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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCATTTCCCACTTGCGTATCTGTGAACAACACTGTATGTCACTTCTCTCCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtacttcagtttggacccattttttatttaattctggtttacagaagtaggttacttgaggattttttctaggttctcattctatttttggaac...

Basic information

species Physcomitrella patens
transcript PP1S119_137V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S119_137V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA03G07420.1 (Glycine max), 5'ss of exon 4
TTGCATTTCCCACTTGCGTATCTGTGAACAACACTGTATGTCACTTCTCTCCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtacttcagtttggacccattttttatttaattctggtttacaga-agtaggttacttgaggatttttt-----ctaggttctcattctatttttggaac-------
|||| || || || || || ||||||||||||||||| ||||||||||||||| | ||  | || ||  |     | |  |     ||| |||| |||||||||||   |||   |||||| |  ||||||  | |    | ||  | | |  |||| | | ||  |   || ||     || | |  | ||  | | || ||          
TTGCCTTCCCTACATGTGTGTCTGTGAACAACACTGTCTGTCACTTCTCTCCTCTTGCCAGTGATGAAACAGTGTTGGAAGATGGTGATATAGTGAAAATgtaagt---cttt--tttggagcattttttttgtgatagatagtgaaaaaatggtagataattttggttgttattggtgactggatggtaatagtgtgttcggttggttacag

upper sequence: PP1S119_137V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA01G29420.1 (Glycine max), 5'ss of exon 4
TTGCATTTCCCACTTGCGTATCTGTGAACAACACTGTATGTCACTTCTCTCCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtacttcagtttggacccattttttat--ttaattctggtttacagaagtaggt-tacttgaggattttt----tctaggttctcattctatttttggaac-------
|||| || || || || || ||||||||||||||||| ||||||||||||||| | ||  | || ||  |     | |  |     ||| |||| ||||||||||| | |||   |||||| | ||| ||| |  |  ||  ||    |  |   ||| | || |||    || ||     || | |  | |   | | |||||  |       
TTGCCTTCCCGACATGTGTGTCTGTGAACAACACTGTCTGTCACTTCTCTCCTCTTGCCAGTGATGAAACAGTGTTGGAAGACGGTGATATAGTGAAAATgtaagtctccttt--tttggagcaattgtttgtgatagatggtgaaaaaatggtatagatatatttggctgttattggtgactggatgttaaaagtgtgtttggttcgttacag

upper sequence: PP1S119_137V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv06s0004g06870.t01 (Vitis vinifera), 5'ss of exon 4
TTGCATTTCCCACTTGCGTATCTGTGAACAACACTGTATGTCACTTCTCTCCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtacttcagtttggacccattttttatttaattctggtttacagaagtaggttacttgaggattttttctaggttct-cattctatttttggaac
|||||||||| |||||| | || || ||||||||||| ||||||||||| ||  || |  | || ||| |     | |  |||   ||| || | || |||||||| | |||  | ||| | |  ||     |  |              ||||| |  |  | | | |  ||||| | || | |    |  ||   |   
TTGCATTTCCGACTTGCATTTCAGTAAACAACACTGTTTGTCACTTCTCACCACTGTCAAGTGATGAGACATTGTTGGAAGCAGGTGATATATTAAAGATgtaagttt-cttgtgcttgtaactgttcaaggtagagaaaaaaaacctgtaagtatgaaaaataaaggtcctttctggttttttcgggttggttgcag---

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|67569798|gb|BJ942622.1|BJ942622
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
EST: gi|208397136|gb|DC908150.1|DC908150
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
EST: gi|100439250|gb|BY980169.1|BY980169
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGAATG-ATTCGTAGCTGTTGTTGCACATACCC
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGA-TGGATTCGTAGCTGTTGTTGCACATACCC
EST: gi|100384797|gb|BY950787.1|BY950787
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
EST: gi|162183958|gb|FC359328.1|FC359328
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
EST: gi|100445208|gb|BY982837.1|BY982837
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
EST: gi|67719527|gb|BJ969786.1|BJ969786
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
EST: gi|162161202|gb|FC337265.1|FC337265
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
EST: gi|100397823|gb|BY990419.1|BY990419
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
EST: gi|67716276|gb|BJ966536.1|BJ966536
EST:     CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAAT                         ACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA
genomic: CCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCA

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: 33 (upstream exon), 29 (downstream exon)
Score: 15

TTGCATTTCCCACTTGCGTATCTGTGAACAACACTGTATGTCACTTCTCTCCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtac ... taatgtgcagACATCTCGGTTGCCACGTCGATGGATTCGTAGCTGTTGTTGCACATACCCATGTGCTTTGTGAAGGACCCATTACAGGTCGTGCAGCAGACGTCCTGGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCATTTCCCACTTGCGTATCTGTGAACAACACTGTATGTCACTTCTCTCCTTTGGCTGGAGACGAGTCCACTCTCGCGGCAAACGATCTAGTCAAAATgtaagtgtacttcagtttggacccattttttatttaattctggtttacagaagtaggttacttgaggattttttctaggttctcattctatttttggaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA