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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagtctgggtacttcaatgtccattgactgggcgaccagagtttaggataagagattttgccatcctctccaatggcctctttgtggaatgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCATAACGCCCACTGCGCTGGACAGATGGGAGGATAGACTGGAAGATATCTT

Basic information

species Physcomitrella patens
transcript PP1S323_70V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S323_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os12g43130.1 (Oryza sativa), 3'ss of exon 2
agagtctgggt-acttcaatgtccattgactgggcgacca------------gagtttaggataa----gagattttgccatcctctccaatggcctctttgtgga-atgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCATAACGCCCACTGCGCTGGACAGATGGGAGGATAGACTGGAAGATATCTT
   || ||| | | || | | | ||||||     |    |             |  ||  |||||     |   ||||      | |  | |     ||||||     | |   ||||| |||||||||||||||||||| ||||| ||||| || ||  | ||   ||| || || |  || || ||  |||||||| | ||| | |||||| ||||
---gtatggattagttaactattcattgatctaccagttactctcacttgtgaaaattcagataacttcaattgtttgtggaatttttaattcttacctttgtttttgtctttggcagTATGGTGCAGAAGAACTGATGAACTGGTAGATGGCCCTAACTCGTCTTACATTACACCAAAGGCACTTGATCGATGGGAGAAGAGATTAGAAGATCTCTT

upper sequence: PP1S323_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G149317_T01 (Zea mays), 3'ss of exon 2
--agagtctgggtacttcaatgtcc---attgactgggcgaccagagtttaggataaga-gattttgccatcctctccaatggcctctttgtggaatgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCATAACGCCCACTGCGCTGGACAGATGGGAGGATAGACTGGAAGATATCTT
  |   ||| | | | |  |   ||     ||  |    | ||      |||     |  |||| ||        |   | |  ||||||      || || ||||||||||||||||||||||| ||||| || || || ||||| || ||   ||| ||||| || || || ||| | |||||| |  | ||||| ||| ||||
gtatgatctcgatccatataaaccctgcgctgtttacttgccccatccctagctcgtgttgattctgaagcaacat---acgttctctttccct--tgcgc-gcagTGTGGTGCAGAAGAACTGACGAGCTAGTGGACGGTCCCAACGCGTCCTACATCACGCCGACCGCTCTCGACCGCTGGGAGAAGCGGCTGGAGGATCTCTT

upper sequence: PP1S323_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA02G45270.1 (Glycine max), 3'ss of exon 2
agagtctgggtacttcaatgtccattgactgggcgaccagagtttaggataagagattttgccatcctctccaat-ggcctctttgtggaatgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCATAACGCCCACTGCGCTGGACAGATGGGAGGATAGACTGGAAGATATCTT
   || || ||  ||  || |  ||| ||      ||     |||  | |     | |  | | |  | |  ||| | |   | |      ||   |||||||||||||||||||||||||||||| || ||||| || ||||| |||| ||| || |||   ||  ||||||| |||||| |  |||||   ||| | ||
---gtatgtgtgattagat-tagatt-acacactcactgctatttcagcttctccagtgagacttgttttggaattgacaattattcattgtgcattgcagTGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCGCACATCACCCCCGGGGCCTTGGACAGGTGGGAGCAACGACTGAGTGATGTTTT

upper sequence: PP1S323_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA14G03500.1 (Glycine max), 3'ss of exon 2
agagtctgggt--acttcaatgtccattgactgggcgaccagagtttaggataagagattttgccatcctctccaatggcctctttgtggaatgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCATAACGCCCACTGCGCTGGACAGATGGGAGGATAGACTGGAAGATATCTT
 |  | ||  |  | |  | |   || | ||||      |||  | |    | |||| | ||       |    | || |   | |  |   ||   |||||||||||||||||||||||||||||| || ||||| || ||||| || | ||| || ||    ||  ||||||| |||||| |  || ||   ||| | ||
-gtatgtgattagattatattacacactcactgctacttcagcttctccagtgagagttatt-------ttggaattgacaattattcgttgtgcattgcagTGTGGTGCAGAAGAACTGATGAGCTAGTGGATGGCCCAAATGCTTCACACATCACCCCTGGGGCCTTGGACAGGTGGGAGCAACGATTGAGTGATGTTTT

upper sequence: PP1S323_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA18G13700.1 (Glycine max), 3'ss of exon 2
agagtctgggtacttcaatgtccattgactgggcgaccagagtttaggataagagattttg--ccatcctctccaat----ggcctctttgtggaatgtgc-tgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCATAACGCCCACTGCGCTGGACAGATGGGAGGATAGACTGGAAGATATCTT
   || || || |||  ||    |||| |    | || | || |||    | |||  || |  ||||  |     ||        |   |      ||||| ||||||||||||||||||||| ||||| || || |||||||| ||||| || | ||| || || |  ||  ||||||| |||||| | |||||  | ||| | | 
--ggtatgtgtgctt--atcctaattggc-attctacaaaagcttatccaatgaggcttgggtccatttttatttattttgaaattgactacactttgtgcatgcaGTGTGGTGCAGAAGAACCGATGAACTAGTGGATGGACCTAATGCTTCTCACATCACACCAAAGGCCTTGGACAGGTGGGAGCAAAGACTATACGATGTTT-

upper sequence: PP1S323_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA08G41890.1 (Glycine max), 3'ss of exon 3
---------------agagtctgggtacttcaa-----tgtccattga--ctgggcgaccagagtttaggataagagattttgccatcctctccaa--tggcctctttgtggaatgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCATAACGCCCACTGCGCTGGACAGATGGGAGGATAGACTGGAAGATATCTT
                 | |  |  | || |||     | |||| |||  || |  | |||   |||   ||      | ||   |   |    ||  || |  |  | ||   ||   ||||||||||||||||||||| ||||| || || |||||||| ||||| || | ||| || || |  ||  ||||||| |||||| | ||| |    ||| | ||
gtatgtgtgcttatcctaattggcatgctacaaaagcttatccaatgaagcttgtggtccattcttttttatttttattattattactattattaaattgactacactttg---tgcattgcagTGTGGTGCAGAAGAACAGATGAACTAGTGGATGGACCTAATGCTTCTCACATCACACCAAAGGCCTTGGACAGGTGGGAGCAAAGATTATCTGATGTTTT

upper sequence: PP1S323_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv12s0028g00960.t01 (Vitis vinifera), 3'ss of exon 2
agagtctgggtacttcaatgtccattgactgggcgac-cagagtttaggataagagattttgccatcctctccaatggcctctttgtggaatgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCATAACGCCCACTGCGCTGGACAGATGGGAGGATAGACTGGAAGATATCTT
     ||  ||   |||   ||  |   |         |||||  | |     |  |        | ||   || | |  || | |     | | ||||||||||||||||||| || || ||||| || |||||||| ||||| || | |||  | ||||  || || |||||||||||  | ||  |    ||  | ||
tttagctatgtttctcatcttctgtcttccacatattacagagccttgagattgccagacaaattttcttggcagttgaatcat-gcattttcttctgcagTGTGGTGCAGAAGGACCGACGAGCTTGTGGATGGACCTAATGCTTCACACATGTCACCCAAGGCCCTTGACAGATGGGAACAAAGGTTAATTGACCTATT

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|162195318|gb|FC370839.1|FC370839
EST:     AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG                         TGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
genomic: AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATGgtacgttcag ... tgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
EST: gi|162194279|gb|FC368501.1|FC368501
EST:     AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG                         TGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
genomic: AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATGgtacgttcag ... tgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
EST: gi|67507624|gb|BJ940505.1|BJ940505
EST:     AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG                         TGTGGTGCAAAANANCTGATGAGC
genomic: AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATGgtacgttcag ... tgtgctgcagTGTGGTGCAGAAGAACTGATGAGC
EST: gi|162196412|gb|FC373558.1|FC373558
EST:     AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG                         TGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
genomic: AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATGgtacgttcag ... tgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
EST: gi|162213600|gb|FC389680.1|FC389680
EST:     AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG                         TGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
genomic: AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATGgtacgttcag ... tgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
EST: gi|162263003|gb|FC438811.1|FC438811
EST:     AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG                         TGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
genomic: AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATGgtacgttcag ... tgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
EST: gi|162167423|gb|FC343126.1|FC343126
EST:     AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG                         TGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
genomic: AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATGgtacgttcag ... tgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
EST: gi|162221129|gb|FC397770.1|FC397770
EST:     AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG                         TGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
genomic: AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATGgtacgttcag ... tgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
EST: gi|162178499|gb|FC354951.1|FC354951
EST:     AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG                         TGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
genomic: AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATGgtacgttcag ... tgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
EST: gi|162279509|gb|FC455820.1|FC455820
EST:     AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG                         TGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
genomic: AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATGgtacgttcag ... tgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
EST: gi|162162258|gb|FC338040.1|FC338040
EST:     AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATG                         TGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA
genomic: AACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATGgtacgttcag ... tgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCA

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), 32 (downstream exon)
Score: 26

GAACCAAGCTAATGACCCCTGAGAGGCAACGCGCTATCTGGGCGATATATGgtacgttcag ... tgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCATAACGCCCACTGCGCTGGACAGATGGGAGGATAGACTGGAAGATATCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggataagagattttgccatcctctccaatggcctctttgtggaatgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCATAACGCCCACTGCGCTGGACAGATGGGAGGATAGACTGGAAGATATCTT
        agatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagtctgggtacttcaatgtccattgactgggcgaccagagtttaggataagagattttgccatcctctccaatggcctctttgtggaatgtgctgcagTGTGGTGCAGAAGAACTGATGAGCTGGTCGATGGACCCAATGCATCGCGCATAACGCCCACTGCGCTGGACAGATGGGAGGATAGACTGGAAGATATCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA