Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTCCGAACATGATCGTTATTCGGTCGTTCGATGTCAACAAGCCTGGTGCCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgttgtcaagtgtgataatgtaatcggccaatcagacatatgtgttgggttcatgtccggacatggctgcagggttaagttgatcaggtagtcc...

Basic information

species Physcomitrella patens
transcript PP1S207_94V6.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S207_94V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 5'ss of exon 7
TCCTCCGAACATGATCGTTATTCGGTCGTTCGATGTCAACAAGCCTGGTGCCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgt-tgttgtcaagtgtgataatgtaatcggccaatcagacatatgtgttgggttcatgtccggacatggctgcagggttaagttgatcaggtagtcc
 ||||| |||||||| |||||||| || || |||||||||||||||||| | || ||||| ||||| | |||||| || ||||||||||| ||||| || |||||| |  | ||  ||   |||||  |||     ||||||   | | |  ||   | | ||  |  |      | |  | |  |||   |||       
CCCTCCAAACATGATTGTTATTCGCTCCTTTGATGTCAACAAGCCTGGTTCAGAGGTTGATGAAATTAGGGGTGGTGTAGCTGGTGGCAGCATTCTCAGAgtatgtgttctctcctgtaacataattaaatattttaatcagtagttttttatg---ttaagtatgagctgaatggtaatgcttcgtt--ccag-------

upper sequence: PP1S207_94V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 5'ss of exon 7
TCCTCCGAACATGATCGTTATTCGGTCGTTCGATGTCAACAAGCCTGGTGCCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgttgtcaagtgtgataatgtaatcggccaatcagacatatgtgttgggttcatgtccggacatggct-gcagggttaagttgatcaggtagtcc
 ||||| |||||||| || ||||| || || |||||||||||||||||| | || ||||| ||||| | |||||| || ||||||||||| || || || ||||||  ||  |  ||||| | |||||||  |    |    ||    | |||||||  |     |  ||| ||   |  || | | |  |    |||   
CCCTCCAAACATGATTGTCATTCGCTCCTTTGATGTCAACAAGCCTGGTTCAGAGGTTGATGAAATTAGGGGTGGTGTAGCTGGTGGCAGCATCCTCAGAgtatgt-attccctcgtgtg-tcatgtaattagattttttatcactacttttgggttatta----ggtatgacttaaattgtgatgcttcttttatag---

upper sequence: PP1S207_94V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G107654_T01 (Zea mays), 5'ss of exon 7
TCCTCCGAACATGATCGTTATTCGGTCGTTCGATGTCAACAAGCCTGGTGCCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgttgtcaagtgtgataatgtaatcggccaatcagacatatgtgttgggttcatgtccggacatggctgcagggttaagttgatcaggtagtcc
 ||||| |||||||| |||||||| || || ||||| |||||||||||| | || || || ||||||| |||||| || |||||||| |||||||| |||||||||   | | |    ||  |  |   |    ||||| |   | |    || ||| |  |  | |||   |  ||  | ||  ||  |   |      
ACCTCCCAACATGATTGTTATTCGCTCCTTTGATGTTAACAAGCCTGGTTCAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacatcttagtcatggcatggcgcta---caatctgt--tttccactgtgttta-atgtgaacaaaacatcaatggtatttttttacag------

upper sequence: PP1S207_94V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G117900_T02 (Zea mays), 5'ss of exon 7
TCCTCCGAACATGATCGTTATTCGGTCGTTCGATGTCAACAAGCCTGGTGCCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgttgtcaagtgtgataatgtaatcggccaatcagacatatgtgttgggttcatgtccggacatggctgcagggttaagttgatcaggtagtcc
 ||||| |||||||| |||||||| || || ||||| |||||||||||| | || ||||||||||| |  ||||| || |||||||||||||| || |||||||||   | | |   || ||  ||  | |   |  |    ||| | ||||   |  |||  |  | || ||    |  ||                  
GCCTCCCAACATGATTGTTATTCGTTCCTTTGATGTTAACAAGCCTGGTTCAGAGGTTGACGAAATTAGAGGTGGTGTAGCTGGTGGCAGTATCCTCAGGgtatgtatatctta---gtcatggtgctaccattctgttctccat-tatgtttaat--atgaacaaa-atagcaatggttttgctacag-----------

upper sequence: PP1S207_94V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA08G18240.2 (Glycine max), 5'ss of exon 7
TCCTCCGAACATGATCGTTATTCGGTCGTTCGATGTCAACAAGCCTGGTGCCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgtt--gtcaagtgtgataatgtaatcggccaatcagacatatg-tgttgggttcatgtccggacatggctgcagggttaagttgatcaggtagtcc
||| || |||||||| ||||||||||| || |||||||| || ||||||   || ||||| ||||| || || || || |||||||| || |||||||||||| |||| |  ||||| |   |  || | ||     |     ||  ||  |     | |    |    |  ||  |  |    |||      || |  ||||
TCCACCTAACATGATTGTTATTCGGTCATTTGATGTCAATAAACCTGGTTATGAGGTTGATGAAATTAAAGGAGGTGTAGCTGGTGGAAGCATTCTGAGGgtaggttggttggtcaatttccaatatatcatgcttgatctgcactgataattccatgctacaatttcaaagtgattttacaaataat---gccatggtgtcc

upper sequence: PP1S207_94V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA15G40750.1 (Glycine max), 5'ss of exon 7
TCCTCCGAACATGATCGTTATTCGGTCGTTCGATGTCAACAAGCCTGGTGCCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgttgtcaagtgtgataatgtaatcggccaatcagacatatgtgttgggttcatgtccggacatggctgcagggttaagttgatcaggtagtcc--
|||||| || ||||||||||||||||| || |||||||| || ||||||   || ||||| ||||| || || || || |||||||| || ||| |||||||| ||  ||        |    |||||    ||        ||     ||      ||  |    | ||  |  ||    |   | ||     || |    
TCCTCCTAATATGATCGTTATTCGGTCATTTGATGTCAATAAACCTGGTTATGAGGTTGATGAAATAAAAGGAGGTGTAGCTGGTGGGAGCATTTTGAGGgtaggtcttttcgtcaatttcccatgtatcatgcttgatttgcactgacgtcactcacagatattaatat--ccccaataatgtatggaatgcataattttt

upper sequence: PP1S207_94V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: Vv13s0074g00310.t01 (Vitis vinifera), 5'ss of exon 7
TCCTCCGAACATGATCGTTATTCGGTCGTTCGATGTCAACAAGCCTGGTGCCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgttgtcaagtgtgataat-gtaatcggccaatcagacatatgtgttgggttcatgtccg-gacatggctgcagggttaagttgatcaggtagtcc--
 || || || ||||| ||||||||||| || |||||||||||||||||    || ||||| || || |  ||||| || |||||||| || ||||| ||||||||||  | |||  | | ||    |   |  |  | | |||  |||||   || ||||  |    |   | | ||||   |    |||||| | |    |  
ACCACCAAATATGATTGTTATTCGGTCATTTGATGTCAACAAGCCTGGGTTTGAGGTTGATGAGATAAGAGGTGGTGTTGCTGGTGGAAGCATTCTCAGGgtatgtt--tctcatttattatttcagaggtttggtagtaagaactatgtaaaggcttcacattgatgctgttggtgcaaaat--gcttgatctgcttccacat

upper sequence: PP1S207_94V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EFJ26525 (Selaginella moellendorffii), 5'ss of exon 5
TCCTCCGAACATGATCGTTATTCGGTCGTTCGATGTCAACAAGCCTGGTGCCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgttgtcaagtgtgataatgtaatcggccaatcagacatatgtgttgggttcatgtccggacatggctgcagggttaagttgatcaggtagtcc
 || || |||||||| || ||  | || ||||| || |||||||| || || || || |||||||||||||| || |||||||| || |||||||| |||||| ||    || || | | | | |   | | || ||  |  ||   || || |   | | |||       |                            
CCCACCAAACATGATTGTCATCAGATCTTTCGACGTGAACAAGCCGGGAGCGGAGGTGGACGAAATCAAGGGCGGAGTGGCTGGCGGGAGTATTCTCAGGgtacgt----gtaaaatctaaaacttgcagctgc-aactactcactcgttttcg---cgtttcctcgtccag----------------------------

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|162272017|gb|FC448435.1|FC448435
EST:     CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGG                         GGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
genomic: CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgtt ... ctttgtgcagGGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
EST: gi|37829627|gb|BJ587639.1|BJ587639
EST:     GGTGNCAGTATTCTGAGG                         GGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
genomic: GGTGGCAGTATTCTGAGGgtatgttgtt ... ctttgtgcagGGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
EST: gi|162264526|gb|FC441160.1|FC441160
EST:     CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGG                         GGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
genomic: CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgtt ... ctttgtgcagGGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
EST: gi|37825347|gb|BJ583413.1|BJ583413
EST:     ATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGG                         GGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
genomic: ATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgtt ... ctttgtgcagGGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
EST: gi|162262330|gb|FC437657.1|FC437657
EST:     CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGG                         GGAGTGTTACGGGTGGGGCAA-GAATCGAAGTGCGGCCTGGAATCACTA
genomic: CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgtt ... ctttgtgcagGGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTA
EST: gi|67720573|gb|BJ970832.1|BJ970832
EST:     CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGNCAGTATTCTGAGG                         GGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
genomic: CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgtt ... ctttgtgcagGGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
EST: gi|67726044|gb|BJ976303.1|BJ976303
EST:     CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGG                         GGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
genomic: CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgtt ... ctttgtgcagGGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
EST: gi|37850546|gb|BJ608554.1|BJ608554
EST:     CAGTATTCTGAGG                         GGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGNCCTGGAATCACTACC
genomic: CAGTATTCTGAGGgtatgttgtt ... ctttgtgcagGGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
EST: gi|208365366|gb|DC954807.1|DC954807
EST:     CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGG                         GGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
genomic: CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgtt ... ctttgtgcagGGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
EST: gi|22132033|gb|BQ826944.1|BQ826944
EST:     CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGG                         GGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
genomic: CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgtt ... ctttgtgcagGGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
EST: gi|37841543|gb|BJ599551.1|BJ599551
EST:     CTGGTGGCAGTATTCTGAGG                         GGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
genomic: CTGGTGGCAGTATTCTGAGGgtatgttgtt ... ctttgtgcagGGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
EST: gi|67720595|gb|BJ970854.1|BJ970854
EST:     CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGG                         GGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
genomic: CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgtt ... ctttgtgcagGGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
EST: gi|37838292|gb|BJ596300.1|BJ596300
EST:     GTGGCAGTATTCTGAGG                         GGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
genomic: GTGGCAGTATTCTGAGGgtatgttgtt ... ctttgtgcagGGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
EST: gi|162272016|gb|FC448434.1|FC448434
EST:     CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGG                         GGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC
genomic: CCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgtt ... ctttgtgcagGGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACC

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: 31 (upstream exon), 35 (downstream exon)
Score: 13

TCCTCCGAACATGATCGTTATTCGGTCGTTCGATGTCAACAAGCCTGGTGCCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgtt ... ctttgtgcagGGAGTGTTACGGGTGGGGCAAAGAATCGAAGTGCGGCCTGGAATCACTACCAAGGACGAGAGTGGTGGAATCAAGTGCACACCAATTTTCTCGCGAATCA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTCCGAACATGATCGTTATTCGGTCGTTCGATGTCAACAAGCCTGGTGCCGAAGTTGACGAAATCAAGGGTGGCGTGGCTGGTGGCAGTATTCTGAGGgtatgttgttgtcaagtgtgataatgtaatcggccaatcagacatatgtgttgggttcatgtccggacatggctgcagggttaagttgatcaggtagtcc

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