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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcctacttgcgttgataactcaatcttcctggactaagcacaggttttctctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG

Basic information

species Physcomitrella patens
transcript PP1S58_234V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 12
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcctacttgcgttgataactcaatcttcctggactaagcacaggttttctctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG
                                                          |  ||  || |      |  || |   | ||| |    |    | | |   |     |   ||||  | ||      || ||||    |   ||||| | || |  ||| || |||| || ||||||||||| ||||||||||| |||||  | || |||||||| |||||||| ||||| || |||||||||||      |||||  |||||||
---------------------------------------------------------actgtggggt-tacgatttatgtgcagtaatgactaatgacctcatactttca-----ggatataaggctat------gggctaatacta---tttctttattgcacttccat-agGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG

upper sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G007229_T01 (Zea mays), 3'ss of exon 12
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcctacttgcgttgataactcaatcttcctggactaagcacaggttttctctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG
                                                            |  |  |  ||| | |     || |    | |   |||  | |  || |||||  ||  | ||   ||        | | ||  |    |||  || |||  |  |   | ||||||| ||||||||||||||||||||||||||||| ||||| || ||||| |||||||| ||||| || || ||||||||   |   || || || ||||
------------------------------------------------------------tcaaaataatttacttattatcctcctcaactactaatattgc--tcatactt-tgtgtacaatgtaa--------gtcaaattatcattttcttcatttattactt--ttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTG

upper sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcctacttgcgttgataactcaatcttcctggactaagcacaggttttctctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG
                                                                  || ||| | |     || |    | |    ||  | |  || |||||  ||  | ||   || |       ||||   |    |||| | ||  | | ||   | ||||||| ||||||||||||||||||||||||||||| ||||| ||||| || |||||||| ||||| || || ||||||||   |   || || || ||||
----------------------------------------------------------------aatgatttgcttattatcctccacaactactcatattgc--tcatactt-tgtgtacaatgtaagcc----aaactatcaatc--tttttttttaatttattactttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG

upper sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G167886_T01 (Zea mays), 3'ss of exon 11
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcctacttgcgttgataactcaatcttcctggactaagcacaggttttctctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG
                                                                          || |  |  |  |     ||||   | ||| |  | |  || |  | |     |    | | | ||||  |      || |  |||||   |     |||| ||  |||||||||| ||||||||||| ||||| ||||| ||||  |  || ||||| ||||| || |||||||||||      |||    |||||||
-----------------------------------------------------------------------cggctaaccctaatgg--gccggcagcccaacagtggtgccggcctacacacactcacacacatagtctaacaagtatcattgttgttttccactgccatagGTGTATCGAGTTTCAGACATGGAGCTTGTAAGAGTTCTTCCTAGTGTAGGAGAGGAAGTCAATGTTGCATGTTTTCATCCTTCCCCTGGATCAGGTCTTG

upper sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 11
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattcta-cattcctacttgcgttgataactcaatcttcctggactaagcacag-gttttctctttttctgt-tcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG
                                                                              | | || | ||  || || |  || |||   | |     |||       |||  |  | | || |    |  || ||    ||| || | ||  | ||||||||||||| ||||||||||| ||||| || || ||||| ||||| || ||||| || |||||||| || ||||||||    |  || || || || |
---------------------------------------------------------------------------gccggcacaaattgt-tgtcattcatatcatctatgccctttttgtagttctaatggttttagtctgaatttaatgtctttgaatttgctttgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGATGAGGTCAATGTGGCATGCTTTCATCCTTTTGCCGGAGGAGGACTAG

upper sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA03G32620.4 (Glycine max), 3'ss of exon 11
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcctacttgcgttgataactcaatcttcctggactaagcacaggttttctctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG
                                                          |    ||   || || |  | ||  |   |  ||| |  || |  | | | | | |  || ||  || ||| |     | ||| | |   | ||| ||||||           ||||||||| ||| ||||||||||| ||||| || || ||||| ||||| || || || || |||||||| || ||||||||    | ||| || || || |
---------------------------------------------------------gctggcacaaattgttgcc-attcatatcatctatgccctttttgtagttcaaatggttttaat--ctgaatttaat--gtctatgaatttgctttgtctttt-----------agGTATACAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGACGAGGTCAATGTGGCATGCTTTCATCCTTTTGCTGGGGGAGGACTAG

upper sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: AT5G43930.1 (Arabidopsis thaliana), 3'ss of exon 11
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcctacttgcgttgataactcaatcttcctggactaagcacaggttttctctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG
                                                                                      || ||     || ||||      |     ||| | ||||           ||   | |||||   || | | | |  |  |  |||| ||||||||||||||||||||||||||||||||||||| || ||| | |||||||||||||| || ||||||||||||||      ||| || |||||||
--------------------------------------------------------------------------------------gtaaagccttatgctactagtacatccatgttcagaacttgg-------agatataacacagaacttgtttgtgtgggc-cggtcagATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG

upper sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 11
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcctacttgcgt-tgataactcaatcttcctggactaagcacaggttttctctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG
                   || |||    |||    |  ||  | ||      | |  |          | ||            ||   ||| || || || ||   ||  |   |    |      ||| | |  || |    || |  ||| ||  ||||| |||  |||| | |||||||||||||||||||| || |||||||||||||| ||  | ||||||||||| ||||| || || ||||||||      ||| || |||||||
-------------------gtaacgtctatgct--ccagtagttatgaatttctagaccagcagaacaatgttt-----------agcagatgcca-ttttatatcattaactatatacacttggaatatcatacaagagtttagactgtgtttttccctttctattccttcagATTTACAGAGTTTCAGATATGGAACTGGTGAGAGTACTTCCAAGCTCAGAGGATGAAGTTAATGTTGCTTGCTTTCATCCTTCTCCTGGGGGAGGTCTTG

upper sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv05s0077g00140.t01 (Vitis vinifera), 3'ss of exon 11
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcct-acttgcgttgataactcaatcttcctggactaagcacaggttttctctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG
                                                             ||     | | |  ||| |   | || ||||   | |  |  |||  | | ||   ||  ||  || || ||  |          ||  |||     | || |  |||  ||||| ||||||||||| |||||||| ||||||||||| ||||| ||||| |||||||| || ||||| || || ||||||||    ||||| || || ||||
-------------------------------------------------------------tgctacttatgttgtgatt---atag-gaataaaactcttggattttttatttatttttttatttctattttattt---------caactttcaaaatatttttatcatgcagGTCTACAGAGTTTCTGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTG

upper sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcctacttgcgttgataactcaatcttcctggactaagcacaggttttct---ctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG
                            |  ||  ||   || |   |  | || |    |  |  || |  |   ||   |||     | ||    |     | |      |  ||| | | || | | ||| ||  ||     ||||| |      || ||| ||| || |||||| ||| |||| ||||||||||| ||||| ||||| |||||||||||||| ||||| || ||||| || || ||||||||   |  ||| || |||||||
---------------------------gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttc-tgatct---ttcaggtctcacaggctctttttgt-cactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG

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|162268390|gb|FC444159.1|FC444159
EST:     TCGTGGACGGCTCAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAG                         GTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
genomic: TCGTGGACGGCTCAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAGgtttgaatat ... gttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
EST: gi|37838922|gb|BJ596930.1|BJ596930
EST:     TCGTGGACGGCTCAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAG                         GTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
genomic: TCGTGGACGGCTCAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAGgtttgaatat ... gttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
EST: gi|162254782|gb|FC430759.1|FC430759
EST:     CAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAG                         GTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
genomic: CAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAGgtttgaatat ... gttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
EST: gi|162179705|gb|FC355763.1|FC355763
EST:     TTGTGGACGGCTCAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAG                         GTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
genomic: TCGTGGACGGCTCAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAGgtttgaatat ... gttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
EST: gi|162201536|gb|FC378250.1|FC378250
EST:     TTGTGGACGGCTCAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAG                         GTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
genomic: TCGTGGACGGCTCAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAGgtttgaatat ... gttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
EST: gi|162179706|gb|FC355764.1|FC355764
EST:     TTGTGGACGGCTCAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAG                         GTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
genomic: TCGTGGACGGCTCAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAGgtttgaatat ... gttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
EST: gi|162193793|gb|FC368707.1|FC368707
EST:     TTGTGGACGGCTCAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAG                         GTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
genomic: TCGTGGACGGCTCAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAGgtttgaatat ... gttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
EST: gi|162247571|gb|FC420535.1|FC420535
EST:     TTGTGGACGGCTCAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAG                         GTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
genomic: TCGTGGACGGCTCAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAGgtttgaatat ... gttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
EST: gi|162209696|gb|FC386195.1|FC386195
EST:     TTGTGGACGGCTCAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAG                         GTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
genomic: TCGTGGACGGCTCAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAGgtttgaatat ... gttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
EST: gi|162209695|gb|FC386194.1|FC386194
EST:     ACACTATTCTCGAG                         GTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG
genomic: ACACTATTCTCGAGgtttgaatat ... gttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAG

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: 32 (upstream exon), 32 (downstream exon)
Score: 13

CATATTGCTTGCATATGGTAGACGCCACAATTCACTTCTTAGAAGCCTTGTCGTGGACGGCTCAGCAACTATTCCAATTCGAGTGTACACTATTCTCGAGgtttgaatat ... gttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataactcaatcttcctggactaagcacaggttttctctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG
 tgataac  putative branch site (score: 13)
                               ttttctctttttctgt  putative PPT
                                    tcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcctacttgcgttgataactcaatcttcctggactaagcacaggttttctctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG