |  | |||||          |||| | |      | |    ||  ||| |    ||||| ||||| ||||| || ||||| || ||||||||||| |||||||| |||||||| || |||||||||||  | || || ||  | ||||||||||| |
gtaagctctcaagtcttgtttgagctctcttgcattgcttcgtttctagttcgtagtttttcttctggactgattgaaacgggttcttttcgtgttttgacgagagtttttgtttttctcttcacttctgccaagagtttttcgtttcttcgtgatgtagtaacttacgctggtatgtcgcttgctcagGTGTTTGTGCGTGCCGTGCACGAAGCAAAGTGGATGAGCGAGATGGAGATCAGCATCTACGACTCGTGGTTCGACCCGGTGGTAGCCGAGCTTCCCGGTT

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|162197342|gb|FC372304.1|FC372304
EST:     GTATCAAGCCTCTGCGTTTGATGGAGCGGAGTGTCTTCAGTGATCGAATG                         GTCTTTGTTCGTGCAGTACACGAGGCGAAGTGGATGAGTGAGATGGAAATC
genomic: GTATCAAGCCTCTGCGTTTGATGGAGCGGAGTGTCTTCAGTGATCGAATGgtaagctcca ... cgtgatgcagGTCTTTGTTCGTGCAGTACACGAGGCGAAGTGGATGAGTGAGATGGAAATC
EST: gi|162243951|gb|FC422306.1|FC422306
EST:     GTATCAAGCCTCTGCGTTTGATGGAGCGGAGTGTCTTCAGTGATCGAATG                         GTCTTTGTTCGTGCAGTACACGAGGCGAAGTGGATGAGTGAGATGGAAATC
genomic: GTATCAAGCCTCTGCGTTTGATGGAGCGGAGTGTCTTCAGTGATCGAATGgtaagctcca ... cgtgatgcagGTCTTTGTTCGTGCAGTACACGAGGCGAAGTGGATGAGTGAGATGGAAATC
EST: gi|162278218|gb|FC454453.1|FC454453
EST:     GTATCAAGCCTCTGCGTTTGATGGAGCGGAGTGTCTTCAGTGATCGAATG                         GTCTTTGTTCGTGCAGTACACGAGGCGAAGTGGATGAGTGAGATGGAAATC
genomic: GTATCAAGCCTCTGCGTTTGATGGAGCGGAGTGTCTTCAGTGATCGAATGgtaagctcca ... cgtgatgcagGTCTTTGTTCGTGCAGTACACGAGGCGAAGTGGATGAGTGAGATGGAAATC

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: 28 (upstream exon), 24 (downstream exon)
Score: 2

GAACTACGTATTTGTAACTCGTCTAATGCAGGAGCGAGAGTCTGCTCATGGTATCAAGCCTCTGCGTTTGATGGAGCGGAGTGTCTTCAGTGATCGAATGgtaagctcca ... cgtgatgcagGTCTTTGTTCGTGCAGTACACGAGGCGAAGTGGATGAGTGAGATGGAAATCAGCATATATGACTCGTGGTTTAATCCAGTTGTGTCAGAGCTTCCCGGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttctgttttaaaactacttttttgatatggatgtctctacttcgtgatgcagGTCTTTGTTCGTGCAGTACACGAGGCGAAGTGGATGAGTGAGATGGAAATCAGCATATATGACTCGTGGTTTAATCCAGTTGTGTCAGAGCTTCCCGGAT
                      ttttgat  putative branch site (score: 2)
                                    tctctacttc  putative PPT
        ttttaaaactactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctccatgacgtggttgtttcatgcttttcgggacgcttgaatttttttctgttttaaaactacttttttgatatggatgtctctacttcgtgatgcagGTCTTTGTTCGTGCAGTACACGAGGCGAAGTGGATGAGTGAGATGGAAATCAGCATATATGACTCGTGGTTTAATCCAGTTGTGTCAGAGCTTCCCGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT