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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attggttggcatggattaccgcagtgtgtcttaggccctcagaacaaatgtgttcctaaggatataagttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG

Basic information

species Physcomitrella patens
transcript PP1S76_212V6.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S76_212V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os05g49300.1 (Oryza sativa), 3'ss of exon 2
-attggttggcatggattaccgcagtgtgtcttaggccctcagaacaaatgtgttcctaaggatataagttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG
  |    |   || |  | ||||  |||| ||          |  || | |  ||  |  |   ||  |     |  ||        ||  || | | |||||| || || ||||| ||||| || || ||||| ||| | ||||||||||||||||| || ||||| ||||| || || |||||||| ||  |  | |||
cttacaatcctattgtcttccgcc-tgtggctagcattgcttgggcacaagctttattgtgctcattggagttctattgacttatcatgtcctgttttcagTGAGATAGCGAAGCATCTATCGCTTCCGCCTGTAAAGCTCCACTGCAGCATGCTTGCAGAGGATGCAATCAAGGCCGCCGTGAAGGATTATGAAGCGAAG

upper sequence: PP1S76_212V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G141252_T01 (Zea mays), 3'ss of exon 2
-----------attggttggcatggattaccgcagtgtgtcttaggcc-ctcagaacaaatgtgttcctaaggatataagttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG
           || ||   | ||    |    |  ||  |   |     ||  |      |||  |  || |  ||||    |     |     ||| |    ||| ||||| || || || |||||||| ||||| ||||| |||||| |||||||||||||||| ||||| || || ||||| || || |||||||| ||| || | |||
gtaagtttcgaatcggcctggatatggtcgtcccatgcattccatatttcttggggttgttgtactgatacgtctatatac-acgcctttccattgtct----tttttgcagCGAGATTGCGAAGCACCTGTCTCTTCCACCAGTGAAGCTGCACTGCAGCATGCTCGCTGAGGACGCAATCAAGGCCGCCGTGAAGGATTACGAGGCAAAG

upper sequence: PP1S76_212V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA17G09670.2 (Glycine max), 3'ss of exon 2
attggttggcatggattaccgcagtgtgtcttaggccctcagaacaaatgtgttcctaaggatataagttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG------------------------------------------------
                                         |  |   | ||||  | ||      |  |  |||  |   ||  |  ||  | ||||||||| || || ||||| || || || ||||| || ||| | |||||||||||||||||||||||||||||||||||||| || || |||||  |  | |||                                                
-----------------------------------------gttctggtttgttgttgag------atcttgatgtggcaaataagc-aatgtcctgcagtgaaattgcaaagcatctttcacttccaccagttaagctccactgcagCATGCTTGCTGAAGATGCTATCAAAGCGGCCGTTAAAGACTATGAAGCTAAGCGTGCTAAGGCAACTGCTAGCGGAGAGGCAGCAACAGAAGAGAAGCCT

upper sequence: PP1S76_212V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA17G09670.1 (Glycine max), 3'ss of exon 2
-attggttggcatggattaccgcagtgtgtcttaggccctcagaacaaatgtgttc---ctaaggatataagttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG
 ||    |||||   ||      ||| |   ||| ||  |||  |   ||   |      |   | |   |  |  |||  |   ||  |  ||  | ||||||||| || || ||||| || || || ||||| || ||| | |||||||||||||||||||||||||||||||||||||| || || |||||  |  | |||
catca--tggca-aaatagttatagttttggttatgctttcatgatggatagttctggtttgttgttgagatcttgatgtggcaaataagc-aatgtcctgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCCGTTAAAGACTATGAAGCTAAG

upper sequence: PP1S76_212V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA05G02260.1 (Glycine max), 3'ss of exon 2
attggttggcatggattaccgcagtgtgtcttaggccctcagaacaaatgtgtt---cctaaggatataag-ttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG
     |        ||      ||| |   ||| |   |||  |   |||  |     ||   | ||| || |      |||| ||    |  |  |  |||||||| || || ||||| || || || ||||| || ||| | |||||||||||||||||||||||||| |||||||| || || || |||||  |  | |||
----atcatagcaaatagttctagttttggttatgttttcatgatggatggttctggtctgttgttatgagatcttgatgtggcgaataatcgatgtcgtgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCATGCTTGCTGAAGATGCCATCAAAGCAGCCGTTAAAGACTATGAAGCTAAG

upper sequence: PP1S76_212V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA06G19310.1 (Glycine max), 3'ss of exon 2
attggttggcatggattaccgcagtgtgtcttaggccctcagaac-aaatgtgttcctaaggatataagttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG
  | |   |  | |     |  | ||| |  |      ||  |      | || |  | ||  ||| | || ||  |     ||   | ||  || |||||||| || || ||||| || || || ||||| || ||| | |||||||||||||||||||| |||||||| ||||| || || || || ||  |  | |||
tctagggagtttagtcatgctaaatgttttatgattaatcgcatttgtctctggttattagtctatgaattgaagtg-acacataatttaatgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG

upper sequence: PP1S76_212V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA13G21010.1 (Glycine max), 3'ss of exon 2
-attggttggcatggattaccgcagtgtgtcttaggccc-tcagaacaaatgtgttcctaaggatataagttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG
   |   |       |       | | |   | |      ||   ||   |  | |  | ||  ||| | || ||  |||        ||||  || | |||||| || || ||||| || || || ||||| || ||| | |||||||||||||||||||| |||||||| ||||| || || || || ||  |  | |||
agcttagtcatgctaaaggttttattattaatcacatttgtctccacctctccggttattagtttatgaattgaa--gtgacacataatgaatgtttttcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG

upper sequence: PP1S76_212V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv01s0127g00460.t01 (Vitis vinifera), 3'ss of exon 1
attggttggcatggattaccgcagtgtgtcttaggccctcagaacaaatgtgttcctaa---ggatataagttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG
      | ||||    |     | |||  ||   |   ||   |    | | ||  |||      | |   |    || || | || | |||      || || || || ||||| || || ||||| || || |||||| |||||||||||||||||||||| ||||| || || || || || || || ||  |  |||||
---aacttgcattatattttttattgttgctactgatttctcgaagtttttatttttaatttttgtctttttgttctgatgtgtatatttgatgacaatgaagGGAGATTGCCAAACATCTCTCTCTTCCTCCAGTGAAGCTGCACTGCAGCATGCTTGCTGAGGATGCAATTAAGGCAGCTGTCAAAGATTATGAAGCCAAG

upper sequence: PP1S76_212V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ10697 (Selaginella moellendorffii), 3'ss of exon 2
attggttggcatggattaccgcagtgtgtcttaggccctcagaacaaatgtgttcctaaggatataagttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG
                               ||     ||      |  |  || ||  |    |||| |   |          | |    | |  ||||||||||||||||||| || || ||||| || |||||| | ||||||||||||||||| || ||||| |||||||| ||| | || || ||| |  | |||
------------------------------gtaacttttcttcttgagaggatttctccgaggctaagctctct--------cctctttcttcttcgcagTGACATCGCCAAGCATCTGTCGCTGCCGCCAGTGAAGCTCCACTGCAGCATGCTTGCCGAGGATGCGATCAAAGCCGCGATCAAAGATTACGACGCGAAG

upper sequence: PP1S76_212V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ35746 (Selaginella moellendorffii), 3'ss of exon 2
attggttggcatggattaccgcagtgtgtcttaggccctcagaacaaatgtgttcctaaggatataagttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG
                    | | | | ||||    | | |||  |    | || |  ||| |  ||| | | |          | |    | |  ||||||||||||||||||| || || || || || |||||| | ||||||||||||||||| || ||||| |||||||| ||| | || || ||| |  |||||
--------------------gtaatttttctt----cttgagagga----tttttccgaggct--aagctcatt--------cctctttcttcttcgcagTGACATCGCCAAGCATCTGTCGCTACCGCCAGTGAAGCTCCACTGCAGCATGCTTGCCGAGGATGCGATCAAAGCCGCGATCAAAGATTACGACGCCAAG

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|18332989|gb|BJ165003.1|BJ165003
EST:     CAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: CAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162224580|gb|FC400476.1|FC400476
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|67508569|gb|BJ941432.1|BJ941432
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162250386|gb|FC426248.1|FC426248
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|37824297|gb|BJ582363.1|BJ582363
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162250385|gb|FC426247.1|FC426247
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162177237|gb|FC353394.1|FC353394
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162177238|gb|FC353395.1|FC353395
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|67691788|gb|BJ952021.1|BJ952021
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|208372787|gb|DC952674.1|DC952674
EST:     AGTGGATCAAGGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: AGTGGATCAA-GGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162224579|gb|FC400475.1|FC400475
EST:     GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAG                         TGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGGCTATGGAAGAAGCAGTGAGCATTAAGAACAGgtaaataagc ... ctttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgtgttcctaaggatataagttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG
                                             ctttctgc  CT-rich tract
                atataagttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attggttggcatggattaccgcagtgtgtcttaggccctcagaacaaatgtgttcctaaggatataagttaaatggtggggatgtgtgaactttctgcagTGACATCGCCAAGCACCTATCTCTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCGGTGAAGGACTACAAGTCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG