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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcagttttgcgcaatccagaccatcattttttcttgacggtagtttctagttttggtgaagtgatggatgatgatttctctagagcgaccgctcacgcttctttcgctcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCATTGAAGATTATCCCTACGCAGCCGACGGGCTTGAAGTTTGGGGCGCCATG

Basic information

species Physcomitrella patens
transcript PP1S419_7V6.1
intron # 7
splice site 3'
intron type U2

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|162194293|gb|FC369516.1|FC369516
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|100423902|gb|BY976582.1|BY976582
EST:     GACTTTTGGACATTTGACTCANATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162158128|gb|FC333923.1|FC333923
EST:     GACTTTTGGACATTTGACTCANATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162249202|gb|FC421545.1|FC421545
EST:     GACTTTTGGACATTTGACTCANATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|67571398|gb|BJ944222.1|BJ944222
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162273902|gb|FC450041.1|FC450041
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162215903|gb|FC392320.1|FC392320
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162196986|gb|FC375211.1|FC375211
EST:     GTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162250241|gb|FC425492.1|FC425492
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162167391|gb|FC343094.1|FC343094
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162178773|gb|FC354510.1|FC354510
EST:     GACTTTTGGACATTTGACTCANATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162164877|gb|FC341366.1|FC341366
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162180667|gb|FC357024.1|FC357024
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162194838|gb|FC370515.1|FC370515
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162265442|gb|FC440768.1|FC440768
EST:     CGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: CGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162246078|gb|FC423566.1|FC423566
EST:     TGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: TGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162165033|gb|FC342224.1|FC342224
EST:     GACTTTTGGACATTTGACTCANATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162211125|gb|FC387149.1|FC387149
EST:     CGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: CGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|100386618|gb|BY970159.1|BY970159
EST:     GACTTTTGGACATTTGACTCANATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162173204|gb|FC349986.1|FC349986
EST:     GACTTTTGGACATTTGACTCANATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162235808|gb|FC412359.1|FC412359
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162245537|gb|FC423272.1|FC423272
EST:     GACTTTTGGACATTTGACTCANATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162264390|gb|FC440556.1|FC440556
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|100388490|gb|BY952092.1|BY952092
EST:     GACTTTTGGACATTTGACTCANATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|100423651|gb|BY976495.1|BY976495
EST:     GACTTTTGGACATTTGACTCANATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162154367|gb|FC330706.1|FC330706
EST:     GACTTTTGGACATTTGACTCANATGCGTTGCCGAACGACCTCATCANGAG                         GGGTATGGCGGTACCAG
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAG
EST: gi|100361047|gb|BY946887.1|BY946887
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGGCCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162167824|gb|FC344554.1|FC344554
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|100426164|gb|BY958760.1|BY958760
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162276105|gb|FC452381.1|FC452381
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162200069|gb|FC376531.1|FC376531
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|100442367|gb|BY981391.1|BY981391
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|67573583|gb|BJ946407.1|BJ946407
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
EST: gi|162191586|gb|FC367631.1|FC367631
EST:     GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAG                         GGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT
genomic: GACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCAT

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), 35 (downstream exon)
Score: 37

TCTATACGCCTCGTGAGTACGTCGTGCGAATGGCTTCTGCTGCCTACCGAGACTTTTGGACATTTGACTCAAATGCGTTGCCGAACGACCTCATCAGGAGgtatcagttt ... tcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCATTGAAGATTATCCCTACGCAGCCGACGGGCTTGAAGTTTGGGGCGCCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatggatgatgatttctctagagcgaccgctcacgcttctttcgctcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCATTGAAGATTATCCCTACGCAGCCGACGGGCTTGAAGTTTGGGGCGCCATG
                           cgctcac  putative branch site (score: 37)
                                 cgcttctttcgctc  CT-rich tract
        atgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcagttttgcgcaatccagaccatcattttttcttgacggtagtttctagttttggtgaagtgatggatgatgatttctctagagcgaccgctcacgcttctttcgctcgacttcagGGGTATGGCGGTACCAGACCCTAACGCTAAACACGGAGTCAGGCTTACCATTGAAGATTATCCCTACGCAGCCGACGGGCTTGAAGTTTGGGGCGCCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG