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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTCGACGGCTACGCGCACCTTTCATCTGGATTGTCGTGTGGGTTGGCTGGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcag

Basic information

species Physcomitrella patens
transcript PP1S200_79V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
TGTTCGACGGCTACGCGCACCTTTCATCTGGATTGTCGTGTGGGTTGGCTGGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcag
| || |||||||| || ||||| || || ||  |  | |||||  | ||||| ||  | ||||||||||||||||| ||||| || ||||||||||| |||||       ||| |      | |    || | |    ||| | ||||  ||| | |   ||| | |||   ||        |   |||  |||    |  |  |  |  |                                                                           
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgta-------aagacgcttcctcttatcatattctgctatatgctttg--gtttg-gctgataatatgctggtcaatgcagcagcagtaatggcag-gcacttctaaaact---------------------------------------------------------------------------

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G101020_T01 (Zea mays), 5'ss of exon 2
TGTTCGACGGCTACGCGCACCTTTCATCTGGATTGTCGTGTGGGTTGGCTGGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctt-tacgttcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcag
| || |||||||| || ||||| || |||||  |  | |||||  | ||||| ||  | ||||||||||||||||| ||||| || ||||||||||| ||||    |||||    ||||  | |     |||      ||| | ||||| | |   |   ||| | ||    |    || || |  |||  |||    || |  |  |                                                                               
TCTTTGACGGCTATGCCCACCTGTCGTCTGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtgaa-gacaa----ttgctttatcatattgtg-----atatgctttgatggtttggctgataatatgttggt--aaatgcagta-gtaatggcaggcacttctaaacctcca--------------------------------------------------------------------------

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA04G00950.2 (Glycine max), 5'ss of exon 1
TGTTCGACGGCTACGCGCACCTTTCATCTGGATTGTCGTGTGGGTTGGCTGGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgcac-gtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcag
| || || || || || || || || |||||  |  | ||||| |||||||| || || || |||||||| |||||||| ||||| |||||||||||||||||      || || ||   |  | |   |  |     ||| | ||||         |   |  | |    || ||  || ||    | |  |  || |  |  ||||  |||| ||                                                                      
TCTTTGATGGTTATGCACATCTCTCCTCTGGTCTTGCCTGTGGCTTGGCTGGCCTTTCTGCTGGCATGGCTATTGGTATTGTCGGTGATGCTGGTGTTAGgtat-----aatgcttttttactttgtttttcat----atatgatttg---------tttcttatttcttgatgtg--tttaaggtcttgttgaattgcaatattgcatagtgacattca-------------------------------------------------------------------

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA12G04090.1 (Glycine max), 5'ss of exon 2
TGTTCGACGGCTACGCGCACCTTTCATCTGGATTGTCGTGTGGGTTGGCTGGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgc---acgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcag
| || || || || || || || || |||||  |  | |||||| |||||||||| || || |||||||| |||||||| || || |||||||||||||||||       ||  |||      | |     || |    || | ||  || | ||     ||    |   | |||| | ||      || ||  || | | | || |   | |||||                                                                        
TCTTTGATGGTTATGCACATCTCTCCTCTGGTCTTGCCTGTGGGCTGGCTGGTCTCTCTGCTGGCATGGCTATTGGTATTGTTGGTGATGCTGGTGTTAGgtat------aattcttctgccttagtatcttatc----tatgatt-aaactcggtactgatttgatcttattctgaagtc------tacagatttcatggtgatacttaatgtgat------------------------------------------------------------------------

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA11G11760.1 (Glycine max), 5'ss of exon 2
TGTTCGACGGCTACGCGCACCTTTCATCTGGATTGTCGTGTGGGTTGGCTGGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgt-tcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcag
| || || || || || || || || |||||  |  | |||||| ||||||| || || || |||||||| |||||||| || || |||||||||||||||||        |    | |  |   ||  ||    |  ||    | || | ||  | |  ||| | | |  || ||    |  ||  ||    | | |  |   ||||                                                                               
TCTTTGATGGTTATGCACATCTCTCCTCTGGTCTTGCCTGTGGGCTGGCTGGCCTCTCTGCTGGCATGGCTATTGGTATTGTTGGTGATGCTGGTGTTAGgtat-------aattcttctcttctgccttgccttagtatcttatctgtaattaaacttgatact-tactgatttgatcactgtttttactcacatgatttgctatgc-------------------------------------------------------------------------------

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA06G00980.1 (Glycine max), 5'ss of exon 2
TGTTCGACGGCTACGCGCACCTTTCATCTGGATTGTCGTGTGGGTTGGCTGGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagt----ctgccaatctggattcaattcgtagaggctttacgttcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcag
| || || || || || || || || |||||  |  | ||||| |||||||| || || || |||||||| |||||||| || || ||||| ||||||||||||     ||||||||   |  | |     |||     || ||||| | ||   | | ||| |      |||  |     | |||| || |       | ||                                                                                       
TCTTTGATGGTTATGCACATCTCTCTTCTGGTCTTGCCTGTGGCTTGGCTGGCCTTTCTGCTGGCATGGCTATTGGTATTGTTGGTGATGCCGGTGTTAGgtaca----aaagcctttttactttgtttcttacttctgtatgttttaaggtcttattgaattgcaatattgcatagtgacactcaactcttgatccactgact--------------------------------------------------------------------------------------

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT1G75630.2 (Arabidopsis thaliana), 5'ss of exon 2
TGTTCGACGGCTACGCGCACCTTTCATCTGGATTGTCGTGTGGGTTGGCTGGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcag
| ||||| ||||| || || || || |||||  |  | |||||  | |||||||| || || || ||||| ||||| |||||||| ||||||||||||||||| |||  |   |  ||| |  ||      || |    |   |   | | ||    || ||  ||  |   | | ||      |   | ||  ||   |||  |                                                                                 
TATTCGATGGCTATGCTCATCTCTCTTCTGGGCTAGCTTGTGGTCTTGCTGGTCTCTCTGCTGGTATGGCTATTGGAATCGTCGGTGATGCTGGTGTTAGgtaattgctat--ctctgctacatgat--cttaactgtttgattgcagcaattttgatcgattttc-acttgtttagaagtttctgagatagctttgttgtttgt---------------------------------------------------------------------------------

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT4G38920.1 (Arabidopsis thaliana), 5'ss of exon 2
TGTTCGACGGCTACGCGCACCTTTCATCTGGATTGTCGTGTGGGTTGGCTGGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcag
| |||||||| || || || || || |||||  |  | |||||| | |||||||| || || || |||||||| |||||||| || ||||||||||| ||||||       | |||     |||| |  | |    | || |  | |     |  || |  || | ||| ||    || ||||||  || |      | ||  ||   | | ||   | || ||                                                              
TCTTCGACGGATATGCTCATCTCTCTTCTGGTCTTGCTTGTGGGCTAGCTGGTCTTTCAGCTGGAATGGCCATAGGTATCGTTGGCGATGCTGGTGTCAGgtac------gatcctc----tgtgtccttctttgcagattcactct-----tatagcc--taatttgctaaa--agactcaattt-tata-----caagtatatctcccttatgaatcagaata-------------------------------------------------------------

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|162275184|gb|FC451771.1|FC451771
EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
EST: gi|162207190|gb|FC382512.1|FC382512
EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
EST: gi|162212908|gb|FC388916.1|FC388916
EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
EST: gi|67709770|gb|BJ965586.1|BJ965586
EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
EST: gi|67723846|gb|BJ974105.1|BJ974105
EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
EST: gi|67721529|gb|BJ971788.1|BJ971788
EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCCGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
EST: gi|162275185|gb|FC451772.1|FC451772
EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
EST: gi|162207189|gb|FC382511.1|FC382511
EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTTGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTTTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
EST: gi|162262065|gb|FC437886.1|FC437886
EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
EST: gi|162262064|gb|FC437885.1|FC437885
EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
EST: gi|162212907|gb|FC388915.1|FC388915
EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
EST: gi|6167058|gb|AW145377.1|AW145377
EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
EST: gi|19783928|gb|BQ040091.1|BQ040091
EST:     GGTCTATCGGCAGGCATGGACATTGGTATCGTCGGAGATGCTGGAGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT

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), 31 (downstream exon)
Score: 12

TGTTCGACGGCTACGCGCACCTTTCATCTGGATTGTCGTGTGGGTTGGCTGGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGATTTTCGCCGAGGCGCTGGCTTTATACGGACTTATCGTGGGTATCATTCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTCGACGGCTACGCGCACCTTTCATCTGGATTGTCGTGTGGGTTGGCTGGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG