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'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGTACTTCGTGGAGCACATCACGAAGGCATATCAAGCACTAACGGATCCTGTATCAAGAGAGAATTACGAGAAGTATGGTCACCCCGATGGACGCCAGgtttgcaccttcatcattttcatgtgggccaaactttactgttgataattaactttgcaaccgcggatcctctttgtaacatattggacggctactgttg...

Basic information

species Physcomitrella patens
transcript PP1S241_31V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S241_31V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os04g24180.1 (Oryza sativa), 5'ss of exon 5
CAAGTACTTCGTGGAGCACATCACGAAGGCATATCAAGCACTAACGGATCCTGTATCAAGAGAGAATTACGAGAAGTATGGTCACCCCGATGGACGCCAGg---tttgcaccttcatcatttt---catgtgggccaaactttactgttgataattaac--tttgcaaccgcggatcctctttgtaacatattggacggctactgttg
||||||||| || ||    ||  | ||||||||||| ||  |||| |||||||||||  | || || || ||||||||||||||||| |||||||||||||   | || || |   | ||| |   ||        |||  | |   |  | |  | |   ||          ||  |      |||||   ||      |  |   |
CAAGTACTTTGTTGAATTTATATCCAAGGCATATCAGGCTTTAACTGATCCTGTATCTCGTGAAAACTATGAGAAGTATGGTCACCCAGATGGACGCCAGgtaatatggacatctgttattcttgacactctacttaaaactaaacatatacatgtgatgtttcatggtgttcgagacaaacattaacacggtgtgtttgtggtccag

upper sequence: PP1S241_31V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G167868_T01 (Zea mays), 5'ss of exon 4
CAAGTACTTCGTGGAGCACATCACGAAGGCATATCAAGCACTAACGGATCCTGTATCAAGAGAGAATTACGAGAAGTATGGTCACCCCGATGGACGCCAGgtttgcaccttcatcattttcatgtgggccaaactttactgttgataattaactttgcaaccgcggatcctctttgtaac--atattggacggctac---tgttg------------
 |||||||| || ||  | ||  | ||||||||||||||| |||| |||||| ||||  |||||||||| || || ||||||||||| ||||| || |||||          || |   ||||  |  || ||  |  |  |  |   | || ||| ||||  |  ||    |    | |  |   |    |||||    | |||            
TAAGTACTTTGTTGAATATATATCCAAGGCATATCAAGCATTAACTGATCCTATATCTCGAGAGAATTATGAAAAATATGGTCACCCTGATGGGCGGCAGgtaa-------tattagcatcattagatcctaatgtctcaatgaaatctaaattttacaacgtcatatttcatgaacagctaaagctaacaggctatacatcttgtttatgattcag

upper sequence: PP1S241_31V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G007871_T02 (Zea mays), 5'ss of exon 4
CAAGTACTTCGTGGAGCACATCACGAAGGCATATCAAGCACTAACGGATCCTGTATCAAGAGAGAATTACGAGAAGTATGGTCACCCCGATGGACGCCAGgtttgcaccttcatcattttcatgtgggccaaactttactgttgataattaactttgcaaccgcggatcctctttgtaacatattggacggctactgttg----------------
 || |||||| | ||  | ||  | ||||||||||||||| |||| |||||| ||||  | |||||||| ||||| ||||||||||| ||||| || |||||          || |   ||||  |  || ||  |  |  |      | || ||||||||    | |||      |   | |    |||| || |                    
TAAATACTTCATTGAATATATATCCAAGGCATATCAAGCATTAACTGATCCTATATCTCGTGAGAATTATGAGAAATATGGTCACCCTGATGGGCGGCAGgtaa-------tattagcatcattagatcctaatgtctcaatcagagctaaattttgcaacacatgttccatgaactgctaaagctaacgggtaatacatcttgtttatgattcag

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|208385127|gb|DC911373.1|DC911373
EST:     CTGTATCAAGAGAGAATTACGAGAAGTATGGTCACCCCGATGGACGCCAG                         GGAATGCAAATGGGTATTGCCTTGCCTTCTTTCCTTCTCAATATTCAAGGA
genomic: CTGTATCAAGAGAGAATTACGAGAAGTATGGTCACCCCGATGGACGCCAGgtttgcacct ... ctcactgcagGGAATGCAAATGGGTATTGCCTTGCCTTCTTTCCTTCTCAATATTCAAGGA
EST: gi|67709776|gb|BJ965592.1|BJ965592
EST:     CTGTATCAAGAGAGAATTACGAGAAGTATGGTCACCCCGATGGACGCCAG                         GGAATGCAAATGGGTATTGCCTTGCCTTCTTTCCTTCTCAATATTCAAGGA
genomic: CTGTATCAAGAGAGAATTACGAGAAGTATGGTCACCCCGATGGACGCCAGgtttgcacct ... ctcactgcagGGAATGCAAATGGGTATTGCCTTGCCTTCTTTCCTTCTCAATATTCAAGGA
EST: gi|162257847|gb|FC434045.1|FC434045
EST:     CTGTATCAAGAGAGAATTACGAGAAGTATGGTCACCCCGATGGACGCCAG                         GGAATGCAAATGGGTATTGCCTTGCCTTCTTTCCTTCTCAATATTCAAGGA
genomic: CTGTATCAAGAGAGAATTACGAGAAGTATGGTCACCCCGATGGACGCCAGgtttgcacct ... ctcactgcagGGAATGCAAATGGGTATTGCCTTGCCTTCTTTCCTTCTCAATATTCAAGGA
EST: gi|162169401|gb|FC345757.1|FC345757
EST:     CTGTATCAAGAGAGAATTACGAGAAGTATGGTCACCCCGATGGACGCCAG                         GGAATGCAAATGGGTATTGCCTTGCCTTCTTTCCTTCTCAATATTCAAGGA
genomic: CTGTATCAAGAGAGAATTACGAGAAGTATGGTCACCCCGATGGACGCCAGgtttgcacct ... ctcactgcagGGAATGCAAATGGGTATTGCCTTGCCTTCTTTCCTTCTCAATATTCAAGGA
EST: gi|100401075|gb|BY973089.1|BY973089
EST:     ATGGTCACCCCGATGGACGCCAG                         GGAATGCAAATGGGTATTGCCTTGCCTTCTTTCCTTCTCAATATTCAAGGA
genomic: ATGGTCACCCCGATGGACGCCAGgtttgcacct ... ctcactgcagGGAATGCAAATGGGTATTGCCTTGCCTTCTTTCCTTCTCAATATTCAAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGTACTTCGTGGAGCACATCACGAAGGCATATCAAGCACTAACGGATCCTGTATCAAGAGAGAATTACGAGAAGTATGGTCACCCCGATGGACGCCAGgtttgcaccttcatcattttcatgtgggccaaactttactgttgataattaactttgcaaccgcggatcctctttgtaacatattggacggctactgttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA