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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctactttctctctctctactatgtcaattatgtattgggatcatatattgtattagttacttgttcaatcccaattctgttctgacttgcacgcagcttccagcttccttggcgaagtatgttgatccttttctggactatgaactcaatgcttgtttttcgtttattgcatgcagCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA

Basic information

species Physcomitrella patens
transcript PP1S207_23V6.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 3'ss of exon 7
gtctactttctctctctctactatgtcaattatgtattgggatcatatattgtattagttacttgttcaatcccaattctgttctgacttgcacgcagcttccagcttccttggcgaagtatgttgatccttttctggactatgaactcaatgcttgtttttcgtttattgcatgcagCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA
                                                                ||     |||  | || ||   | |   |   | | | ||| ||  |  || | ||  | | |   |  |    |     ||    ||  |    | |   || |||   |||| |  |  | |||||||| |||||||| || ||||| ||||| ||||||||||| |||||||||||||||||||| || || || ||| |  | || ||||
----------------------------------------------------------------gtaagcaccctgtactattagca-tcatatagatcctgcagatt--tgagcaatgtcagctaaatttaattgtaatggataatctgatattaacctgtttctttttgtg-gcagTTGCTTGATTTGAGTGGTATTCTTACGGTGTTCTTCTGTGGTATTGTAATGTCGCACTATACCTGGCATAATGTAACAGAGAGTTCCAGGGTCACAACCA

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 9
gtctactttctctctctctactatgtcaattatgtattgggatcatatattgtattagttacttgttcaatcccaattctgttctgacttgcacgcagcttccagcttccttggcgaagtatgttgatccttttctggac--tatgaactcaatgcttgtttttcgt---ttattgca---tgcagCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA
                                                                                   || | ||    | ||| | ||     ||  |     | |||| ||||||||    ||   ||||   |||   |||||| |  |   || || ||   | ||||| ||  || ||||||| ||||||||||||||||| ||||| || |||||||| || || || ||||||||||| || ||||| ||  |  | |||||||
-----------------------------------------------------------------------------------cttatttttgtgtagcatgcactgatctgagttt--tctgtt-atccttttgcaaacaacatgataccaagatttgtttctaatattttcttccaattttcagCTGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCA

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA20G37370.1 (Glycine max), 3'ss of exon 9
gtctactttctctctctctactatgtcaattatgtattgggatcatatattgtattagttacttgttcaatcccaattctgttctgacttgcacgcagcttccagcttccttggcgaagtatgttgatccttttctggactatgaactcaatgcttgtttttcgtttattgcatgcagCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA
                                                                                    | | ||  |   |  ||      |  ||   | |   || ||   | ||| |     || |||  | ||||  | | || |  ||    ||||| | | |||  ||||||| ||||| ||||| ||||||||||| ||||| ||||| || ||||||||||||||||| ||||| || ||  |||| || ||||
-----------------------------------------------------------------------------------gtaagttttaaagaattttagtaatgttttatgga---tgctgcaacatttgt----cattaacata-tgctgatgtatc-tacatcttctgcagTTGTCCTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGGATTGTCATGTCTCATTATACCTGGCATAATGTGACTGAGAGTTCAAGAATCACTACCA

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 8
gtctactttctctctctctactatgtcaattatgtattgggatcatatattgtattagttacttgttcaatcccaattctgttctgacttgcacgcagcttccagcttccttggcgaagtatgttgatccttttctggactatgaactcaatgcttgtttttcgtttattgcatgcagCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA
                                                      | ||||  ||    ||   ||    | || ||    | | |    ||  ||||            ||| |  ||  |||  ||    | |      ||   |  |    |||       ||||| | |  ||  ||||||| ||||||||||| ||||| ||||| ||||| ||||| || ||||| ||||||||||| ||||| |||||  ||||||| ||||
-----------------------------------------------------gtaagtt--ttaaagaacttcagaaatattttgtagagtatgtctttttgagctc-----------tatatctattttttcttgtgaaagggttctgatatat-ctacaagttc------tgcagTTATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 8
gtctactttctctctctctactatgtcaattatgtattgggatcatatattgtattagttacttgttcaatcccaattctgttctgacttgcacgcagcttccagcttccttggcgaagtatgttgatccttttctggactatgaactcaatgcttgtttttcgtttattgcatgcagCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA
                                                      | ||||  ||    ||   ||    |||||||    | | |    ||      ||  |  | |  | | |||    | |  |  | |    | ||| |    | || |  | ||||   ||||| | |  ||  ||||||| ||||| ||||| ||||| ||||| ||||| ||||| || ||||| ||||||||||| ||||| |||||  ||||||| ||||
-----------------------------------------------------gtaagtt--ttaaagaacttcagaaatgttctgtacagtatgtcttttttgagctctatatcta--ttttttg---ttgtggtacattcattaatcattaacgggttctgatatattc--tgcagTTATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCA

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 9
gtctactttctctctctctactatgtcaattatgtattgggatcatatattgtattagttacttgttcaatcccaattctgttctgacttgcacgcagcttccagcttccttggcgaagtatgttgatccttttctggactatgaactcaatgcttgtttttcgtttattgcatgcagCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA
                                                                                    | | ||| |   |  ||      |  ||   | |   |||  |   || ||       |  ||   |||||  | | || |  ||    ||||| | |  ||  ||||||| ||||| ||||| ||||||||||| ||||| ||||| || |||||||||||||| || || || || ||  |||| || ||||
-----------------------------------------------------------------------------------gtaagttgtaaagaattttagtaatgttttatggatgctgtcaacatttgtc------gttgacatgatgctgatgtatc-tacatctgttgcagTTATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCA

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv14s0128g00020.t01 (Vitis vinifera), 3'ss of exon 8
--------gtctactttct---ctctctctactatgtcaattatgtattgggatcatatattgtattagttacttgttcaatcccaattctgttctgacttgcacgcagcttccagcttccttggcgaagtatgttgatccttttctggactatgaa---ctcaatgcttgtttttcgtttattgcatgcagCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA
        | ||   ||||      | | |  ||       ||| | || | |  | || |  | || |       | || | | || |   |  |    |        |      ||    |   |||   |||  ||   || || || | |  |    | ||   |  |   |   ||||| | |||||||||| |   ||||||||||| | || || ||||| ||||||||||| ||||| || || || |||||||||||||| |||||||| |||||||| ||||
gtaccaaagactggattctgaaaattttattttaaacactatatttctttgtaaaacatgtcctctttgccttccatacagtac-aactgaatggtactctttggttgacaagggactgg--tactgaaaactgtgaatatattccttgattgtagattgtttaaaattgataaatttgttatttcttgcagCTTTTATCTCTGAGTGGGATTTTAACAGTTTTCTTCTGTGGCATTGTCATGTCGCATTACACATGGCATAATGTTACCGAAAGCTCGCGAATAACAACCA

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 3'ss of exon 8
gtctactttctctctctctactatgtcaattatgtattgggatcatatattgtattagttacttgttcaatcccaattctgttctgacttgcacgcagcttccagcttccttggcgaagtatgttgatccttttctggactatgaactcaatgcttgtttttcgtttattgcatgcagCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA
||    ||||| |||  |    | |    ||   |||  | |||  ||   ||  |      |||    || | |   || |  |      ||  ||  |    ||||  |  |   | |||  | ||||  |||||  || |      | || || |   |  | |    ||| ||| | ||||| || ||||| ||||| ||||| |||||||| || ||||| ||||| ||||| ||||||||||| || |||||||| ||  || | ||||| |
gtaagatttctttctacccttcaagcacctt---tataagaatctcatcaagttctg----tttgaaatatacaaggactatcat------catccaattctgtgctttataag--gattattatcatccacttctgtgctttactgatagtgtttataaattctgttcatcatccagTTGTTCTATTTAAGTGGCATTCTCACTGTATTCTTTTGCGGGATTGTCATGTCACACTACACCTGGCATAACGTGACTGAAAGTTCAAGAGTCACCACAA

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 3'ss of exon 8
gtctactttctctctctctactatgtcaattatgtattgggatcatatattgtattagttacttgttcaatcccaattctgttctgac-ttgcacgcagcttccagcttccttggcgaagtatgttgatccttttctggactatgaactcaatgcttgtt-tttcgtttattgcatgcagCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA
                                 |||  |   || | ||   | || |  ||||       |||  || | |  || | |||   |     |  || |||    |   | ||| |  ||| |||   |   |       || || | ||   || | || |  | ||||||| ||||| |||||||| ||||| || || || || ||||| |||||||||||||| || || ||||| |||||||| || || ||  || | || ||||
---------------------------------gtaa-gatttcttttaacttcttgggcacttccctggcccctgttgtctattggcattgagtgttctatttagattcaacagtaga-tatatcaatcatttaaagtctt-----tccattgttagtaactttggttgt--cctgcagCTATTCTATTTGAGTGGCATTCTCACGGTATTTTTCTGTGGGATTGTAATGTCCCATTACACGTGGCACAATGTTACAGAGAGTTCAAGAGTCACTACCA

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 9
gtctactttctctctctctactatgtcaattatgtattgggatcatatattgtattagttacttgttcaatcccaattctgttctgacttgcacgcagcttccagcttccttggcgaagtatgttgatccttttctggactatgaactcaatgcttgtttttcgtttattgcatgcagCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA
                                 |||  |  |||  | |   |  | |  | |  |||   ||  |  |   | ||   |  |   |   ||  |   ||      ||| |  | || | |       | | || | |   |  |||| ||              ||||| ||||| || ||||  ||||| ||||| |||||||| || ||||| ||||| ||||| || ||||||||||| |||||||| ||  || | || ||||
---------------------------------gtaa-gatatcccacaacttgctgggaaatccttc---cctgacccctgtttgctctttatttatactcttgagccccaaaataagcacatggacctt------aattttggaattgttatttgtctt-------------acagCTGTTCTATTTAAGTGCCATTCTCACTGTGTTCTTTTGCGGGATTGTCATGTCTCACTACACATGGCATAATGTGACTGAAAGTTCAAGAGTGACTACCA

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ05720 (Selaginella moellendorffii), 3'ss of exon 7
gtctactttctctctctctactatgtcaattatgtattgggatcatatattgtattagttacttgttcaatcccaattctgttctgacttgcacgcagcttccagcttccttggcgaagtatgttgatccttttctggactatgaact--caatgcttgtttttc----gtttattgcatgc-agCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA
                                                                                                                         || |  |  ||||||| |    ||  |  || | ||| || |||    |  |||  ||| | |||| |||||| |||||||||| || || |||||||||||||||||||| ||||| || ||||| ||||| || || || || |||||  |||| || ||||
------------------------------------------------------------------------------------------------------------------------gtgatagtttttttctgtatagagaggtagcatttcttcttgttctcatgcgtatgccattccagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCA

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ32893 (Selaginella moellendorffii), 3'ss of exon 7
gtctactttctctctctctactatgtcaattatgtattgggatcatatattgtattagttacttgttcaatcccaattctgttctgacttgcacgcagcttccagcttccttggcgaagtatgttgatccttttctggactatgaactcaatgcttgttttt-cgtttattgcatgc-agCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA
                                                                                                                 | ||    | ||  | || |   |     |    |   | |||||| |   |  |||  ||| | |||| |||||| |||||||||| || || |||||||||||||||||||| ||||| || ||||| ||||| || || || || |||||  |||| || ||||
-----------------------------------------------------------------------------------------------------------------gtgagagttttt--ttctgtatagagaggtagcatttcttcttgttctcatgcgtatgccattccagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCA

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: 14 (upstream exon), 22 (downstream exon)
Score: 2

GCATTCTACTGACCGTGAAATTGCATTAATGACCATTATGGCTTACTTGTCATATATCTTGGCCGAGgtctactttc ... ttgcatgcagCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatccttttctggactatgaactcaatgcttgtttttcgtttattgcatgcagCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA
 tgttgat  putative branch site (score: 2)
                               ttgttttt  TA-rich tract