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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgtcgaagcataatttggacacgatcatcttgtattaccaactttggctaaatgaagaattctccgggacgagcgagaaatgaggttgttaaacctttagtatacttggactggtggttctgggactgattattactttcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCTTGTTGCAAATCTGTTTCAAATGGCCCGTGAAGCTGCTCCATCCATCATC

Basic information

species Physcomitrella patens
transcript PP1S76_197V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S76_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
gtaactgtcgaagcataatttggacacgatcatcttgtattaccaactttggctaaatgaagaattctccgggacgagcgagaaatgaggttgttaaacctttagtatacttggactggtggttctgggactgattattactttcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCTTGTTGCAAATCTGTTTCAAATGGCCCGTGAAGCTGCTCCATCCATCATC
                                             |  ||| |  |||||  |||    |        | | |        | ||   | |  | |||| ||    |  || |||    | | | | |   |    | |||||||| || || |||||| | || ||||| ||||||||||||||||| || ||||||||||| || || |||||||| || |||   ||||| ||||| |||
-------------------------------------------tgatgttgcc--aatgatcaatat--caatgtataccatattcatttgtattgttcgtgcaatatatttta--ttatgtttc----atttaatgtgtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC

upper sequence: PP1S76_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g04840.1 (Oryza sativa), 3'ss of exon 2
gtaactgtcgaagcataatttggacacgatcatcttgtattaccaactttggctaaatgaagaattctccgggacgagcgagaaatgaggttgttaaacctttagtatacttggactggtggttctgggactgattattactttcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCTTGTTGCAAATCTGTTTCAAATGGCCCGTGAAGCTGCTCCATCCATCATC
                                  || | || |     || |||       |      |  | || || |    |||   |||||    ||||  |    ||  |      ||| ||  |  |||| |   |||| |  |||| || || || |||||| | || ||||| ||||||||||| |||||||| || ||||| ||||| || || ||||||||||||  |||||| ||||| |||
----------------------------------ttctctttcttttctttgct-------gctactgctagtactagtgcagtatgct-ttgtt----ctttgtttctgtttcat-----gttatgttaacgattttggttttctt--gcagCATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAAAGTGAGAAACTAGTTGCTAATCTTTTCCAGATGGCCCGTGAAAATGCTCCCTCCATTATC

upper sequence: PP1S76_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os02g06490.1 (Oryza sativa), 3'ss of exon 2
gtaactgtcgaagcataatttggacacgatcatcttgtattaccaactttggctaaatgaagaattctccgggacgagcgagaaatgaggttgttaaacctttagtatacttggactggtggttctgggactgattattactttcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCTTGTTGCAAATCTGTTTCAAATGGCCCGTGAAGCTGCTCCATCCATCATC
                                    | |||   || |||||  |||         ||  ||   || |    |      |||||      ||||| || ||  |||  |  |   | ||| |||    ||    | ||||||||| || || || ||  |  | || |||||||||||||| ||||||||||| ||  | || ||||| || ||||||||||||  ||| || ||||| |||
------------------------------------gcattgttaaatttggacaaaa--------ctatggagtgatctgtcatct---ttgttctgttattagtgtaatt--actaatc-tgaagtgacggatggacaca---cactgcagTATATCTTCGTCGGATCTTCTCTCCAAGTGGATGGGAGAAAGTGAGAAGCTGGTGACGAACCTGTTCCAGATGGCCCGTGAAAATGCACCCTCCATTATC

upper sequence: PP1S76_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 2
gtaactgtcgaagcataatttggacacgatcatcttgtattaccaactttggctaaatgaagaattctccgggacgagcgagaaatgaggttgttaaacctttagtatacttggactggtggttctgggactgattattactttcct-ctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCTTGTTGCAAATCTGTTTCAAATGGCCCGTGAAGCTGCTCCATCCATCATC
                                               ||    | | ||   |||      ||| |    || |||     | |   ||| || || | ||  | |   |  || ||  | |    | |  |    | ||||||||| || ||||||||  |||| |||||||||||||| || ||||||||  | |||||||||||||| |||||||| || |||  ||| || ||||| |||
----------------------------------------------tttcacttgattggtcaat------ggatg--ttagcaatactaatatcctaccatttgttttctatgccgtatctttatgatatttcacactgttgctttactgcagTATATCTTCTTCAGATCTGGTTTCAAAGTGGATGGGTGAAAGTGAGAAATTAGTTGCAAATCTGTTCCAAATGGCTCGGGAAAATGCCCCTTCCATTATC

upper sequence: PP1S76_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G126860_T01 (Zea mays), 3'ss of exon 2
gtaactgtcgaagcataatttggacacgatcatcttgtattaccaactttggctaaatgaagaattctccggg-acgagcgagaaatgaggttgttaaac-ctttagtatacttggactggtggttctgggactgattattactttcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCTTGTTGCAAATCTGTTTCAAATGGCCCGTGAAGCTGCTCCATCCATCATC
                                                    |||| |    | || |  |   ||   |  ||   |    ||| | |  |  || |||||||    |  || |  |    |  | | || ||||  |  ||||||| || ||||||||  |||| |||||||||||||| || || |||||  | || |||||||| || |||||||| ||||||  ||| || ||||| |||
--------------------------------------------------atctaacttgcaattttttagtttacatacttgattggtcaatgtaagataccctactatactttttttcatgatattt---cacaatgttgctttatt--gcagTATATCTTCTTCAGATCTGGTTTCAAAGTGGATGGGTGAAAGCGAGAAATTAGTCGCAAATCTTTTCCAAATGGCTCGTGAAAATGCCCCTTCCATTATC

upper sequence: PP1S76_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA12G09300.1 (Glycine max), 3'ss of exon 2
gtaactgtcgaagcataatttggacacgatcatcttgtattaccaactttggctaaatgaagaattctccgggacgagcgag-aaatgaggttgttaaacctttagtatacttggactggtggttctgggactgattattactttcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCTTGTTGCAAATCTGTTTCAAATGGCCCGTGAAGCTGCTCCATCCATCATC
                                     | | |   | ||||  | ||  |  |  || |       || |   |  | |||| |  |    |||  || |          || ||       | | | ||   ||| ||  |||| |||| || |||||| |||| ||||||||||||||||| ||||| ||||| ||  ||||||| || |||||||| || |||  ||| || || ||||| 
-------------------------------------tgtcagtgattttgtttgaaaaataaggtcgcaaatgtaagtgcttaggttaggtgggcatttttttgctaca----------tgttt-------taactttttaattcttcaccagTGTTTCTTCGTCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCTGGTCTCAAATCTTTTCCAAATGGCACGCGAAAGTGCACCTTCTATCATA

upper sequence: PP1S76_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA11G19120.1 (Glycine max), 3'ss of exon 2
gtaactgtcgaagcataatttggacacgatcatcttgtattaccaactttggctaaatgaagaattctccgggacgagcgagaaatgaggttgttaaacctttagtatacttggactggtggttctgggactgattattactttcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCTTGTTGCAAATCTGTTTCAAATGGCCCGTGAAGCTGCTCCATCCATCATC
                                                    ||  |    || ||     | |  |   |    || |  ||| |   |||| ||   | |   || |  |     |   | | | ||   ||| ||  |||| |||| || |||||| |||| ||||||||||||||||| ||||| ||||| ||  ||||||| || |||||||| || |||  ||| || || || || 
---------------------------------------------------ccttgacagtgattttgtttgaaataaaaaaggttgtgaatgtgagtgctttggtgggcattttcttgcagcat--gttttaacttttgaattcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCTGGTCTCAAATCTTTTCCAAATGGCTCGCGAAAGTGCACCTTCTATAATA

upper sequence: PP1S76_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 2
gtaactgtcgaagcataatttggacacgatcatcttgtattaccaactttggctaaatgaagaattctccgggacgagcgagaaatgaggttgttaaacctttagtatacttggactggtggttctgggactgattattact-ttcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCTTGTTGCAAATCTGTTTCAAATGGCCCGTGAAGCTGCTCCATCCATCATC
                                                      || |       | |    |   | ||     |     |  |      ||  |   ||| | |   |   |  |  | ||   | | || ||| | |||||| | || ||||||||| |||| |||||||||||||| || ||||| ||| | ||| ||||||| ||||||||||| || ||   |||||| |||||||||
------------------------------------------------------aagtctgtttctgtttctggttatcgtatttttctcctccttttatgttcatgagcttaggccaataagttggcaagtgccaactgctgttcttttgcagTGTCTCTTCTTCAGACCTGGTTTCAAAGTGGATGGGTGAAAGTGAAAAGTTAGTTTCAAATCTTTTTCAAATGGCTCGGGAGAGTGCTCCTTCCATCATC

upper sequence: PP1S76_197V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv13s0106g00490.t01 (Vitis vinifera), 3'ss of exon 2
gtaactgtcgaagcataatttggacacgatcatcttgtattaccaactttggctaaatgaagaattctccgggacgagcgagaaatgaggttgttaaacctttagtatacttggactggtggttctgggactgattattactttcct-ctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCTTGTTGCAAATCTGTTTCAAATGGCCCGTGAAGCTGCTCCATCCATCATC
                                               |       || ||||  ||  |    |      ||| |   | || ||      ||  || |||||  |             | ||   | || | || | |  |||| | || || || ||  | || ||||| |||||||| || ||||| ||||| ||  ||||||||||||||||||| ||||||  |||||| |||||||| 
-----------------------------------------------tacaaacgaaagaagggttggctta-atatcatagatacaggtttatt------ttgatagacttgagcctacaaagtcacaaatgccaaatattgtctttccacagTGTGTCTTCATCTGATCTAGTTTCAAAATGGATGGGTGAAAGTGAAAAGCTAGTCTCAAATCTGTTTCAAATGGCTCGTGAAAGTGCTCCTTCCATCATT

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|162243142|gb|FC416742.1|FC416742
EST:     TCGTATCTTGCAAAAGCTGTTGCTACGGAAGCTGATTCTACATTCTTTAG                         TATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCT
genomic: TCGTATCTTGCAAAAGCTGTTGCTACGGAAGCTGATTCTACATTCTTTAGgtaactgtcg ... tcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCT
EST: gi|162181631|gb|FC357933.1|FC357933
EST:     TCGTATCTTGCANAAGCTGTTGCTACGGAAGCTGATTCTACATTCTTTAG                         TATTTCCTCTTCAGACTTGGTGTCAAAGTGGATG
genomic: TCGTATCTTGCAAAAGCTGTTGCTACGGAAGCTGATTCTACATTCTTTAGgtaactgtcg ... tcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATG
EST: gi|162154850|gb|FC331892.1|FC331892
EST:     TCGTATCTTGCAAAAGCTGTTGCTACGGAAGCTGATTCTACATTCTTTAG                         TATTTCCCTCT-CAGACTTGGTGTC
genomic: TCGTATCTTGCAAAAGCTGTTGCTACGGAAGCTGATTCTACATTCTTTAGgtaactgtcg ... tcctctgcagTATTTCC-TCTTCAGACTTGGTGTC
EST: gi|162149984|gb|FC326515.1|FC326515
EST:     TCGTATCTTGCAAAAGCTGTTGCTACGGAAGCTGATTCTACATTCTTTAG                         TATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCT
genomic: TCGTATCTTGCAAAAGCTGTTGCTACGGAAGCTGATTCTACATTCTTTAGgtaactgtcg ... tcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCT
EST: gi|208397729|gb|DC911980.1|DC911980
EST:     TCGTATCTTGCAAAAGCTGTTGCTACGGAAGCTGATTCTACATTCTTTAG                         TATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCT
genomic: TCGTATCTTGCAAAAGCTGTTGCTACGGAAGCTGATTCTACATTCTTTAGgtaactgtcg ... tcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCT
EST: gi|162196819|gb|FC373887.1|FC373887
EST:     TCGTATCTTGCAAAAGCTGTTGCTACGGAAGCTGATTCTACATTCTTTAG                         TATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCT
genomic: TCGTATCTTGCAAAAGCTGTTGCTACGGAAGCTGATTCTACATTCTTTAGgtaactgtcg ... tcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCT

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), 29 (downstream exon)
Score: 12

GAAGACCATGGCGAGCATTTTTGTTGTATGGGCCCCCCGGGACTGGAAAATCGTATCTTGCAAAAGCTGTTGCTACGGAAGCTGATTCTACATTCTTTAGgtaactgtcg ... tcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCTTGTTGCAAATCTGTTTCAAATGGCCCGTGAAGCTGCTCCATCCATCATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttagtatacttggactggtggttctgggactgattattactttcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCTTGTTGCAAATCTGTTTCAAATGGCCCGTGAAGCTGCTCCATCCATCATC
                              gactgat  putative branch site (score: 12)
                                    ttattactttcctct  CT-rich tract
                                   attattacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactgtcgaagcataatttggacacgatcatcttgtattaccaactttggctaaatgaagaattctccgggacgagcgagaaatgaggttgttaaacctttagtatacttggactggtggttctgggactgattattactttcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCTTGTTGCAAATCTGTTTCAAATGGCCCGTGAAGCTGCTCCATCCATCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT