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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatacctcttctagattgcggttgaaatctttctcgaactctcacaatgaaactgtacaccaatttgaatgtatgtagtatcaggttttctacatggtccaactggatgttgtagctctttgctgagtcttcgtaagatgatcccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAGTATAACTTTGATCACCCTG

Basic information

species Physcomitrella patens
transcript PP1S19_94V6.1
intron # 2
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|208397640|gb|DC912258.1|DC912258
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
EST: gi|100401165|gb|BY990863.1|BY990863
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
EST: gi|208399535|gb|DC908532.1|DC908532
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GGTTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
EST: gi|100444887|gb|BY982715.1|BY982715
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTA-TCAG                         GATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
EST: gi|100418660|gb|BY957527.1|BY957527
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTTTCTACCCGCGG-CTGAAACCCGAAGAGATGGCTAAATGT-GGAG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACC-GCGGGCTGAAACCCGAAGAGATGGCTAA-TGTTGGAG
EST: gi|100421604|gb|BY976229.1|BY976229
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
EST: gi|100413766|gb|BY974978.1|BY974978
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
EST: gi|208359964|gb|DC939296.1|DC939296
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
EST: gi|100434157|gb|BY978986.1|BY978986
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
EST: gi|100380032|gb|BY968812.1|BY968812
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
EST: gi|100449796|gb|CJ973940.1|CJ973940
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTT-CTACCGCGG-CTGAA
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAA
EST: gi|100426311|gb|BY958834.1|BY958834
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTTTCTACCCGCGG-CTGAAACCCGAAGAGATGGCTAATGTTGGAGA
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACC-GCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGA
EST: gi|100417096|gb|BY957165.1|BY957165
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTTTCTACCGCGGGCTGAAAACCGAAGAGATGGCTAATGTTGGAGAG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
EST: gi|208352244|gb|DC901737.1|DC901737
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
EST: gi|100355920|gb|BY946105.1|BY946105
EST:     ACATGATTATTCAACAGGTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTTTCTACCGCGGGCTGAAACCCGAAGA
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGA
EST: gi|100450661|gb|CJ974375.1|CJ974375
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTTTCTACCGCGGGCTGAA-CCCGAAGAGATGGCTAATGTTGAA-AG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
EST: gi|208359017|gb|DC957765.1|DC957765
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
EST: gi|208383715|gb|DC911453.1|DC911453
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTANTCAG                         GATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
EST: gi|100446804|gb|CJ971103.1|CJ971103
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
EST: gi|100385991|gb|BY951185.1|BY951185
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
EST: gi|100446201|gb|CJ970500.1|CJ970500
EST:     ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG                         GATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG
genomic: ACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAG

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: 23 (upstream exon), 28 (downstream exon)
Score: 4

GTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAGgtattatacc ... cccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAGTATAACTTTGATCACCCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaactggatgttgtagctctttgctgagtcttcgtaagatgatcccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAGTATAACTTTGATCACCCTG
                                            tcccgtt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatacctcttctagattgcggttgaaatctttctcgaactctcacaatgaaactgtacaccaatttgaatgtatgtagtatcaggttttctacatggtccaactggatgttgtagctctttgctgagtcttcgtaagatgatcccgttacagGATTCTTTCTACCGCGGGCTGAAACCCGAAGAGATGGCTAATGTTGGAGAGTATAACTTTGATCACCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA