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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcaaaacgtagataaatttctgtcgtttatatcatttctctgcgctagtcaagcctacatgctgcttattagccgaatctatttgtgcatatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT

Basic information

species Physcomitrella patens
transcript PP1S29_256V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S29_256V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 9
ttttcaaaacgtagataaatttctgtcgtttatatcatttctctgcgctagtcaagcctacatgctgcttattagccgaatctatttgtgcatatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT
       |   | | ||       |    |  |   | |||| ||    |   ||   || |  |||   ||   |   |||||  |    ||   ||||||||||||| || ||||| |||||||| |||||||| |||||||| ||||| 
-----gtattttggttatgccatagaaagtccttataattctatgtttca--taaatttaga--ctgacaatattcatgatctaaata---atgatacagATATGGTGGTGGTATGAGTTCTGCCAAAGCTGCACTGGAGAGTGATACACGA

upper sequence: PP1S29_256V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA12G03060.1 (Glycine max), 3'ss of exon 10
ttttcaaaacgtagataaatttctgtcgtttatatcatttctctgcgctagtcaagcctacatgctgcttattagccgaatctatttgtgcatatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT
       |   | | ||    |     ||   ||| |||   ||  | |    ||   || |  |||   ||   |   |||||  |    ||   ||||||||||||| || ||||| ||||| || |||||||| |||||||| ||||| 
-----gtatgttggttatgcatagaaagtccttataatt---ctatgtttcataaatttaga--ctgacaatattcatgatctaaata---atgatacagATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCACTGGAGAGTGATACACGA

upper sequence: PP1S29_256V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 8
ttttcaaaacg-----tagataaat--ttctgtcgtttatatcatttctctgcgctagtcaagcctacatgctgcttattagccgaatctatttgtgcatatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT
   | |  | |     |  | || |  |||    |   | |  | | | |     ||   | | | |||   | || |  ||    |||| |||     | || ||| ||||||||||| ||||| |||||||| |||||||| |||||||||||||| 
--gtaaggatggcttcttcacaagttattcaaaggaacaaactaatgcacacacataacgatgtcaacacatt-ctcacaagt---atctctttcattctgtg-cagGTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGG

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|162169757|gb|FC345294.1|FC345294
EST:     GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|37845305|gb|BJ603313.1|BJ603313
EST:     CTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: CTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|18327390|gb|BJ159392.1|BJ159392
EST:     GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|162182768|gb|FC359515.1|FC359515
EST:     GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|67720249|gb|BJ970508.1|BJ970508
EST:     CTGCACTTTCTCTTACTTACNTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: CTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|67727192|gb|BJ977451.1|BJ977451
EST:     GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|18334218|gb|BJ166234.1|BJ166234
EST:     CGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: CGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|67726751|gb|BJ977010.1|BJ977010
EST:     GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|162171617|gb|FC347558.1|FC347558
EST:     GAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|162181163|gb|FC357608.1|FC357608
EST:     GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|37824766|gb|BJ582832.1|BJ582832
EST:     GGTTCTGCAC-TTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|18335658|gb|BJ167678.1|BJ167678
EST:     CGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: CGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|67727852|gb|BJ978111.1|BJ978111
EST:     GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGTCAAGGCTGCACTTGAGAGTGACACACG
genomic: GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|162223700|gb|FC399772.1|FC399772
EST:     GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|19789330|gb|BQ041244.1|BQ041244
EST:     GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|162176594|gb|FC353063.1|FC353063
EST:     GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|162223699|gb|FC399771.1|FC399771
EST:     GTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|162182767|gb|FC359514.1|FC359514
EST:     GAGAAGATTATCCCNGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|162167231|gb|FC342796.1|FC342796
EST:     GAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|18333553|gb|BJ165568.1|BJ165568
EST:     GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|67725967|gb|BJ976226.1|BJ976226
EST:     CTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCCCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: CTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|67720690|gb|BJ970949.1|BJ970949
EST:     GGTTCTGCACTTTCTCTTACTTACTNGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|208375034|gb|DC944815.1|DC944815
EST:     GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|67720235|gb|BJ970494.1|BJ970494
EST:     GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
EST: gi|162241271|gb|FC416902.1|FC416902
EST:     GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG                         ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG
genomic: GGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACG

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: 24 (upstream exon), 31 (downstream exon)
Score: 11

GTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGGgtaagattga ... catatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctagtcaagcctacatgctgcttattagccgaatctatttgtgcatatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT
                                 aatctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcaaaacgtagataaatttctgtcgtttatatcatttctctgcgctagtcaagcctacatgctgcttattagccgaatctatttgtgcatatgacagATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA