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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaatgtcagattgtattggtggattatgttcctgaaagttaggttaatatcgacgtggagcacacaagttcttgtttcattcccctctccctttctacaatgcgaatctattaggactgttggtagtgatgctatgctggtattatttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACTCAATTGGTGGTGGGCCGGGGCAAGAAGATGTGCAGTTGCGTGCCAGCAA

Basic information

species Physcomitrella patens
transcript PP1S46_127V6.1
intron # 5
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|208392104|gb|DC949550.1|DC949550
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|37826977|gb|BJ584989.1|BJ584989
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|162279433|gb|FC455549.1|FC455549
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|18339275|gb|BJ171302.1|BJ171302
EST:     GAGGTNACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGNCGATTAGGTCTTTTATGTGGAGACGNATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|162272341|gb|FC448200.1|FC448200
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|208364026|gb|DC950374.1|DC950374
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|208383174|gb|DC928216.1|DC928216
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|208360734|gb|DC946458.1|DC946458
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|208371151|gb|DC955971.1|DC955971
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGCCGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|37849036|gb|BJ607044.1|BJ607044
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|37847526|gb|BJ605534.1|BJ605534
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|208363146|gb|DC954346.1|DC954346
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|208377301|gb|DC927017.1|DC927017
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|208396773|gb|DC929068.1|DC929068
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|162271211|gb|FC447174.1|FC447174
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|37847911|gb|BJ605919.1|BJ605919
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|208366230|gb|DC943804.1|DC943804
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCATATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|208363024|gb|DC957979.1|DC957979
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTCGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|37848042|gb|BJ606050.1|BJ606050
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|67692292|gb|BJ952525.1|BJ952525
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|37840472|gb|BJ598480.1|BJ598480
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|208394573|gb|DC953612.1|DC953612
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|208358561|gb|DC946522.1|DC946522
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|18337354|gb|BJ169378.1|BJ169378
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|162206621|gb|FC382379.1|FC382379
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|208352798|gb|DC917762.1|DC917762
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|37845773|gb|BJ603781.1|BJ603781
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|37841703|gb|BJ599711.1|BJ599711
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
EST: gi|208359294|gb|DC954189.1|DC954189
EST:     GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAG                         TGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT
genomic: GAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACT

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: 35 (upstream exon), 33 (downstream exon)
Score: 46

GCTACTTAGAGATAATCTGACCCTGTGGACATCTGACCTTCAGGACGAGGGAGGTGACGACCAGGGAAAGGGAGATGATATGAGGCCCGAGGAGGCTGAGgtatgaaatg ... ttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACTCAATTGGTGGTGGGCCGGGGCAAGAAGATGTGCAGTTGCGTGCCAGCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgaatctattaggactgttggtagtgatgctatgctggtattatttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACTCAATTGGTGGTGGGCCGGGGCAAGAAGATGTGCAGTTGCGTGCCAGCAA
                                       tattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaatgtcagattgtattggtggattatgttcctgaaagttaggttaatatcgacgtggagcacacaagttcttgtttcattcccctctccctttctacaatgcgaatctattaggactgttggtagtgatgctatgctggtattatttggatgcagTGATGACGATTAGGTCTTTTATGTGGAGACGAATTTGCAAATCACTTCACTCAATTGGTGGTGGGCCGGGGCAAGAAGATGTGCAGTTGCGTGCCAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG