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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtccgtctagccctttctttctggttaacggattttagggttaatcttctagtatttgggaatgacgaaagtgaaatttgtatggccttcttaatcaagtttcttgtatttatttgtgatgtctccttgtgagctaatcaagaatatgcaaggctttttttaacaagttgttttcaacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGATTTCCATTATGCTCGCGGGGACCTTCAGCAAGCCTTCAAGTGCTACGTGC

Basic information

species Physcomitrella patens
transcript PP1S31_338V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S31_338V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g02540.1 (Oryza sativa), 3'ss of exon 1
gtgtccgtctagccctttctttctggttaacggattttagggttaatcttctagtatttgggaatgacgaaagtgaaatttgtatggccttcttaatcaagtttcttgtatttatttgtgatgtc-tccttgtgagctaatcaagaatatgcaaggctttttttaacaagttgttttcaacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGATTTCCATTATGCTCGCGGGGACCTTCAGCAAGCCTTCAAGTGCTACGTGC
                                                                               |||  | |    |||  |     | ||| ||||     |||||| | | ||| |     || | | | | | |  |  || ||||          ||    ||||| ||||| ||||||||||||||  ||||||| ||||||||| | || ||||||   |||||||  ||  |||||    | ||||||||  ||||| | |
-------------------------------------------------------------------------------ttgctttgtggccttgttgtgcgtacttctattctaaggtgatggcatacttattgaagaaacta-acttttctggatttattttgtttctcaaatt---gcagACCAACCTTATCAAAGAGAGCATCAGAATGGGTTACAATGACATTGGTGATTTCTTCTATGCTCATGGCCACCTTTCAGATGCCTTCAAAAGCTACATCC

upper sequence: PP1S31_338V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G153152_T01 (Zea mays), 3'ss of exon 1
gtgtccgtctagccctttctttctggttaacggattttagggttaatcttctagtatttgggaatgacgaaagtgaaatttgtatggccttcttaatcaagtttcttgtatttatttgtgatgtctccttgtgagctaatcaagaatatgcaaggctt--tttttaacaagttgttttcaacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGATTTCCATTATGCTCGCGGGGACCTTCAGCAAGCCTTCAAGTGCTACGTGC
                                                                                   || | | || |   ||         |  | |      |||||    |||||     ||||   | |  ||   |   | |  |   | |   || |  ||||| ||| | ||||||||||||||  ||||||||||||||||| | |||||||||   ||||| |  ||  | |||    ||||        |   || | 
-----------------------------------------------------------------------------------attgtcctcgtgcgcagaacgtcaatcctcagaaa-aatgtccttgtgtgatgacgtcaatcctctataactttcaatctacattgattctcttactgcagACTAACTTAATCAAAGAGAGCATCAGAATGGGCTACAATGACATTGGCGATTTCTTCTATGCCCATGGCCAACTTTCAAAAGCTACATCAGGACTCGGGA

upper sequence: PP1S31_338V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G062210_T02 (Zea mays), 3'ss of exon 1
gtgtccgtctagccctttctttctggttaacggattttagggttaatcttctagtatttgggaatgacgaaagtgaaatttgtatggccttcttaatcaagtttcttgtatttatttgtgatgtctccttgtgagctaatcaagaatatgcaaggctttttttaacaagttgtttt-caacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGATTTCCATTATGCTCGCGGGGACCTTCAGCAAGCCTTCAAGTGCTACGTGC
                                                                                  | |  | |||| || | |        |||  ||     ||| |    ||   | |  ||||   | |  ||  |   | |  |    || | || |  ||||| ||| | ||||||||||||||  ||||||||||||||||| | || ||||||   ||||| |  ||  | |||    | || |||||  ||||| |  
---------------------------------------------------------------------------------atttcccattctaaagcgacaagtgcttatcaatgaa-aatgccattctgcatgttg-tcaatcctctctaattcaaatctacattgattctcttactgcagACTAACTTAATCAAAGAGAGCATCAGAATGGGCTACAATGACATTGGTGATTTCTTCTATGCCCATGGCCAACTTTCAGATGCTTTCAAAAGCTACATCA

upper sequence: PP1S31_338V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ08729 (Selaginella moellendorffii), 3'ss of exon 1
gtgtccgtctagccctttctttctggttaacggattttagggttaatcttctagtatttgggaatgacgaaagtgaaatttgtatggccttcttaatcaagtttcttgtatttatttgtgatgtctccttgtgagctaatcaagaatatgcaaggctttttttaacaagttgttttcaacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGATTTCCATTATGCTCGCGGGGACCTTCAGCAAGCCTTCAAGTGCTACGTGC
                                                                                 |||  ||    |  | ||    |||| | ||| |||    | ||  || ||  |  ||  ||||          || | |||     |||   ||   ||||| || || ||||| ||||||||||| |||||||||||||| || || ||||||   ||    || || || || |||||||| |||||||||||||| |
---------------------------------------------------------------------------------gtaccgctcgatcgagcagtcctcttctctttcttttctttctcgtctcgtagg--aactaagat---------ctctctttggatcgtttccttgcgcagACCAATCTCATCAAGGAGAGCATTCGCATGGGCTACAATGATCTGGGAGATTTCTTCTACAGCCGTGGAGATCTCCAGCAAGCTTTCAAGTGCTACGTCC

upper sequence: PP1S31_338V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ06457 (Selaginella moellendorffii), 3'ss of exon 1
gtgtccgtctagccctttctttctggttaacggattttagggttaatcttctagtatttgggaatgacgaaagtgaaatttgtatggccttcttaatcaagtttcttgtatttatttgtgatgtctccttgtgagctaatcaagaatatgcaaggctttttttaacaagttgttttcaacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGATTTCCATTATGCTCGCGGGGACCTTCAGCAAGCCTTCAAGTGCTACGTGC
                                                                                                           ||||   | | |    | || || |   ||  |    | || |     | |||  |  |             ||||| || || ||||| ||||||||||| |||||||||||||| || || ||||||   ||    || || || || |||||||| |||||||||||||| |
-----------------------------------------------------------------------------------------------------------gtatcgctcttt--cttttctttctcgtctcgtaggaactaagaggatcgtttccttgcg------------cagACCAATCTCATCAAGGAGAGCATTCGCATGGGCTACAATGATCTGGGAGATTTCTTCTACAGCCGTGGAGATCTCCAGCAAGCTTTCAAGTGCTACGTCC

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|100367711|gb|BY984780.1|BY984780
EST:     GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGG                         ACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGAT
genomic: GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGGgtgtccgtct ... ttttcaacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGAT
EST: gi|162169510|gb|FC346074.1|FC346074
EST:     GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGG                         ACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGAT
genomic: GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGGgtgtccgtct ... ttttcaacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGAT
EST: gi|208348050|gb|DC905373.1|DC905373
EST:     GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGG                         ACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGAT
genomic: GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGGgtgtccgtct ... ttttcaacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGAT
EST: gi|100404512|gb|BY973615.1|BY973615
EST:     GGCTGCACAGCGGCAGGAGAAGCTTNGAA-TGGAGCTCAATGGATATAGG                         G
genomic: GGCTGCACAGCGGCAGGAGAAGCTT-GAAATGGAGCTCAATGGATATAGGgtgtccgtct ... ttttcaacag-
EST: gi|100404512|gb|BY973615.1|BY973615
EST:     GGCTGCACAGCGGCAGGAGAAGCTTNGAA-TGGAGCTCAATGGATATAGG                         G
genomic: GGCTGCACAGCGGCAGGAGAAGCTT-GAAATGGAGCTCAATGGATATAGGgtgtccgtct ... ttttcaacag-
EST: gi|67717537|gb|BJ967796.1|BJ967796
EST:     GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGG                         ACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGAT
genomic: GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGGgtgtccgtct ... ttttcaacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGAT
EST: gi|100438439|gb|BY979957.1|BY979957
EST:     GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGG                         ACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGAT
genomic: GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGGgtgtccgtct ... ttttcaacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGAT
EST: gi|67719857|gb|BJ970116.1|BJ970116
EST:     GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGG                         ACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGAT
genomic: GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGGgtgtccgtct ... ttttcaacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGAT
EST: gi|18365655|gb|BJ197732.1|BJ197732
EST:     GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGG                         ACAAACCTGATCA
genomic: GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGGgtgtccgtct ... ttttcaacagACAAACCTGATCA
EST: gi|100416138|gb|BY957095.1|BY957095
EST:     GGGCTGCACAGCGCCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGG                         ACAAACCTGATCAAAGAGAGCATTCGAATGAGCTACAATGACCTC
genomic: GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGGgtgtccgtct ... ttttcaacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTC
EST: gi|19789755|gb|BQ041491.1|BQ041491
EST:     GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGG                         ACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGAT
genomic: GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGGgtgtccgtct ... ttttcaacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGAT
EST: gi|18357096|gb|BJ189155.1|BJ189155
EST:     GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGG                         ACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGAT
genomic: GGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGGgtgtccgtct ... ttttcaacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGAT

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: 30 (upstream exon), 34 (downstream exon)
Score: 6

AGGGCCTGGTTACGGATTGGACCAGGAGTGGATTGATACGGTGGAGCGCCGGGCTGCACAGCGGCAGGAGAAGCTTGAAATGGAGCTCAATGGATATAGGgtgtccgtct ... ttttcaacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGATTTCCATTATGCTCGCGGGGACCTTCAGCAAGCCTTCAAGTGCTACGTGC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtgagctaatcaagaatatgcaaggctttttttaacaagttgttttcaacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGATTTCCATTATGCTCGCGGGGACCTTCAGCAAGCCTTCAAGTGCTACGTGC
                                ttttaac  putative branch site (score: 6)
                                          ttgttttc  putative PPT
                             tttttttaacaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtccgtctagccctttctttctggttaacggattttagggttaatcttctagtatttgggaatgacgaaagtgaaatttgtatggccttcttaatcaagtttcttgtatttatttgtgatgtctccttgtgagctaatcaagaatatgcaaggctttttttaacaagttgttttcaacagACAAACCTGATCAAAGAGAGCATTCGAATGGGCTACAATGACCTCGGCGATTTCCATTATGCTCGCGGGGACCTTCAGCAAGCCTTCAAGTGCTACGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG