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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattagggtttttcctcctgtggcccgttggggtttggttaggtgcttgtgcaagtgttcgtttttggtgcgagggcgcgggggtttggttcggagggaagtggtttgtgatagtgggctgttgacgagggtagtgacgtcgttttttattttgtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCGCGAGGGTGATTGCTGCCATCGAGAACCCCCAGGACATCATCGTCCAGTC

Basic information

species Physcomitrella patens
transcript PP1S48_103V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S48_103V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g08440.2 (Oryza sativa), 3'ss of exon 1
gtaattagggtttttcctcctgtggcccgttggggtttggttaggtgcttgtgcaagtgttcgtttttggtgcgagggcgcgggggtttggttcggagggaagtggt-ttgtgatagtgggctgttgacgagggtagtgacgtcgttttttattttgtg-tgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCGCGAGGGTGATTGCTGCCATCGAGAACCCCCAGGACATCATCGTCCAGTC
                                                                   |||       ||   |     || | |   |     || | || |  | |  || | |    ||   |    ||||     |   |  ||   |    |||||| | |||||||||  | |||||||| |  || |||||| |||| || ||||||||||||| |||||| |||||||||||||||||||| ||||||||
------------------------------------------------------------------gtggcatagttgcattgcaacctgttgcaaggtatgctgctgttcttttgggagggtatct-tgaatatgaatacgtgaacatcgttgctgcaattcatagGTATCTACATCATCAACCTCGGCAAGACATGGGAGAAGCTGCAGCTCGCGGCGAGGGTGATTGTTGCCATTGAGAACCCCCAGGACATCATTGTCCAGTC

upper sequence: PP1S48_103V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g28410.1 (Oryza sativa), 3'ss of exon 1
gtaattagggtttttcctcctgtggcccgttggggtttggttaggtgcttgtgcaagtgttcgtttttggtgcgagggcgcgggggtttggttcggagggaagtggtt-tgtgatagtgggctgttgacgagggtagtgacgtcgttttttattttgtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCGCGAGGGTGATTGCTGCCATCGAGAACCCCCAGGACATCATCGTCCAGTC
                                                 |||| |||   || ||  |  |||     |    | | | | |||         || || ||| | | |||  || |||| || |    |   || ||   ||||||   |   |||| ||||||||||| ||  | ||||| ||||  || |||||  ||||||| || || ||||||| |||||| |||||||| |||||||||||||| |||||
------------------------------------------------atgtgaaaggcctccttcatc-tgcattctcataagcgatagattct--------tgattatgtaacaatgg--tgatgacaagag----gctatccttgcatattttcctt---cagGCATTTTCATCATTAACCTTGGCAAAACCTGGGAGAAGCTTCAGCTGGCTGCCAGAGTGATTGTTGCCATTGAGAACCCACAGGACATCATCGTGCAGTC

upper sequence: PP1S48_103V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 1
gtaattagggtttttcctcctgtggcccgttggggtttggttaggtgcttgtgcaagtgttcgtttttggtgcgagggcgcgggggtttggttcggagggaagtggtttgtgatagtgggctgttgacgagggtagtgacgtcgttttttattttgtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCGCGAGGGTGATTGCTGCCATCGAGAACCCCCAGGACATCATCGTCCAGTC
                                                            | | | |   |    | || | |  |    | |     |    |  | |   | | ||   |||||     | ||   || |   |  |  |||| | | | |||| || | |||||||||| | |||||||| |  || || ||  |||| || |||||||| || | ||||||||||||||| ||||||||||||||||||||
------------------------------------------------------------tagctgtgaattgtggagcaccgtagc--agcttaatagcgcttcatcttcaaga-tgaattgttgggtgtgatat--acattcatgctactttttttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC

upper sequence: PP1S48_103V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G126821_T01 (Zea mays), 3'ss of exon 1
gtaattagggtttttcctcctgtggcccgttggggtttggttaggtgcttgtgcaagtgttcgtttttggtgcgagggcgcgggggtttggttcgga--gggaagtggtttgtgatagtgggctgttgacgagggtagtgacgtcgttttttattttgtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCGCGAGGGTGATTGCTGCCATCGAGAACCCCCAGGACATCATCGTCCAGTC
                                                       ||  |  |  |||  |  | ||     |   || | |  |      | ||   |||  |    |   |  |   | ||  |  ||     ||||||             |||| || | |||||||||  | |||||||| |  || || ||| |||| || |||||||| || | ||||||||||||||| ||||||||||||||||||||
------------------------------------------------------cagcatgaggcttt--tatggggatctagtaattagctgtgatctatggagcacttttagcagcttctccatcttcaagattcttgctactgttttt-----------atcagGCATCTACATCATCAACCTTGGCAAGACATGGGAGAAACTGCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC

upper sequence: PP1S48_103V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G099657_T01 (Zea mays), 3'ss of exon 1
gtaattagggtttttcctcctgtggcccgttggggtttggttaggtgcttgtgcaagtgttcgtttttggtgcgagggcgcgggggtttggttcggagggaagtggtttgtgatagtgggctgttgacgagggtagtgacgtcgttttttattttgtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCGCGAGGGTGATTGCTGCCATCGAGAACCCCCAGGACATCATCGTCCAGTC
                                                                 |  |||||    | |  |  | ||  |  | | | | ||  ||     |         |||    | ||  |    |  |  | |   || | |   |||| || | |||||||||  |||||||||| |  || |||||  |||| || |||||||| |||| |||||| |||||||| || |||||||||||||||||
-------------------------------------------------------------taactgcggtgca---gtgtagcagcttaata-gcatgtatgttcttcacagtcaatatgaattgttaggtgtgatattctattcctgttactttttttatcagGCATCTACATCATCAACCTGGGCAAGACATGGGATAAGCTCCAGCTCGCGGCGAGGGTTATTGTTGCCATTGAGAACCCACAAGACATCATCGTCCAGTC

upper sequence: PP1S48_103V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G099657_T04 (Zea mays), 3'ss of exon 1
gtaattagggtttttcctcctgtggcccgttggggtttggttaggtgcttgtgcaagtgttcgtttttggtgcgagg-gcgcgggggtttggttcggagggaagtggtttgtgatagtgggctgttgacgagggtagtgacgtcgttttttattttgtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCGCGAGGGTGATTGCTGCCATCGAGAACCCCCAGGACATCATCGTCCAGTC
                                                   |  |  |  ||    | ||   ||   | |    | |   | |||  | || |  |||  || |     ||  ||||  |       ||| || |  |  | |  |   |  |   ||    || | |   |||   ||||  |  || |   |     ||||| ||    |  || ||||  |   | | |||      | ||| |   |||  
-------------------------------------------------catctacatcatcaacctgggcaagacatgggataagctccagctcgcggcgagg--gttattgtt-----gccattgagaacccacaagacatcatcgtccagtcgGCCCGCCCC--TACGGCCAGCGT-GCTGTCCTCAAGTTC-GCGCAGTAC----ACTGGC-GCCCATGCCATCGCTGGGAGGCACACCCCTGGTACCTTCACCAATCAGC-

upper sequence: PP1S48_103V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G72370.2 (Arabidopsis thaliana), 3'ss of exon 1
gtaattagggtttttcctcctgtggcccgttggggtttggttaggtgcttgtgcaagtgttcgtttttggtgcgagggcgcgggggtttggttcggagggaagtggtttgtgatagtgggctgttgacgagggtagtgacgtcgttttttattttgtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCGCGAGGGTGATTGCTGCCATCGAGAACCCCCAGGACATCATCGTCCAGTC
                                            ||  |||||| |||||  ||| ||| |||         |   |||    |    | |||||||  || || |      |||   || | |          ||  | ||| |       ||||||||| |||| ||||  | ||||| || |  ||||||||  || |||| || || || |||| |||||| |||||||| ||||||||||||||||||||
--------------------------------------------gtatttgtgctagtgtgtgttattgttgctcttttattgtaattta---caattgtaagtggtgagt-atggaacttagtttttgaagtt----------ttcgtcattct-------cagGTATTTACATCTTCAACCTTGGCAAAACATGGGAAAAGCTCCAGATGGCTGCTAGAGTTATTGTTGCCATTGAGAACCCACAGGACATCATCGTCCAGTC

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|162236069|gb|FC412228.1|FC412228
EST:     GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTCATCATCAACGTGGGCAAGACCTACGAGAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
EST: gi|162274933|gb|FC450584.1|FC450584
EST:     GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTCATCATCAACGTGGGCAAGACCTACGAGAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
EST: gi|162260986|gb|FC436899.1|FC436899
EST:     GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTCATCATCAACGTGGGCAAGACCTACGAGAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
EST: gi|162200638|gb|FC377847.1|FC377847
EST:     GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATG                         GTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
EST: gi|162156223|gb|FC332598.1|FC332598
EST:     GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTCATCATCAACGTGGGCAAGACCTACGAGAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
EST: gi|162259869|gb|FC436004.1|FC436004
EST:     GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTCATCATCAACGTGGGCAAGACCTACGAGAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
EST: gi|162270986|gb|FC447391.1|FC447391
EST:     GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTCATCATCAACGTGGGCAAGACCTACGAGAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
EST: gi|162228209|gb|FC404925.1|FC404925
EST:     GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATG                         GTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
EST: gi|162256326|gb|FC432336.1|FC432336
EST:     GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATG                         GTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
EST: gi|18368861|gb|BJ200946.1|BJ200946
EST:     GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATG                         GTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
EST: gi|162269653|gb|FC445586.1|FC445586
EST:     GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATG                         GTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
EST: gi|18329169|gb|BJ161175.1|BJ161175
EST:     GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATG                         GTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
EST: gi|162269859|gb|FC445389.1|FC445389
EST:     GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTCATCATCAACGTGGGCAAGACCTACGAGAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
EST: gi|162253576|gb|FC429599.1|FC429599
EST:     GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATG                         GTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
EST: gi|162268481|gb|FC444354.1|FC444354
EST:     GAACTGCGACTTCCATATGGAGCGCTACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTCATCATCAACGTGGGCAAGACCTACGAGAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
EST: gi|162224636|gb|FC401884.1|FC401884
EST:     GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATG                         GTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
EST: gi|67570351|gb|BJ943175.1|BJ943175
EST:     GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCCGATG                         GCATTTTCATCATCAACGTGGGCAAGACCTACGAGAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
EST: gi|162223268|gb|FC400237.1|FC400237
EST:     GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATG                         GTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG
genomic: GAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCG

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: 34 (upstream exon), 35 (downstream exon)
Score: 18

GAGAGCGATGTGCAGATGATGCTGGCTGCCGACGTGCACCTAGGCACCAAGAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattaggg ... gtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCGCGAGGGTGATTGCTGCCATCGAGAACCCCCAGGACATCATCGTCCAGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatagtgggctgttgacgagggtagtgacgtcgttttttattttgtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCGCGAGGGTGATTGCTGCCATCGAGAACCCCCAGGACATCATCGTCCAGTC
           tgttgac  putative branch site (score: 18)
                                  ttttttattttgtgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattagggtttttcctcctgtggcccgttggggtttggttaggtgcttgtgcaagtgttcgtttttggtgcgagggcgcgggggtttggttcggagggaagtggtttgtgatagtgggctgttgacgagggtagtgacgtcgttttttattttgtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCGCGAGGGTGATTGCTGCCATCGAGAACCCCCAGGACATCATCGTCCAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC