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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctttgtttctccgctttacatgaaaagtttgctcgtgtactattagaccatcttttgtgaccatgttatgactcatcaggttgtatgatgttttgcagTTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGATAGTGCTGCTAAGAAATACGATTTGGAGGCATGGTTTCCAGCTTCCAAGA

Basic information

species Physcomitrella patens
transcript PP1S142_120V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S142_120V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 7
ctctttgtttctccgctttacatgaaaagtt-tgctcgtgtactattagaccatcttttgtgaccatgttatgactcatcaggttgtatgatgttttgcagTTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGATAGTGCTGCTAAGAAATACGATTTGGAGGCATGGTTTCCAGCTTCCAAGA
              |   ||      | ||| || || |       |||    || |   |||   |  | | | |  | |  |  | |    | |||||| | || || || || | ||| || ||||| |||||||| || ||||| |||  ||||||||||||||| |||||||| |||||||| || || || ||||
--------------gtaataatcagtatgttgtgatctttataacctagtttgtcctccctga--gttgtctaaatttttatttaatgtc-catcttgcagATTGGGCTACCATACCAAGTTGTTTCCATTGTCTCTGGCGCTCTTAATGATGCTGCTGCTAAGAAATATGATTTGGAAGCATGGTTCCCTGCATCAAAGA
















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|208396648|gb|DC929027.1|DC929027
EST:     GGAAGATGCACGANGAAATGTTGAAGAATTCAGAAGACTTCTANCAACAG                         TTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGAT
genomic: GGAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAACAGgtaccgaatt ... tgttttgcagTTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGAT
EST: gi|162204299|gb|FC380487.1|FC380487
EST:     GGAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAACAG                         TTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGAT
genomic: GGAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAACAGgtaccgaatt ... tgttttgcagTTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGAT
EST: gi|67724461|gb|BJ974720.1|BJ974720
EST:     GGAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAACAG                         TTGGGTCTTCCTTATCGAGTGGTATCCAT--TCTCTGGAGCACTTAACGAT
genomic: GGAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAACAGgtaccgaatt ... tgttttgcagTTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGAT
EST: gi|208353284|gb|DC926167.1|DC926167
EST:     GGAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTNTACCAACAG                         TTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGAT
genomic: GGAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAACAGgtaccgaatt ... tgttttgcagTTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGAT
EST: gi|67697454|gb|BJ957687.1|BJ957687
EST:     GGAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAACAG                         TTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGAT
genomic: GGAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAACAGgtaccgaatt ... tgttttgcagTTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGAT
EST: gi|162204300|gb|FC380488.1|FC380488
EST:     GGAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAACAG                         TTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGAT
genomic: GGAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAACAGgtaccgaatt ... tgttttgcagTTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGAT
EST: gi|37839193|gb|BJ597201.1|BJ597201
EST:     GAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAACCAG                         TTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGA
genomic: GAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAA-CAGgtaccgaatt ... tgttttgcagTTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGA
EST: gi|208368352|gb|DC955535.1|DC955535
EST:     GGAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAACAG                         TTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGAT
genomic: GGAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAACAGgtaccgaatt ... tgttttgcagTTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGAT
EST: gi|37838367|gb|BJ596375.1|BJ596375
EST:     GAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAACCAG                         TTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGA
genomic: GAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAA-CAGgtaccgaatt ... tgttttgcagTTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGA
EST: gi|67725840|gb|BJ976099.1|BJ976099
EST:     GGAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAACAG                         TTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGAT
genomic: GGAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAACAGgtaccgaatt ... tgttttgcagTTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGAT

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), 33 (downstream exon)
Score: 6

TGAGAAGGTGGAGCAGTTTTGTATTACCAGCCCTAATGACGACGAATCTTGGAAGATGCACGAAGAAATGTTGAAGAATTCAGAAGACTTCTACCAACAGgtaccgaatt ... tgttttgcagTTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGATAGTGCTGCTAAGAAATACGATTTGGAGGCATGGTTTCCAGCTTCCAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaccatcttttgtgaccatgttatgactcatcaggttgtatgatgttttgcagTTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGATAGTGCTGCTAAGAAATACGATTTGGAGGCATGGTTTCCAGCTTCCAAGA
      atctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctttgtttctccgctttacatgaaaagtttgctcgtgtactattagaccatcttttgtgaccatgttatgactcatcaggttgtatgatgttttgcagTTGGGTCTTCCTTATCGAGTGGTATCCATCGTCTCTGGAGCACTTAACGATAGTGCTGCTAAGAAATACGATTTGGAGGCATGGTTTCCAGCTTCCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG