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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaaactacattctaaacatcctacacccttttcagactaaattatatcagaccatagattctgtctttgggcaggcaagaccatgcttggttactatgaacatcactttacttgagtgtaaactaggaatattacgacgtaacagtaaatatgaaatcagtacttgacatgtttctatggcagGACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTGACGTGGAGATCCTTGACGAAATTATCCAG

Basic information

species Physcomitrella patens
transcript PP1S71_187V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S71_187V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ24611 (Selaginella moellendorffii), 3'ss of exon 5
gtacaaaactacattctaaacatcctacacccttttcagactaaattatatcagaccatagattctgtctttgggcaggcaagaccatgcttggttactatgaacatcactttacttgagtgtaaactaggaatattacgacgtaacagtaaatatgaaatcagtacttgacatgtttctatggcagGACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTGACGTGGAGATCCTTGACGAAATTATCCAG
                                                                                                                         |||  || | | |      ||||   | |    ||  ||  |||  | | | |||        |||| || || ||||||||||||||||| || || ||||||||  ||||||| ||||| || |||||||||||| | || |||
-------------------------------------------------------------------------------------------------------------------------gtatgcttgtattggctt-acgttgaattgctcatagaa--agtggtggtcttgt--------cagGTCCGCATAAGATTCAGGGTATTGGTGCGGGATTCATTCCAAGCATTCTAGACGTAGAAATCCTTGACGAAGTCATTCAG

upper sequence: PP1S71_187V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ13264 (Selaginella moellendorffii), 3'ss of exon 5
gtacaaaactacattctaaacatcctacacccttttcagactaaattatatcagaccatagattctgtctttgggcaggcaagaccatgcttggttactatgaacatcactttacttgagtgtaaactaggaatattacgacgtaacagtaaatatgaaatcagtacttgacatgtttctatggcagGACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTGACGTGGAGATCCTTGACGAAATTATCCAG
                                                                                                                                        ||     | ||  | ||| ||    ||| |  ||    || |   || |||| || || ||||||||||||||||| || || ||||||||  ||||||| ||||| || |||||||||||| | || |||
---------------------------------------------------------------------------------------------------------------------------------------gtattgtcttacgttgaat-tgctcacagaaagtggtg-gtct---tgtcagGTCCGCATAAGATTCAGGGTATTGGGGCGGGATTCATTCCAAGCATTCTAGACGTAGAAATCCTTGACGAAGTCATTCAG
















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|208385470|gb|DC953089.1|DC953089
EST:     TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAG                         GACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
genomic: TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAGgtacaaaact ... tctatggcagGACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
EST: gi|67694755|gb|BJ954988.1|BJ954988
EST:     TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAG                         GACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
genomic: TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAGgtacaaaact ... tctatggcagGACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
EST: gi|67575491|gb|BJ948315.1|BJ948315
EST:     TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAG                         GACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
genomic: TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAGgtacaaaact ... tctatggcagGACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
EST: gi|162171775|gb|FC348951.1|FC348951
EST:     TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAG                         GATCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTNCT-
genomic: TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAGgtacaaaact ... tctatggcagGACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATT-CTT
EST: gi|162219672|gb|FC395876.1|FC395876
EST:     TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAG                         GACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
genomic: TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAGgtacaaaact ... tctatggcagGACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
EST: gi|67698963|gb|BJ959196.1|BJ959196
EST:     TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAG                         GACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
genomic: TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAGgtacaaaact ... tctatggcagGACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
EST: gi|15590673|gb|BI675289.1|BI675289
EST:     TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAG                         GACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
genomic: TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAGgtacaaaact ... tctatggcagGACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
EST: gi|162184261|gb|FC359683.1|FC359683
EST:     ATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAAGGCA-GCCAG                         GACCTCACAAGATTCAGGGTATTG
genomic: ATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGA-GGCAAGCCAGgtacaaaact ... tctatggcagGACCTCACAAGATTCAGGGTATTG
EST: gi|208381504|gb|DC919506.1|DC919506
EST:     TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAG                         GACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
genomic: TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAGgtacaaaact ... tctatggcagGACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
EST: gi|162202798|gb|FC379780.1|FC379780
EST:     TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAG                         GACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
genomic: TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAGgtacaaaact ... tctatggcagGACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
EST: gi|16137490|gb|BI894354.1|BI894354
EST:     TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAG                         GACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
genomic: TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAGgtacaaaact ... tctatggcagGACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
EST: gi|18339257|gb|BJ171284.1|BJ171284
EST:     TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAG                         GACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG
genomic: TATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAGgtacaaaact ... tctatggcagGACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTG

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: 34 (upstream exon), 31 (downstream exon)
Score: 6

GTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAGgtacaaaact ... tctatggcagGACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTGACGTGGAGATCCTTGACGAAATTATCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattacgacgtaacagtaaatatgaaatcagtacttgacatgtttctatggcagGACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTGACGTGGAGATCCTTGACGAAATTATCCAG
                                         tgtttct  CT-rich tract
               agtaaatatgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaaaactacattctaaacatcctacacccttttcagactaaattatatcagaccatagattctgtctttgggcaggcaagaccatgcttggttactatgaacatcactttacttgagtgtaaactaggaatattacgacgtaacagtaaatatgaaatcagtacttgacatgtttctatggcagGACCTCACAAGATTCAGGGTATTGGAGCAGGGTTCATTCCTGGCATTCTTGACGTGGAGATCCTTGACGAAATTATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC