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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGCATCTGCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggttgtacacgtcgttggagctgttgttccgtgaatgttggtctttgtgtaagcgaggatgtgaggttgaaatggtaggatggtgggaggggg...

Basic information

species Physcomitrella patens
transcript PP1S69_31V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S69_31V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EDO98738 (Chlamydomonas reinhardtii), 5'ss of exon 4
GTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGCATCTGCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggttgtacacgtcgttggagctgttgt--tccgtgaatgttggtctttgtgtaagcgaggatgtgaggttgaaatggtaggatggtgggaggggg-
             || | |||||||||| | || ||  | || |||||||||||||| ||||| || || |||||||||||||| || ||||| || |||||  ||     |    ||  |  |||  |  ||   | | |        | |   |   |    |  ||||   |   ||  || |||      || |   | 
-------------GTGTACCACCCCAACGTGAACAGCCAGGGCAGCATCTGCCTGGACATTCTCAAAGACCAGTGGAGCCCTGCCCTGACCATTTCCAAGgtaagtcaagcgccggcgg-gcgggacttcatggcattcatcggcagcaggcccaggaca--ttacaatgttgcgggaaagcgggaggtgccctggtgaccgc

upper sequence: PP1S69_31V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ27529 (Selaginella moellendorffii), 5'ss of exon 3
GTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGCATCTGCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggttgtac-acgtcgttggagctgttgttccgtgaat--gttggtctttgtgtaagcgaggatgtgaggttgaaatggtaggatggtgggaggggg
 ||||| || ||||| || || |||||||||||||| ||||| |||||||| || || ||||| ||||||||||||||||| ||  | || || || |||||  |||  ||   | ||            |  ||| ||||       |||  |||   |         | |   | |     | | |   | |      |  
ATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGCATCTGTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctttcctcgacaaaaccaagagagaggtttcgtgttctaaatggcttttcgttccttttctttctctcgctcgctcgatcgatcgatttaccag--

upper sequence: PP1S69_31V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ35297 (Selaginella moellendorffii), 5'ss of exon 3
GTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGCATCTGCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggttgtac----acgtcgttggagctgttgttccgtgaatg-ttggtctttgtgtaagcgaggatgtgaggttgaaatggtaggatggtgggaggggg
 ||||| || ||||| || || |||||||||||||| ||||| |||||||| || || ||||| ||||||||||||||||| ||  | || || || |||||  |||  ||   |    ||   |   ||||| | ||    | |||| ||  || ||   |       | |     | |  |  | | |  |     |      
ATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGCATCTGTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctttcctcgacaaccaagagagagctctcgtgttctaaatggtttttcgttccttttctttcgctcgctcgctcgatcgatcgatttaccag------

upper sequence: PP1S69_31V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ15547 (Selaginella moellendorffii), 5'ss of exon 3
GTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGCATCTGCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggttgtacacgtcgttggagctgttgttccgtgaatgttggtctttgtgtaagcgaggatgtgaggttgaaatggtaggatggtgggaggggg
|||| |||| || || |||||||| |||||||| || ||||| ||||||||||| || || || ||||||||||||||||| ||  | || || || |||||  |   | | |   |    ||     | |   ||  | |||     ||  |     | |  || |      |   |                      
GTTCCGGACGAAAGTCTTCCACCCAAACATCAACAGCAATGGAAGCATCTGCCTCGACATCCTCAAGGAGCAGTGGAGCCCCGCATTGACGATCTCCAAGgtaagaaagctcttggc----ttttgcttttcactcgatcaat--ccatcactcctcgatcttggtttcttcttcccag---------------------

upper sequence: PP1S69_31V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ11261 (Selaginella moellendorffii), 5'ss of exon 3
GTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGCATCTGCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggttgtacacgtcg---ttggagctgttgttccgtgaat-gttggtctttgtgtaagcgaggatgtgaggttgaaatggtaggatggtgggaggggg
|||| |||| || || |||||||| |||||||| || ||||| ||||||||||| || || || ||||||||||||||||| ||  | || || || |||||| |   | | |     | |   ||    |  |   ||| | | | || | |||| || |   |      |                                
GTTCCGGACGAAAGTCTTCCACCCAAACATCAACAGCAATGGAAGCATCTGCCTCGACATCCTCAAGGAGCAGTGGAGCCCCGCATTGACGATCTCCAAGgtgagaaagctctggcttttgcttttcactcgatcaatccatcactcgtcgatcttggtttcttcttcccag--------------------------------

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|162193815|gb|FC369223.1|FC369223
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|208392917|gb|DC928603.1|DC928603
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|100444703|gb|BY982532.1|BY982532
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTATCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|208368971|gb|DC955056.1|DC955056
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|208354417|gb|DC953823.1|DC953823
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|100380283|gb|BY968931.1|BY968931
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|208367859|gb|DC950940.1|DC950940
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|162249610|gb|FC426490.1|FC426490
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|208358988|gb|DC957736.1|DC957736
EST:     CTGAAGNAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: CTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|208386994|gb|DC956949.1|DC956949
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|162239360|gb|FC416564.1|FC416564
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|208353619|gb|DC946357.1|DC946357
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|208366616|gb|DC955650.1|DC955650
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|208377304|gb|DC927020.1|DC927020
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|208388401|gb|DC957039.1|DC957039
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|22492225|gb|BU052148.1|BU052148
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|37825009|gb|BJ583075.1|BJ583075
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|208385507|gb|DC956677.1|DC956677
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|208370020|gb|DC948115.1|DC948115
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|208390085|gb|DC942386.1|DC942386
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|67727148|gb|BJ977407.1|BJ977407
EST:     AGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCCAAATCCGGATGATCC
genomic: AGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGA-CCCAAATCCGGATGATCC
EST: gi|208398315|gb|DC920714.1|DC920714
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|18336116|gb|BJ168138.1|BJ168138
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|67727765|gb|BJ978024.1|BJ978024
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|208358830|gb|DC957630.1|DC957630
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|18335330|gb|BJ167348.1|BJ167348
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
EST: gi|162193814|gb|FC369222.1|FC369222
EST:     GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAG                         GTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC
genomic: GCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCC

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), 34 (downstream exon)
Score: 68

GTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGCATCTGCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggt ... gttggtgcagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCCCTTGTACCGGAAATCGCTCACATGTACAAGACAGACAGGCATAAGTACG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCAGGACCAAGGTTTTCCACCCCAACATCAATAGTAATGGGAGCATCTGCCTGGATATTCTGAAGGAGCAGTGGAGCCCTGCTCTAACCATATCTAAGgtgcgttggttgtacacgtcgttggagctgttgttccgtgaatgttggtctttgtgtaagcgaggatgtgaggttgaaatggtaggatggtgggaggggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG