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

gtgagtgatgggagaaggggtgaggtgaatgcagcatgtgcgttggttgcgaaagtggtggaggtgtgtggagaggtggggtgtttgacatgggaaggtttgtgggtcggggtaagaaactgagagcagttgtggtgatgaatgcaatgcaatgcagGTATCGTGCTGGACAGTGGAGATGGTGTGACCCACACGGTGCCAATCTACGAGGGTTACGCACTGCCTCACGCCATATTGCGATTAGACTTGGCGGGTCG

Basic information

species Physcomitrella patens
transcript PP1S337_26V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os11g06390.6 (Oryza sativa), 3'ss of exon 3
gtgagtgatgggagaaggggtgaggtgaatgcagcatgtgcgttggttgcgaaagtggtggaggtgtgtggagaggtggggtgtttgacatgggaaggtttgtgggtcggggtaagaaactgagagcagttgtggtgatgaatgcaatgcaatgcagGTATCGTGCTGGACAGTGGAGATGGTGTGACCCACACGGTGCCAATCTACGAGGGTTACGCACTGCCTCACGCCATATTGCGATTAGACTTGGCGGGTCG
                                                                             |   |   | || |   | ||||    | |      || | | | |    | |  ||   |    |||  |   |||||||||||||| |||||  ||| |||||||| | |||||| ||||||||||| || || || || || ||||| |||||  ||||  | ||| | || || ||
-----------------------------------------------------------------------------gtaataactcac-tcacatggttgagagttttaa--aaaatattcactttattcatga--actgttgctct-tgatgcagGTATCGTGTTGGACTCTGGTGATGGTGTCAGCCACACCGTGCCAATCTATGAAGGATATGCCCTTCCTCATGCCATCCTGCGTCTGGACCTTGCTGGGCG

upper sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G053299_T01 (Zea mays), 3'ss of exon 3
gtgagtgatgggagaaggggtgaggtgaatgcagcatgtgcgttggttgcgaaagtggtggaggtgtgtggagaggtggggtgtttgacatgggaaggtttgtgggtcggggtaagaaactgagagcagttgtggtgatgaatgcaatgcaatgcagGTATCGTGCTGGACAGTGGAGATGGTGTGACCCACACGGTGCCAATCTACGAGGGTTACGCACTGCCTCACGCCATATTGCGATTAGACTTGGCGGGTCG
                                 ||| |||      || |     |  |  | || | |  || |     || | |||     |    || |||    |  |  |  |    |   |   |||   | |  |  |  ||   ||||||||| ||||| ||   ||| ||||||||||||||||| ||||||||||||||||| ||||| || ||||| |||||  |  |  | ||  | || || ||
---------------------------------gcacgtgt-ccactttcacctcttattaaagtttttctag-gacaacgtctctgattctcgtca-ttggtgatctgacgacaccattctactacctatgtctcggt--actctgtg---tgcagGTATTGTGCTCGATTCTGGTGATGGTGTGACCCACACCGTGCCAATCTACGAGGGATACGCGCTCCCTCATGCCATTCTTAGGCTGGATCTTGCTGGCCG

upper sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G152328_T02 (Zea mays), 3'ss of exon 2
gtgagtgatgggagaaggggtgaggtgaatgcagcatgtgcgttggttgcgaaagtggtggaggtgtgtggagaggtggggtgtttgacatgggaaggtttg----tgggtcggggtaagaaactgagagcagttgtggtgatgaatgcaatgcaatgcagGTATCGTGCTGGACAGTGGAGATGGTGTGACCCACACGGTGCCAATCTACGAGGGTTACGCACTGCCTCACGCCATATTGCGATTAGACTTGGCGGGTCG
                                                                   |||    | |   ||  |   | |   ||  |        |  | |       |  | |  | |  |  |     ||  | |    |  | ||||||||||||| |||   ||||||||||||| |||||| || || ||||||||||| ||||| || || ||||||||  | ||  | ||| |||| |||||
-------------------------------------------------------------------gtgagctgattccgttctctgcttaacaatttccaaatccgatttgctcctgcagtccgttatctctaatatctgtggcttcccctctct-cagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACGAGGGATACGCCCTCCCCCACGCCATCCTTCGTCTTGACCTGGCCGGTCG

upper sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM5G859691_T01 (Zea mays), 3'ss of exon 8
gtgagtgatgggagaaggggtgaggtgaatgcagcatgtgcgttggttgcgaaagtggtggaggtgtgtggagaggtggggtgtttgacatgggaaggtttgtgggtcggggtaagaaactgagagcagttgtgg-tgatgaatgcaatgcaatgcagGTATCGTGCTGGACAGTGGAGATGGTGTGACCCACACGGTGCCAATCTACGAGGGTTACGCACTGCCTCACGCCATATTGCGATTAGACTTGGCGGGTCG
                                                                   |||    | |   ||  |   | |   ||  |||     ||    |      |||    | ||  |   | |    ||          ||||||||||||| |||   ||||||||||||| |||||| || || ||||||||||| ||| | || || ||||||||  | |   | ||| |||| |||||
-------------------------------------------------------------------gtgagctgattccgttctctgcttaacaa--tttccaaatccaattttctc-ctgcagtccgtaatctctaaaatctgtggcctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACGAGGGATACACCCTCCCCCACGCCATCCTTCATCTTGACCTGGCCGGTCG

upper sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G047055_T01 (Zea mays), 3'ss of exon 3
gtgagtgatgggagaaggggtgaggtgaatgcagcatgtgcgttggttgcgaaagtggtggaggtgtgtggagaggtggggtgtttgacatgggaaggtttgtgggtcggggtaagaaactgagagcagttgtggtgatgaatgcaatgcaatgcagGTATCGTGCTGGACAGTGGAGATGGTGTGACCCACACGGTGCCAATCTACGAGGGTTACGCACTGCCTCACGCCATATTGCGATTAGACTTGGCGGGTCG
                                     ||| | || ||        | |     | | |       ||    ||||  ||   | |  || |||      | |||    |  |   || |||          |    |||    ||||||||||||| |||   ||||||||||| | |||||| || || ||||||||||| ||||| || || ||||||||  | ||  | ||| |||| || ||
-------------------------------------gtgagctgatt-------cgattcgattctattctccactgaaccgtttc-cacttggaaattagtgatcttcgctaattttcaaatctcatttgc---------tctcttgcctctcagGTATCGTGCTCGACTCGGGAGATGGTGTCAGCCACACTGTCCCCATCTACGAGGGATACGCCCTCCCCCACGCCATCCTTCGTCTCGACCTGGCTGGCCG

upper sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G047055_T04 (Zea mays), 3'ss of exon 3
gtgagtgatgggagaaggggtgaggtgaatgcagcatgtgcgttggttgcgaaagtggtggaggtgtgtggagaggtggggtgtttgacatgggaaggtttgtgggtcggggtaagaaactgagagcagttgtggtgatgaatgcaatgcaatgcagGTATCGTGCTGGACAGTGGAGATGGTGTGACCCACACGGTGCCAATCTACGAGGGTTACGCACTGCCTCACGCCATATTGCGATTAGACTTGGCGGGTCG----------------------------------------------
                                                                                               |  || |||      | |||    |  |   || |||          |    |||    ||||||||||||| |||   ||||||||||| | |||||| || || ||||||||||| ||||| || || ||||||||  | ||  | ||| |||| || ||                                              
----------------------------------------------------------------------------------------------gaaattagtgatcttcgctaattttcaaatctcatttgc---------tctcttgcctctcaggtatcgtgctcgactcgggagatggtgtcagccacactgtccccatCTACGAGGGATACGCCCTCCCCCACGCCATCCTTCGTCTCGACCTGGCTGGCCGCGACCTCACCGACTACCTCATGAAGATCCTGACTGAACGCGGCTAC

upper sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 3
gtgagtgatgggagaaggggtgaggtgaatgcagcatgtgcgttggttgcgaaagtggtggaggtgtgtggagaggtggggtgtttgacatgg-gaaggtttgtgggtcggggtaagaaactgagagcagttgtggtgatgaatgcaatgcaatgcagGTATCGTGCTGGACAGTGGAGATGGTGTGACCCACACGGTGCCAATCTACGAGGGTTACGCACTGCCTCACGCCATATTGCGATTAGACTTGGCGGGTCG
                                                                        |   ||   | ||| |||||| ||     | |   | ||  |    || |     ||  |    |   || |||  | |  | ||||||| ||| |||||  ||| |||||||| | |||||| |||||||||||||| ||||| || || ||||| |||||  ||||  | ||| | || || ||
------------------------------------------------------------------------gtaatgat-tctttaacatggtgaccaaatttcattaggacttcccaaatttttccatctcaattatggattgctgttcctt-cagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACCGTGCCAATCTACGAAGGTTATGCCCTTCCTCATGCCATCCTGCGTCTTGACCTTGCTGGGCG

upper sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G18780.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagtgatgggagaaggggtgaggtgaatgcagcatgtgcgttggttgcgaaagtggtggaggtgtgtggagaggtggggtgtttgacatgggaaggtttgtgggtcggggtaagaaactgagagcagttgtggtgatgaatgcaatgcaatgcagGTATCGTGCTGGACAGTGGAGATGGTGTGACCCACACGGTGCCAATCTACGAGGGTTACGCACTGCCTCACGCCATATTGCGATTAGACTTGGCGGGTCG
                                                                          | | |    ||| |        | ||| |       | | |  |  |||    || | || | ||   | || || |   ||||||| ||||||||   ||| ||||||||| | ||||| ||||||||||||||||||| | | || ||||| |||||  | ||  | ||| | || || ||
--------------------------------------------------------------------------gttagtacattttaggctttttg-tttatactcattgatcattatttgaactgagctctgattatct-tccattgaa---cagGTATTGTGCTGGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACGAGGGTTTCTCTCTTCCTCATGCCATCCTCCGTCTTGACCTTGCTGGACG

upper sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EDO98923 (Chlamydomonas reinhardtii), 3'ss of exon 5
gtgagtgatgggagaaggggtgaggtgaatgcagcatgtgcgttggttgcgaaagtggtggaggtgtgtggagaggtggggtgtttgacatgggaaggtttgtgggtcggggtaagaaactgagagcagttgtggtgatgaatgcaatgcaatgcagGTATCGTGCTGGACAGTGGAGATGGTGTGACCCACACGGTGCCAATCTACGAGGGTTACGCACTGCCTCACGCCATATTGCGATTAGACTTGGCGGGTCG
                 | ||||  ||   |          |     | |        |  |    ||        | |     |  ||    |    |        ||  ||      |   | || ||    ||     |      |||   | |||||||||||||||  ||| || || ||||| ||||||||||| ||||||||||| ||||| |                                     
----------------cgcgtgacatgtgcgtgaaggccctggcccctcccctccccatcaaccactgccattgactcgcaccctc-actcccgcgcctccccaccccgccgtccagGCC---GTGCTGTCCCTGTACGCCAGCGGCCGCACCACCGGTATCGTGCTGGACTCTGGCGACGGCGTGACGCACACGGTGCCCATCTACGAGGGCTACGCGC-------------------------------------

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|100404907|gb|BY991341.1|BY991341
EST:     CGTGGCCATTCAGGCAGTGCTGTCACTATATGCCAGTGGACGAACGACCG                         GTATCGTGCTGGACAGTGGAGATGGTGTGACCCACACGGTGCCAATCTACG
genomic: CGTGGCCATTCAGGCAGTGCTGTCACTATATGCCAGTGGACGAACGACCGgtgagtgatg ... tgcaatgcagGTATCGTGCTGGACAGTGGAGATGGTGTGACCCACACGGTGCCAATCTACG




















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), 27 (downstream exon)
Score: 18

GAGAAGATGACGCAGATCATGTTCGAGACGTTCAACGTGCCGGCGATGTACGTGGCCATTCAGGCAGTGCTGTCACTATATGCCAGTGGACGAACGACCGgtgagtgatg ... tgcaatgcagGTATCGTGCTGGACAGTGGAGATGGTGTGACCCACACGGTGCCAATCTACGAGGGTTACGCACTGCCTCACGCCATATTGCGATTAGACTTGGCGGGTCG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggtcggggtaagaaactgagagcagttgtggtgatgaatgcaatgcaatgcagGTATCGTGCTGGACAGTGGAGATGGTGTGACCCACACGGTGCCAATCTACGAGGGTTACGCACTGCCTCACGCCATATTGCGATTAGACTTGGCGGGTCG
          taagaaa  TA-rich tract