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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttctccttctctatgtcctttctatgtttggcatctttcccgtcgtagtcgggccctctcgcacttctgcacttacggttacaagattttaatagtgccttgaagaaattttgtatttcatgtcacaatatggaatgtgtatattgaaaccggtaaaggtcttctgacctttattgggcttgttgaccag

Basic information

species Physcomitrella patens
transcript PP1S223_50V6.1
intron # 6
splice site 5'
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|162185524|gb|FC361248.1|FC361248
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|67722347|gb|BJ972606.1|BJ972606
EST:     AAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
genomic: AAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|37828398|gb|BJ586410.1|BJ586410
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|162155716|gb|FC331329.1|FC331329
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATTTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|208361643|gb|DC950331.1|DC950331
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|67692304|gb|BJ952537.1|BJ952537
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|162172649|gb|FC348030.1|FC348030
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|162180018|gb|FC356089.1|FC356089
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCAT
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCAT
EST: gi|67722359|gb|BJ972618.1|BJ972618
EST:     CCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
genomic: CCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|37842788|gb|BJ600796.1|BJ600796
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATATACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|162190854|gb|FC368052.1|FC368052
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|208372257|gb|DC948060.1|DC948060
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|18335076|gb|BJ167094.1|BJ167094
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|162200375|gb|FC376660.1|FC376660
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|37836649|gb|BJ594657.1|BJ594657
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|208389164|gb|DC945740.1|DC945740
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|208365828|gb|DC951063.1|DC951063
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|18337537|gb|BJ169561.1|BJ169561
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|37851326|gb|BJ609334.1|BJ609334
EST:     CAGTCGTTGCCACAGGAAATGGNTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|162200361|gb|FC376659.1|FC376659
EST:     CCGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATTTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|162174414|gb|FC350485.1|FC350485
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATTTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
EST: gi|208365900|gb|DC951079.1|DC951079
EST:     CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG                         GTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG
genomic: CAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTG

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: 19 (upstream exon), 20 (downstream exon)
Score: 3

GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttc ... tgttgaccagGTGAATGTTACCGCTGACCACAGAATCATCTACGGTGGAGACCTAGCTGTGTTTTTGCAAACATTTGCAGCAATCATTGAGAACCCTACAGAACTTACCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACGgtatcatttctccttctctatgtcctttctatgtttggcatctttcccgtcgtagtcgggccctctcgcacttctgcacttacggttacaagattttaatagtgccttgaagaaattttgtatttcatgtcacaatatggaatgtgtatattgaaaccggtaaaggtcttctgacctttattgggcttgttgaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG