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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgggctgctatcttcattctttccatgagttttctcttggattaacagatgggatgtactataaatgtgcggtttgcattcgctttggaaagactgcccgaccaatcgaatgtttcgttctctgtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGGATGAGGGTGGTTTTGCTCCTAACATTCAG

Basic information

species Physcomitrella patens
transcript PP1S1_527V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_527V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os10g08550.3 (Oryza sativa), 3'ss of exon 8
gtaatgggctgctatcttcattctttccatgagttttctcttggattaacagatgggatgtactataaatgtgcggtttgcattcgctttggaaag-actgcccgaccaatcgaatgtttcgttctctgtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGGATGAGGGTGGTTTTGCTCCTAACATTCAG
                                                          |      |  || | |  |||  |     |    |    ||  |      |||  | |  ||   ||| |  || |||| |||||||||||||| || || ||||||||||| ||||| ||||| ||||||||||||||||||||||||
---------------------------------------------------------gtaattctttcatcttcattttaaaccttttccccatcttacgtcattgaaaattaattaattttatctgtacagTCTGTTATCAAGAAGAAGTATGGTCAGGATGCCACCAATGTTGGTGATGAAGGTGGTTTTGCTCCTAACATTCAG

upper sequence: PP1S1_527V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os03g14450.2 (Oryza sativa), 3'ss of exon 5
gtaatgggctgctatcttcattctttccatgagttttctcttggattaacagatgggatgtactataaatgtgcggtttgcattcgctttggaaagactgcccgaccaatcgaatgtttcgttctctgtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGGATGAGGGTGGTTTTGCTCCTAACATTCAG
                                             | |     | |    | || |||      |   || ||| | | || ||| | |  |    ||||   || | || |  |||  || |||| |||||||||||||| || |||||||| || || ||||| ||||| |||||||||||||| |||||||||
--------------------------------------------gtcactttcttgacatttctttaag-----gaactggatt-gttgtgcaaaaattaac-actcaat---atatctcatgttctacagTCTGTTATCAAGAAGAAGTATGGGCAAGATGCTACTAATGTTGGTGATGAAGGTGGTTTTGCTCCAAACATTCAG

upper sequence: PP1S1_527V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os06g04510.2 (Oryza sativa), 3'ss of exon 6
gtaatgggctgctatcttcattctttccatgagttttctcttggattaacagatgggatgtactataaatgtgcggtttgcattcgctttggaaagactgcccgaccaatcgaatgtttcgttctctgtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGGATGAGGGTGGTTTTGCTCCTAACATTCAG
                                                       |     |  | ||||   |  |||   || |  |  ||||  || |   |    |    ||      | | |  ||  | | |||||||| ||||| || ||||||||||| || || |||||||| ||||| ||||||||||||||||||
-------------------------------------------------------gtgaaaaaaaaaaatcaaccttttcattttgtatctgaaa--cttcagaatgtgttatctgaacttctttatacagAGTATAATCAAGAAAAAGTATGGCCAAGATGCCACAAATGTGGGGGATGAAGGTGGCTTTGCTCCTAACATTCAG

upper sequence: PP1S1_527V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G064302_T01 (Zea mays), 3'ss of exon 8
gtaatgggctgctatcttcattctttccatgagttttctcttggattaacagatgggatgtactataaatgtgcggtttgcattcgctttggaaagactgc-ccgaccaatcgaatgtttcgttctctgtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGGATGAGGGTGGTTTTGCTCCTAACATTCAG
                                             | | ||  |      | ||||  |||| |  |  |  |   |  | | ||        |         |||| |||    |    ||    | ||||||||||||||||| || ||||| || || ||||||||||| ||||||||||| ||||||||||||
--------------------------------------------gtgagcaactaatgcat-ctattgatgtaccttaagtgtggaccctaggaatgtgaagtcagaatgctaaatgcttc--cgtacacagAGCATCATCAAGAAGAAGTACGGTCAGGATGCGACAAATGTTGGGGATGAAGGTGGTTTTGCACCTAACATTCAG

upper sequence: PP1S1_527V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G048371_T03 (Zea mays), 3'ss of exon 8
gtaatgggctgctatcttcattctttccatgagttttctcttggattaacagatgggatgtactataaatgtgcggtttgcattcgctttggaaagactgcccga--ccaatcgaatgtttcgttctctgtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGGATGAGGGTGGTTTTGCTCCTAACATTCAG
                                                 ||  ||    |||       | ||   ||| | ||   |   |  | | |  |  |     ||    | | | ||||  |  || | || ||||| |||||||| || ||||||||||| || ||||| || || |||||||||||||| ||||| |||
------------------------------------------------gcatttgcctcgtatatcttgtttgtccttttctttttgtagtgtcaaagtatcataatttgatatcttttgttgttccttacagTCCGTTATCAAAAAGAAGTATGGGCAAGATGCCACGAATGTTGGTGACGAAGGTGGTTTTGCTCCGAACATCCAG

upper sequence: PP1S1_527V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 8
gtaatgggctgctatcttcattctttccatg-agttttctcttggattaacagatgggatgtactataaatgtgcggtttgcattcgctttggaaagactgcccgaccaatcgaatgtt----tcgttctct-gtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGGATGAGGGTGGTTTTGCTCCTAACATTCAG
              |  |  |||||| |    |  || |||||  |  ||   |    |   |    ||||   |     | |    | ||   |  | ||  |    | |   |||||    |  || |||   |||||||||| || ||||| |||||||| ||||| || |||||||| ||||| ||||| ||||||||||| || |||
-------------gttatagttcttttcgcataacttactcttttacaaaataaaaaaacaaaaacaaaatagacaaaaggaaaaatcattattattagtggtcataaattgagatgttgatgtgtttatcttacagGCTGTGATTAAAAAGAAATACGGACAGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAG

upper sequence: PP1S1_527V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA09G28100.1 (Glycine max), 3'ss of exon 8
gtaatgggctgctatcttcattctttccatgagttttctcttggattaacagatgggatgtactataaatgtgcggtttgcattcgctttggaaagactgcccgaccaatcgaatgtttcgttctctgtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGGATGAGGGTGGTTTTGCTCCTAACATTCAG
                             | |   |||| || |  ||||       |   |  || | | |   ||   |||    |   || |   |||| |   |                  |  ||||||| || || ||||| ||||| || ||||| || |||||||| ||||| ||||| ||||||||||| || |||
----------------------------gttatagttcttttcgcataactctctttaaa-atcattattatttagtggtcataaatt---gagatgttgcctgttta---------------tcttacagGCTGTTATTAAAAAGAAATACGGTCAGGATGCTACTAACGTTGGTGATGAAGGTGGCTTTGCTCCTAATATCCAG

upper sequence: PP1S1_527V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv08s0007g03960.t01 (Vitis vinifera), 3'ss of exon 8
gtaatgggctgctatcttcattctttccatgagttttctcttggattaacagatgggatgtactataaatgtgcggtttgcattcgctttggaaagactgcccgaccaatcg--aatgtttcgttctc-tgtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGGATGAGGGTGGTTTTGCTCCTAACATTCAG
                 |||| | |  ||| | |||  |  || ||| |          ||||| || || |||    | |  || |  ||    | || |    | ||| |  | | | || | ||  |  |||||||||| || ||||| || || || |||||||| || ||||| ||||| ||||| ||||||||||| || |||
----------------ctcatacat--cataaatttcat--tgcattca----------gtact-tacatttgcaaaat-ctctcccactgtttggtcttct--gctaattgctattttctcttgcttattcagGCTGTGATTAAAAAGAAATATGGTCAGGATGCCACAAATGTTGGTGATGAAGGTGGCTTTGCTCCTAATATACAG

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|208357716|gb|DC902282.1|DC902282
EST:     CCTTCACGGAAGCCATGAAGATTGGCTCTGAAGTTTACCACAACTTGAAG                         GCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCA-CGTTGGGGATGAA
genomic: CCTTCACGGAAGCCATGAAGATTGGCTCTGAAGTTTACCACAACTTGAAGgtaatgggct ... ttctctgtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGGATGAG
EST: gi|208384682|gb|DC907127.1|DC907127
EST:     CCTTCACGGAAGCCATGAAGATTGGCTCTGAAGTTTACCACAACTTGAAG                         GCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCA
genomic: CCTTCACGGAAGCCATGAAGATTGGCTCTGAAGTTTACCACAACTTGAAGgtaatgggct ... ttctctgtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCA
EST: gi|100369601|gb|BY948562.1|BY948562
EST:     CTTCACGGAAGCCATGAAAGAT-GGCTCTGAAGTTTACCACA-CTTGAAG                         GCTGTGNATCA-GAAGAAGTACGGACAAGATGCCACCNACGTTGGGGATGA
genomic: CTTCACGGAAGCCATGAA-GATTGGCTCTGAAGTTTACCACAACTTGAAGgtaatgggct ... ttctctgtagGCTGTG-ATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGGATGA
EST: gi|100409225|gb|BY991908.1|BY991908
EST:     CCTTCACGGAAGCCATGAAGATTGGCTCTGAAGTTTACCACAACTTGAAG                         GCTGTGATCAAGAAGAAGTACGGACAAGATGCCAC-AACGTTGGGGGATGA
genomic: CCTTCACGGAAGCCATGAAGATTGGCTCTGAAGTTTACCACAACTTGAAGgtaatgggct ... ttctctgtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGG-ATGA
EST: gi|100448364|gb|CJ972663.1|CJ972663
EST:     CCTTCACGGAAGCCATGAAGATTGGCTCTGAAGTTTACCACAACTTGAAG                         GCTGTGATCAAGAANAAGTACGGACAAGATGCCACCAACGTTGGG
genomic: CCTTCACGGAAGCCATGAAGATTGGCTCTGAAGTTTACCACAACTTGAAGgtaatgggct ... ttctctgtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGG
EST: gi|100401183|gb|BY990872.1|BY990872
EST:     CCTTCACGGAAGCCATGAAGATTGGCTCTGAAGTTTACCACAACTTGAAG                         GCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGGATGAG
genomic: CCTTCACGGAAGCCATGAAGATTGGCTCTGAAGTTTACCACAACTTGAAGgtaatgggct ... ttctctgtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGGATGAG

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), 24 (downstream exon)
Score: 6

GAGTTCATGATCCTGCCAACTGGCGCGTCGTCCTTCACGGAAGCCATGAAGATTGGCTCTGAAGTTTACCACAACTTGAAGgtaatgggct ... ttctctgtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGGATGAGGGTGGTTTTGCTCCTAACATTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcattcgctttggaaagactgcccgaccaatcgaatgtttcgttctctgtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGGATGAGGGTGGTTTTGCTCCTAACATTCAG
                                        tttcgttctct  CT-rich tract
                                    aatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgggctgctatcttcattctttccatgagttttctcttggattaacagatgggatgtactataaatgtgcggtttgcattcgctttggaaagactgcccgaccaatcgaatgtttcgttctctgtagGCTGTGATCAAGAAGAAGTACGGACAAGATGCCACCAACGTTGGGGATGAGGGTGGTTTTGCTCCTAACATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG