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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtaacttacccttctagtgcaggatttcgagtagtataaacgtacaagtaaatcagaatgttcgaccatgtcatttactgtttgtcctgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAGGCTAGGCGTAAGAACGTAGGAGGAAAGGTCTTAGGATTCTTCTATTAAG

Basic information

species Physcomitrella patens
transcript PP1S61_209V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S61_209V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA17G02200.1 (Glycine max), 3'ss of exon 3
catgtaacttacccttctagtgcaggatttcgagtagtataaacgtacaagt--aaatcagaatgttcgacca--tgtcatttactgtttgtcctgt------tgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAGGCTAGGCGTAAGAACGTAGGAGGAAAGGTCTTAGGATTCTTCTATTAAG
     |  ||| || |    || |  || | || |||| ||  |    | ||  ||  || |  ||||  |||  | ||  ||||  ||||   | |      | |||||||||| || ||||||||||| ||||| ||||| || |||||||| || ||||||||| | || || || || || ||||| || || |||||||| ||  
-----agattaaccat----tgaactatattga-tagtttactctgttatgttgaatacaaatggttcctccacctatcccttacattttgatttatggtaattatgcagTTTGGGTATATTGTATTGACTACCTCTGCTGGCATCATGGATCATGAAGAGGCTAGGAGGAAAAATGTTGGTGGTAAGGTATTGGGCTTCTTCTACTAGT

upper sequence: PP1S61_209V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA15G10950.1 (Glycine max), 3'ss of exon 3
catgtaacttacccttctagtgcaggatttcgag---tagtataaacgtacaagtaaatcagaatgttcgaccatgtcatttactgtttgtcctgttgt-gcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAGGCTAGGCGTAAGAACGTAGGAGGAAAGGTCTTAGGATTCTTCTATTAAG
 ||  | ||    | | ||    |   |||  |    | |||||  | |   |   | |    ||  | |||| |  | |||   ||||   |   ||| ||||||||| || ||||| ||||| ||||||||||| || |||||||| || || |||||| | ||||| || |                              
-attaagctggtgcctgtatcctaaattttttaatcatggtataggctttgtacacagtttccattgttgaccctaaccttt---gtttacacaaatgttgcagTTTGGGTATATTGTGTTGACTACCTCAGCTGGCATCATGGATCATGAAGAAGCTAGGAGAAAGAATGTTG------------------------------

upper sequence: PP1S61_209V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA07G38520.1 (Glycine max), 3'ss of exon 3
-catgtaacttacccttctagtg-caggatttcgagtagtataaacgtacaagtaaatcagaatgttcgaccatgtcatttactgtttgtcctgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAGGCTAGGCGTAAGAACGTAGGAGGAAAGGTCTTAGGATTCTTCTATTAAG
  ||  | | |     | || ||   || |     ||  | |  |  ||||| |   ||      ||   || |  | |||  | | |  |   || |||||||||| || ||||||||||| ||||| || || || ||||||||||| || |||||| | || || || || || |||||  | || |||||||| ||  
agattaaccattgaactatactgattggttactctgttatgttga-atacaaatggttcctccacttatcccttaccttttgatttata-ctaattttgcagTTTGGGTATATTGTATTGACTACCTCTGCCGGCATCATGGATCACGAAGAAGCTAGGAGAAAAAATGTTGGTGGTAAGGTACTGGGTTTCTTCTACTAGA

upper sequence: PP1S61_209V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 3
catgtaacttacccttctagtgcaggatttcgagtagtataaacgtacaagtaaatcagaatgttcgaccatgtcatttactgtttgtcctgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAGGCTAGGCGTAAGAACGTAGGAGGAAAGGTCTTAGGATTCTTCTATTAAG
  | |  |||     ||| || ||  |||| |  |    |      |  || ||      || |||    || | |  |   |||  |    ||||||||||||| ||||||||  | |||||||| |||||||||||||| ||||| || || ||| | ||||| || || || |||||  | || ||||| || | | 
-gtctgtcttttaagtcttgttcat-attttggttctggttttttaaagagcaatctt--atattcagtgatcttacattgagttc-ttaaattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAAGCCAGGAGAAAGAATGTTGGTGGCAAGGTTCTTGGCTTCTTTTACTGAA

upper sequence: PP1S61_209V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G46040.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------------------catgtaac--ttacccttctagtgca---ggatttcgagtagtataaacgtaca--agtaaatcagaatgttcgaccatgtcatttactgtttgtcctgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAGGCTAGGCGTAAGAACGTAGGAGGAAAGGTCTTAGGATTCTTCTATTAAG
                                                               |  |  |  || |  || | ||  |   |||| |  |||   || |   | |   | |  |||      |   || |  ||||| |    || ||    |||||||||||| | ||||||  ||||||||||||| || || |||||||| || || |||||| | |||||||| || || || ||  | || ||||| || | | 
gttagtctagagactatatagtagtggtaccaatcaatgttttagctattgatctgctgccttactttgctgttcctattatggtttaattggatgtttagtgtcattactttgccttactttatctttcaatgttacaacttcattgaacacttctcta--tgtgcagTTTGGTTTCATTGTTCTGACGACCTCAGCGGGAATCATGGATCATGAAGAAGCTAGGAGAAAGAACGTTGGTGGCAAAGTTCTTGGGTTCTTTTACTGAA

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|162223680|gb|FC399453.1|FC399453
EST:     GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAG                         TTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
genomic: GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAGgtttgtggtc ... tgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
EST: gi|18367689|gb|BJ199772.1|BJ199772
EST:     GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAG                         TTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
genomic: GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAGgtttgtggtc ... tgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
EST: gi|18356853|gb|BJ188912.1|BJ188912
EST:     GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAG                         TTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
genomic: GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAGgtttgtggtc ... tgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
EST: gi|18373024|gb|BJ204626.1|BJ204626
EST:     GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAG                         TTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
genomic: GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAGgtttgtggtc ... tgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
EST: gi|162200218|gb|FC376584.1|FC376584
EST:     GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAG                         TTGGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
genomic: GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAGgtttgtggtc ... tgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
EST: gi|37852641|gb|BJ610649.1|BJ610649
EST:     GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAG                         TTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
genomic: GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAGgtttgtggtc ... tgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
EST: gi|37843544|gb|BJ601552.1|BJ601552
EST:     GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAG                         TTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
genomic: GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAGgtttgtggtc ... tgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
EST: gi|37836217|gb|BJ594225.1|BJ594225
EST:     GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAG                         TTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
genomic: GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAGgtttgtggtc ... tgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
EST: gi|37848213|gb|BJ606221.1|BJ606221
EST:     GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAG                         TTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
genomic: GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAGgtttgtggtc ... tgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
EST: gi|37839178|gb|BJ597186.1|BJ597186
EST:     GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAG                         TTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
genomic: GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAGgtttgtggtc ... tgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
EST: gi|162200219|gb|FC376585.1|FC376585
EST:     GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAG                         TTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
genomic: GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAGgtttgtggtc ... tgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
EST: gi|18359232|gb|BJ191292.1|BJ191292
EST:     GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAG                         TTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
genomic: GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAGgtttgtggtc ... tgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
EST: gi|18361466|gb|BJ193532.1|BJ193532
EST:     GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAG                         TTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG
genomic: GAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAGgtttgtggtc ... tgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAG

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: 32 (upstream exon), 33 (downstream exon)
Score: 9

CAACGGTAGATTGAACAAGTGTGGTGTAATCAGTCCTCGTTACAACGTCGGAGTTGGTGAATTGGAAGCATGGACTGCTCGGCTCCTACCATCTCGTCAGgtttgtggtc ... tgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAGGCTAGGCGTAAGAACGTAGGAGGAAAGGTCTTAGGATTCTTCTATTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaagtaaatcagaatgttcgaccatgtcatttactgtttgtcctgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAGGCTAGGCGTAAGAACGTAGGAGGAAAGGTCTTAGGATTCTTCTATTAAG
                                      tttgtcct  CT-rich tract
      taaatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtaacttacccttctagtgcaggatttcgagtagtataaacgtacaagtaaatcagaatgttcgaccatgtcatttactgtttgtcctgttgtgcagTTTGGCTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAGGCTAGGCGTAAGAACGTAGGAGGAAAGGTCTTAGGATTCTTCTATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA