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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA

Basic information

species Physcomitrella patens
transcript PP1S81_165V6.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 12
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
                            |    | | |||||| |           | || | ||  |||   ||| ||    |||  | ||   ||    | |||     |     || ||| ||||||||| || |||||||| |||||| ||||||||||||| || ||||| || ||||||||  |||| || || || || || ||||| || ||||| || ||
----------------------------gtaactatgtttgcttcacacaggataaggttgt-tacacatcttattact---ggtctctattgtactaagttgtgaagttccctattattatt-tgcagATCCTACCTACATGATCCGAGCTATTCCAAGCAATGCATCAGACAATGTCTACTGCACGCTGCTGGCCCACAGTGCTATTCATGGTGCAATGGCCGGCTA

upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
---gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
     |  | | |    |  |  ||   |         |      |||| | ||   || || || | |  ||| |  |   | |   | | |  |   ||| | || |   |     |  |      ||||||||||| |||||||| || ||  ||||||||||||| || ||||| || ||||||||  |||| || || || ||||| ||||| || ||||| || ||
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgca-ataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA

upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
                                      |   || ||   |   ||| |  ||| |    |  |   ||  ||||       |  ||   || |      ||  |      | |||||||||||||||||||||| || ||  | ||||||||||||||||| ||||| || |||||  |||| ||||| ||||   |||||||||| ||||| || ||
-------------------------------------gtcagtggttttcttcggtg-tcatatttcagggccagaactgctagttacacacat-ctcagatgt-----ttcttc------tactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA

upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 12
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
                          |     | ||||||  | ||||||   ||   |  ||  ||  | |      || |||    |    |  |   ||   ||| |   |||  |  || || ||||||||| |||||||| || ||| ||||||||||||| || ||||| || || |||||  |||| || ||||| ||||| ||||| || ||||| || ||
-------------------------gtaatcgtcttcttttttacttggtgaacgcagtgtta-gtttgtaa-----tttatagcatgtcaaggaatctgatg-aagtgcctgccatttttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTATTGCACCCTGCTCGCACATAGTGCCATTCATGGTGCAATGGCGGGATA

upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 11
gtggccat-atgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
  |  | | | | | |  |  | | || |   | | | |    || ||| ||    |  || | ||| |||   || |      |  |   | | || |        | | |      |  |||   ||||||||||||| ||||| |||||||||||||||||||||||||||||||||||||||||  | |||||||| || ||  | |||||||| |||||||| ||
--gttcgttaagacaaactatacaattatacgtatgtgtgca-tgtttgatt---atatttatgtatgcattgcatactgaaaggaggaaatcaagcatt-------gcattttttttactatttgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA

upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 11
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaa-attc-cttttagtcgtttttaggcttgaatatgagtactcaccacatg-attctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
                                   | | |   | ||     || ||    ||||    || | |  | |  | |   |      ||||  || |  | | |   |    |   || | |||||||||| || |||||||||||| ||||||||||||||||||||||||||||||||||  | |||||||| || ||  | |||||||| |||||||| ||
----------------------------------gtttgtaaagattaaacttcatggaattataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaatgccttctctttatgttttacagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA

upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
gtggccatatgcccagttgaaaacttttggttttttc-tttgc-tgcttg-gttctcgtgcttctatattcatgaaattccttttagtcgtttttagg--cttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
  |  | ||    ||    |||||| |   ||| | | | ||  | | || || |  || |   || ||| |||       |       |     |||   |  |  ||      |      |  |||   ||||||||||||| ||||| ||||| |||||||||||||||||||||||||||||||||||  | |||||||| || ||  | |||||||| |||||||| ||
--gttcgtaaagacaa---aaaactatatatttatacgtatgtgtacatgtgtgcatgttcgattacatttatgtgtgcattgcatactgaaaggaggaaatcaagcattgcatttttttttactatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA

upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtac--tcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
                                  ||  |      |      || ||    ||| |   |  |    ||   ||  |   |  ||||  || |  | | |  || |       || | |||||||||| || ||||| |||||| ||||||||||||| ||||||||||||||||||||  | |||||||| || ||  | |||||||| |||||||| ||
---------------------------------gtttgtaaagattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaat--ggctgaaagagtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA

upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA10G33820.1 (Glycine max), 3'ss of exon 12
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
                          |    |       || ||   |    |  | ||||| ||||||  |  ||   ||| || |||||     || | ||| |    |       |  ||    ||||||||| ||||||||||| ||| ||||||| ||||| || |||||| | ||||||||| | ||||| ||| | ||  | |||||||||||||| || ||
--------------------------taaaatcaactaatgatgggggcagttgttacttctctattca-aatcttgaattttgttgtttt--atttttattataaaacttgtttgtttactttcatagATCCAACATACATGATTCGGGCTATTCCAAGTAATGCCTCGGACAACATTTACTGCACTCTTCTTGCACATGGTGCTGTTCATGGAGCTATGGCTGGATA

upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 10
--------------------------gtggccatatgcccagttgaaaactt--ttggttttttctttgctgcttggttctc----gtgcttctatattca--tga-----aattccttttagtcg--tttttaggct---tgaatatgagtac-tcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
                           |  |  | || ||  || |   |||  || || |||  |||     | || | |     ||  ||  | |||    |||     |  || ||||| | |  || |  | ||    | ||| || |   |    |    ||    |||||||||| ||||||||||| ||  ||||||||||||| || ||||| || ||||| ||  | |||||||| || ||  ||||||| || |||||||||||
gtcagtttctcttacagcattctcctcttcctttttgacctatttatttcttacttagtctttcatttttatttcggatttgaaaggttttttaaaatttgactgacaattatctcattttaattgagttatctgcctagtgggataagactttgttgttattgtatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA

upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 11
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgct-tctatattcatgaaattccttttagtcgtttttagg---cttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
                                                      || |  | ||||| | |   ||| | ||   ||     |  |   ||||| | |   |  |       | | | | |||||||||| |||||||||||||||||||| |||||||| || ||||| || || || ||  | || ||||| || ||  | || || || ||||| || ||
------------------------------------------------------gtacaatttatatcccttgcattgcattctctccaccatgagtttcttgattgttcatttttcttgtcttaattt-cagATCCAACATACATGATTCGAGCTGTTCCTAGCAATGCGTCAGACAATGTTTATTGTACACTTCTGGCTCAGAGTGCAGTGCACGGTGCAATGGCTGGATA

upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT4G29220.1 (Arabidopsis thaliana), 3'ss of exon 11
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
          |   | | || | ||| ||  |||||||||  ||  ||     | |        ||  || || || ||| |  || ||||| |                           |  | |||||||||| |||||||| ||||||||||| |||||||| || ||||| || | ||||||  |  | ||||| |||||  | |||||||  ||||| || ||
----------gtata-tagatatcttatgagtttttcttttgtgtatgtggaacata-------atagataaagtttcttct--tcttttttggt-------------------------gtctttcagATCCAACCTACATGATACGAGCTGTTCCGAGCAATGCATCAGACAATGTATGCTGCACGCTTTTAGCTCAAAGCGCGGTTCATGGAGTGATGGCTGGTTA

upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 11
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattcct-tttagtcgtttttaggcttgaat-atgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
                                                      || | | | |  ||   ||||||   |  ||     |  |  | ||||| |  | ||     || |  ||  | ||||||| || |||||||| |||||| |||||  |||||| ||||||||||| ||||  ||| | ||||| || |||||  ||||||| || ||||| || ||
------------------------------------------------------gtacgtttgtcctccccaaattcaagtcgagctacatagattcatgaattagaaatatgactcaaaccatgtttcagATCCGACATACATGATCCGAGCTATTCCAGCCAATGCATCTGACAACGTCTACTCAACTCTCCTTGCCCAAAGCGCAGTCCATGGTGCAATGGCTGGCTA

upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 11
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgc-ttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
                                                |||    | |  | | | |  |  | ||      | | |  |    ||  | |  |  ||| ||   |   |  |    ||||||| ||||| ||||| || ||||||||||||||||| |||||||| || || |||||  | |||||||| || ||  | |||||||| |||||||||||
------------------------------------------------gtttgtatacactatctttctaatatatagaagctgggcaatggctggtctaacca--agtgctgcactttttgtctatcagATCCTACGTATATGATCCGTGCTGTTCCAAGCAATGCATCTGACAATGTCTATTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGGTA

upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 11
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
               ||     ||||  | ||| |  ||   |  ||  || ||   ||| || |||       ||  |   | | | || || |||  |   |||||  ||            ||||||||| || |||||||| || ||| ||||| ||||||| |||||||| |||||||||||  | |||||||| || ||  | |||||||| |||||||| ||
---------------gtcagtgacttcagatttgtgtttgtttatttatttttc---cttttagatttg---gcttagtaacaatagattctaagct--atcctgagttgtc-----------ttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA

upper sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv16s0013g01140.t01 (Vitis vinifera), 3'ss of exon 12
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcacca-catgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
                            | |||| |  ||| |  ||| |    ||  |  | | || ||   |||   | ||      |||        ||||   || | |  | | ||  ||| |||||||||| |||||||| |||||| ||||||| ||||| || |||||  | ||||||||  | ||||| ||||| ||  | ||||| || |||||||||||
----------------------------gtttttattgttgata-ttgctaactgt-ttattcttttaataggattttatctaaaaaaatttcaaagattatatttttatttattatcttgtctctacagATCCAACATACATGATCCGAGCTATTCCAAGTAATGCATCAGACAATATCTACTGCACCCTCCTTGCACATAGTGCTGTACATGGGGCCATGGCAGGGTA

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|162256335|gb|FC432345.1|FC432345
EST:     GAATTTAAGGAGCCGCTGAACTTGAAATACATAG                         ATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGT
genomic: GAATTTAAGGAGCCGCTGAACTTGAAATACATAGgtggccatat ... gattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGT




















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: 26 (upstream exon), 27 (downstream exon)
Score: 8

GAACATTTTCTCAAGGAATTTAAGGAGCCGCTGAACTTGAAATACATAGgtggccatat ... gattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA
                                 tactcac  putative branch site (score: 8)
                      ttgaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT