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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcatcagtgttctacttttggccctgctatcattatcttggttcggataggaggggagttagttttctttgactgagcataagtgagcattgctccatagtggacgactactagtaagtcacttgactttctagtatttcttcctgtttcagGCCCCCTGAGCTGCTGATGGGCTCCACAAAGTATACTCCAGCTGTGGACATGTGGTCAGTGGGGTGCATTTTTGCTGAGCTTCTTAATGGGAAACCCATC

Basic information

species Physcomitrella patens
transcript PP1S121_162V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S121_162V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 7
gtaaggcatcagtgttctacttttggccctgctatcattatcttggttcggataggaggggagttagttttctttgactgagcataagtgagcattgctccatagtggacgactactagtaagtcacttgactttctagtatttcttcctgt-ttcagGCCCCCTGAGCTGCTGATGGGCTCCACAAAGTATACTCCAGCTGTGGACATGTGGTCAGTGGGGTGCATTTTTGCTGAGCTTCTTAATGGGAAACCCATC
                                                                     |      |||   ||| ||   |   | |     |     |   ||||      ||| |   || |||     || ||  ||| | ||| || |||||| || |  | ||   ||| | ||||  |||||| || ||||||||||||||||| || ||||||||||||||||| ||||| || || || 
--------------------------------------------------------------------gtatggaaacttcccatgaggaggttcttccattcatatttctcttactttcttttcattgttctctct--ctcttatttgtgtatgcagACCTCCTGAGTTGTTACTCGGGAGCACGAGGTATGGTCCAGCCGTTGACATGTGGTCAGTGGGTTGTATTTTTGCTGAGCTTCTCAATGGAAAGCCAATA

upper sequence: PP1S121_162V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G019267_T01 (Zea mays), 3'ss of exon 7
gtaaggcatcagtgttctacttttggccctgctatcattatcttggttcggataggaggggagttagttttctttgactg-agcataagtgagcattgctccatagtggacgactactagtaa-gtcacttgactttctagtatttctt--cctgtttcagGCCCCCTGAGCTGCTGATGGGCTCCACAAAGTATACTCCAGCTGTGGACATGTGGTCAGTGGGGTGCATTTTTGCTGAGCTTCTTAATGGGAAACCCATC
                                                                |||| || |   ||    |  |     | ||||| | |  |   | |   |||   |   ||  |  |  | |  ||| || ||      | | ||| || || ||| ||||  | ||   ||||||||||   ||||| || ||||||||||||||||| || |||||||| || ||||| |||||||| || || 
-------------------------------------------------------------gtatagtattgtaaaaccatggttttgagaaacattgttgccaaacaggcccttacagttgttgttgcaagcttcttaagtcttcctggattggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATA

upper sequence: PP1S121_162V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA14G04410.1 (Glycine max), 3'ss of exon 7
gtaaggcatcagtgttctacttttggccctgctatcattatcttggttcggataggaggggagttagttttctttgactgagcataagtgagcattgctccatagtggacgactactagtaagtcacttgactttctagtatttcttcctgtttcagGCCCCCTGAGCTGCTGATGGGCTCCACAAAGTATACTCCAGCTGTGGACATGTGGTCAGTGGGGTGCATTTTTGCTGAGCTTCTTAATGGGAAACCCATC
                                                                                   ||  |||  ||||  |  ||  ||    |  |  | |  | || |  |  |  |  | |||     | | | || || |||||| ||||| | ||  | |||||||||   ||||||||||| |||||||| || |||||||||||||||||||||||| | ||||| || || 
--------------------------------------------------------------------------------gtaattggtgt-catttttttatcatgagttatca--aattggccaatgcatgtattgatttttggctatatct-agACCACCTGAGTTGCTGCTAGGAACAACAAAGTATGGGCCAGCTGTGGATATGTGGTCTGTTGGGTGCATTTTTGCTGAGCTTCTTCAAGGGAAGCCTATA

upper sequence: PP1S121_162V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA02G44400.1 (Glycine max), 3'ss of exon 8
gtaaggcatcagtgttctacttttggccctgctatcattatcttggttcggataggaggggagttagttttctttgactgagcataagtga-gcattgctccatagtggacgactactagtaagtcacttgactttctagtatttcttcctgt-ttcagGCCCCCTGAGCTGCTGATGGGCTCCACAAAGTATACTCCAGCTGTGGACATGTGGTCAGTGGGGTGCATTTTTGCTGAGCTTCTTAATGGGAAACCCATC
                                                                                    ||| ||  |   |  |  ||  ||  | |  |    |  | || |  |  |  |  | | | |   | | || || || |||||| ||||| | ||  | |||||||||   ||||||||||| |||||||| || |||||||||||||||||||||||| | ||||| || |||
-----------------------------------------------------------------------------------gtaattggtgtcattttttatcatgatctatga--gattggccaatgcatgtattgatttctttatatatatttagACCACCTGAGTTGCTGCTAGGGACAACAAAGTATGGACCAGCTGTGGATATGTGGTCTGTTGGGTGCATTTTTGCTGAGCTTCTTCAAGGGAAGCCTATC

upper sequence: PP1S121_162V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA20G10960.1 (Glycine max), 3'ss of exon 6
gtaaggcatcagtgttctacttttggccctgctatcattatcttggttcggataggaggggagttagttttctttgactgagcataagtgagcattgctccatagtggacgactactagtaagtcacttgactttctagtatttcttcctgtt-tcagGCCCCCTGAGCTGCTGATGGGCTCCACAAAGTATACTCCAGCTGTGGACATGTGGTCAGTGGGGTGCATTTTTGCTGAGCTTCTTAATGGGAAACCCATC
                                           |  ||    |         |||  ||   ||||||  |   |   |  | |  | | |||  || ||   | |   ||   ||| | | |   |  |||||| |  | || | || ||||||||||||||| | ||  | |||| ||||   |||||||| || |||||||| || |||||||||||||| ||||||||| ||||||| || |||
------------------------------------------gtaatttatgtccataataggtt--ttaattttgacctaagttcttttgggagggttgcatcatgaacttatgcccata---cacattattgatt--tatttcattatattattagACCCCCTGAGCTGCTGCTTGGGACAACAAGGTATGGGCCAGCTGTAGATATGTGGTCTGTAGGGTGCATTTTTGCAGAGCTTCTTCATGGGAAGCCTATC

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|162159147|gb|FC334318.1|FC334318
EST:     GATCAGAATGGTCAACCACTGACAAACAGAGTTATCACTCTTTGGTATAG                         GCCCCCTGAGCTGCTGATGGGCTCCACAAAGTATACTCCAGCTGTGGACAT
genomic: GATCAGAATGGTCAACCACTGACAAACAGAGTTATCACTCTTTGGTATAGgtaaggcatc ... cctgtttcagGCCCCCTGAGCTGCTGATGGGCTCCACAAAGTATACTCCAGCTGTGGACAT
EST: gi|162171355|gb|FC347254.1|FC347254
EST:     GATCAGAATGGTCAACCACTGACAAACAGAGTTATCACTCTTTGGTATAG                         GCCCCCTGAGCTGCTGATGGGCTCCACAAAGTATACTCCAGCTGTGGACAT
genomic: GATCAGAATGGTCAACCACTGACAAACAGAGTTATCACTCTTTGGTATAGgtaaggcatc ... cctgtttcagGCCCCCTGAGCTGCTGATGGGCTCCACAAAGTATACTCCAGCTGTGGACAT

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), 16 (downstream exon)
Score: 1

ATGGAATTTTGAAGCTTGCTGATTTTGGGCTTGCAAGGTCGTTTTCTAATGATCAGAATGGTCAACCACTGACAAACAGAGTTATCACTCTTTGGTATAGgtaaggcatc ... cctgtttcagGCCCCCTGAGCTGCTGATGGGCTCCACAAAGTATACTCCAGCTGTGGACATGTGGTCAGTGGGGTGCATTTTTGCTGAGCTTCTTAATGGGAAACCCATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtggacgactactagtaagtcacttgactttctagtatttcttcctgtttcagGCCCCCTGAGCTGCTGATGGGCTCCACAAAGTATACTCCAGCTGTGGACATGTGGTCAGTGGGGTGCATTTTTGCTGAGCTTCTTAATGGGAAACCCATC
                       acttgac  putative branch site (score: 1)
                                     tatttcttcctgtttc  putative PPT
                                  tagtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggcatcagtgttctacttttggccctgctatcattatcttggttcggataggaggggagttagttttctttgactgagcataagtgagcattgctccatagtggacgactactagtaagtcacttgactttctagtatttcttcctgtttcagGCCCCCTGAGCTGCTGATGGGCTCCACAAAGTATACTCCAGCTGTGGACATGTGGTCAGTGGGGTGCATTTTTGCTGAGCTTCTTAATGGGAAACCCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT