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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTTGACGGCTACGCGCATCTTTCTTCGGGATTGTCTTGCGGGTTGGCAGGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacgaacccttgcaatgtggtgatgtatgggaatacgtagtgaagttggaaagagagatgtaatcgggattgaaatggattcgcagagggttcacggtgatggacatgaggtttgaggatgcagagtgagttatgggagggtttggtgtgttgtggatgtggttgttaacgtggaggatggcatcgtttgcag

Basic information

species Physcomitrella patens
transcript PP1S45_100V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S45_100V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
TGTTTGACGGCTACGCGCATCTTTCTTCGGGATTGTCTTGCGGGTTGGCAGGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcgg-acgaacccttgcaatgtggtgatgtatgggaatacgtag-tgaagttggaaagagagatgtaatcgggattgaaatggattcgcagagggttcacggtgatggacatgaggtttgaggatgcagagtgagttatgggagggtttggtgtgttgtggatgtggttgttaacgtggaggatggcatcgtttgcag
| ||||||||||| || || || || || ||  |  | || ||  | || || ||  | |||||||||||||| || |||||||| ||||||||||| |||||  |   |   | |||   || |  || | ||||        | | |||   |     |    ||| |   |   |       |   |    |    |                                                                                                     
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctcttatcatattctgctatatgctttggtttggctgataatatgctggtcaatgcagcagcagtaatggcaggcacttctaaaact-----------------------------------------------------------------------------------------------------

upper sequence: PP1S45_100V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G101020_T01 (Zea mays), 5'ss of exon 2
TGTTTGACGGCTACGCGCATCTTTCTTCGGGATTGTCTTGCGGGTTGGCAGGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacgaacccttgcaatgtggtgatgtatgggaatacgtag--tgaagttggaaagagagatgtaatcgggattgaaatggattcgcagagggttcacggtgatggacatgaggtttgaggatgcagagtgagttatgggagggtttggtgtgttgtggatgtggttgttaacgtggaggatggcatcgtttgcag
| ||||||||||| || || || || || ||  |  | || ||  | || || ||  | |||||||||||||| || |||||||| ||||||||||| ||||   |       | ||   || | ||||| |      ||   | |  |||   |     |  | ||| | | |  || | |     |||    |   | ||                                                                                                   
TCTTTGACGGCTATGCCCACCTGTCGTCTGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtgaagacaattgctttatcatattgtgatatgctttgatggtttggctgataatatgttggtaaatgcagtagtaatggcaggcacttct--aaacctcca---------------------------------------------------------------------------------------------------

upper sequence: PP1S45_100V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT4G38920.1 (Arabidopsis thaliana), 5'ss of exon 2
TGTTTGACGGCTACGCGCATCTTTCTTCGGGATTGTCTTGCGGGTTGGCAGGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacgaacccttgcaatgtggtg-atgtatgggaatacgtagtgaagttggaaagagagatgtaatcgggattgaaatggat-tcgcagagggttcacggtgatggacatgaggtttgaggatgcagagtgagttatgggagggtttggtgtgttgtggatgtggttgttaacgtggaggatggcatcgtttgcag
| || ||||| || || ||||| ||||| ||  |  |||| ||| | || || || || || || |||||||| ||||||||||| ||||||||||| |||||     ||| ||  ||     |  |      ||         |||   | || |  | | |||   |||    ||  || |  || || |  | |  |||   |                                                                                               
TCTTCGACGGATATGCTCATCTCTCTTCTGGTCTTGCTTGTGGGCTAGCTGGTCTTTCAGCTGGAATGGCCATAGGTATCGTTGGCGATGCTGGTGTCAGgta-----cgatcctctgtgtccttctttgcagattcactcttatagcctaatttgctaaa-agactcaatttt-atacaagtatatctcccttatgaatcagaata----------------------------------------------------------------------------------------------

upper sequence: PP1S45_100V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ33972 (Selaginella moellendorffii), 5'ss of exon 2
TGTTTGACGGCTACGCGCATCTTTCTTCGGGATTGTCTTGCGGGTTGGCAGGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcgga--cgaacccttgcaatgtggtgatgtatgggaatacgtagtgaagttggaaagagagatgtaatcgggattgaaatggattcgcagagggttcacggtgatggacatgaggtttgaggatgcagagtgagttatgggagggtttggtgtgttgtggatgtggttgttaacgtggaggatggcatcgtttgcag
| || || |||||||||||||| ||||| |||||| |||||||| | || || || ||||| || ||||| || || || |||||||| ||||| ||||||||  |    | ||| ||| |   ||  || | | |  || ||  |   |    | ||  |     |||   | | | |         |          | |                                                                                                   
TCTTCGATGGCTACGCGCATCTCTCTTCCGGATTGGCTTGCGGGCTTGCTGGTCTCTCGGCTGGGATGGCGATTGGAATTGTTGGAGACGCTGGAGTGAGgtaaagtttccaaactctttcttcgttttgct-tcttcgactagttcacgcttgtagacggtcgagtgtctgctg-actatctccagctttagctcaactaa---------------------------------------------------------------------------------------------------

upper sequence: PP1S45_100V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ37480 (Selaginella moellendorffii), 5'ss of exon 2
TGTTTGACGGCTACGCGCATCTTTCTTCGGGATTGTCTTGCGGGTTGGCAGGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgt--agcggacgaacccttgcaatgtggtgatgtatgggaatacgtagtgaagttggaaagagagatgtaatcgggattgaaatggattcgcagagggttcacggtgatggacatgaggtttgaggatgcagagtgagttatgggagggtttggtgtgttgtggatgtggttgttaacgtggaggatggcatcgtttgcag
| || || |||||||||||||| ||||| |||||| |||||||| | || || || ||||| || ||||| || || || |||||||| ||||| |||||||  ||    | ||| ||| |   ||  || ||  | | ||||  |   |    | ||  |     |||   | | | |         |          | |                                                                                                   
TCTTCGATGGCTACGCGCATCTCTCTTCCGGATTGGCTTGCGGGCTTGCTGGCCTCTCGGCTGGGATGGCGATTGGAATTGTTGGAGACGCTGGAGTGAGgtcaagtttccaaactctttcttcgttttgctgcttcg-aatagttcacgcttgtagacggtcgagtgtctgctg-actatctccagctttagctcaactaa---------------------------------------------------------------------------------------------------

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|67720441|gb|BJ970700.1|BJ970700
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|6167364|gb|AW145628.1|AW145628
EST:     GCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|162249537|gb|FC426469.1|FC426469
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|37833247|gb|BJ591259.1|BJ591259
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|7286495|gb|AW598982.1|AW598982
EST:     GCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|208382900|gb|DC928325.1|DC928325
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|162239793|gb|FC417192.1|FC417192
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|37833369|gb|BJ591381.1|BJ591381
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|18339672|gb|BJ171699.1|BJ171699
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|162249538|gb|FC426470.1|FC426470
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|37828255|gb|BJ586267.1|BJ586267
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|162239794|gb|FC417193.1|FC417193
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|37829944|gb|BJ587956.1|BJ587956
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|67693162|gb|BJ953395.1|BJ953395
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|67700019|gb|BJ960252.1|BJ960252
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|19787589|gb|BQ040646.1|BQ040646
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|208388270|gb|DC956992.1|DC956992
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|37829724|gb|BJ587736.1|BJ587736
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|37824068|gb|BJ582134.1|BJ582134
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|208346445|gb|DC917398.1|DC917398
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
EST: gi|208366239|gb|DC947511.1|DC947511
EST:     GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAG                         GGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT
genomic: GGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCAT

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), 35 (downstream exon)
Score: 59

TGTTTGACGGCTACGCGCATCTTTCTTCGGGATTGTCTTGCGGGTTGGCAGGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacg ... tcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCATTTTCGCTGAGGCGCTTGCCTTGTATGGACTGATCGTCGGCATTATCTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTTGACGGCTACGCGCATCTTTCTTCGGGATTGTCTTGCGGGTTGGCAGGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcggacgaacccttgcaatgtggtgatgtatgggaatacgtagtgaagttggaaagagagatgtaatcgggattgaaatggattcgcagagggttcacggtgatggacatgaggtttgaggatgcagagtgagttatgggagggtttggtgtgttgtggatgtggttgttaacgtggaggatggcatcgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG