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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTCAGAGTGCGGCAATTACCTGCTCCTTCGTCATGAAGATCTCCGTGAAGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgttgccctgtcttggagttggtgttgcttgcgttcgtggtagggtttggtaatttgaacgggcatcattggtatccgcgtgaacgtttctgta...

Basic information

species Physcomitrella patens
transcript PP1S58_148V6.4
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_148V6.4 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G061620_T05 (Zea mays), 5'ss of exon 1
-GCCTCAGAGTGCGGCAATTACCTGCTCCTTCGTCATGAAGATCTCCGTGAAGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgta---aatcgttgccctgtcttggagttggtgttgcttgcgttcgtggtagggtttggtaatt--tgaacgggcatcattggtatccgcgtgaacgtttctgta
  ||     || || |  |   |  |  |  ||  |||||| ||||||||||||||||||||||   |   ||| || | |||||   |||  | || | ||||   |  | |||| ||  |     || | | | | |   |||  |||  |  || |     |  |     ||     ||||  ||     | |  |  |||  
AACCCTCCGGTTCGACG-TAGGCGCCGGCGGCGAAATGAAGGTCTCCGTGAAGACGCTCAAGGGATCCAGCTTCCATATCGAAGTGGATCCTACCGACAAGgtaggcagcccttgcgctcccgatctgtcgctatggttctagttgctggatgtattggcgggctgcttgttaggttcgtttggggtcta---ggatttggctg--

upper sequence: PP1S58_148V6.4 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G105772_T01 (Zea mays), 5'ss of exon 1
GCCTCAGAGT--GCGGCAATTACCTGCTCCTTCGTCATGAAGATCTCCGTGAAGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgttgccctgtcttggagttggtgtt--gcttgcgttcgtggtagggtttggtaatttgaacgggcatcattggtatccgcgtgaacgtttctgta
   ||   |   ||||| |   |  |   |  ||  |||||| ||||||||||||||||||||||       ||| |  | |||||    ||| | || | ||||       |    |     ||  ||  | |  | ||    | |  |  |  || |      ||    |  |   ||||   |    |     | | ||  
AGTTCGACGCAGGCGGCGACGGC--GGCGCGCCGAGATGAAGGTCTCCGTGAAGACGCTCAAGGGATCTAGCTTCCAGATCGAAGTGGAGCCCACCGACAAGgtactcatcggttgcgctcccgatctgtcgctatgtttctagttgctgatgtattggcggggctgcttcgctagatttggctgctttttaggtttgtttg--

upper sequence: PP1S58_148V6.4 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ33528 (Selaginella moellendorffii), 5'ss of exon 1
GCCTCAGAGTGCGGCAATTACCTGCTCCTTCGTCATGAAGATCTCCGTGAAGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgttgccctgtcttggagttggtgttgcttgcgttcgtggtagggtttggtaatttgaacgggcatcattggtatccgcg----tgaacgtttctgta----
                                  |||||||| ||||| |||||||||||||| ||||| |||||||| || ||    || ||||| |||||||  ||    |  |  || |      ||      || |||  | |                | | ||  |  ||||  | | ||    | |  |||| ||      
----------------------------------ATGAAGATTTCCGTCAAGACGCTCAAGGGCAACCACTTCGATCTCGATGTGCAGCCGGCGGACACGgtaag-cgcgctcgcgaattcgctgctctgcccggcgctttctcgcttttcgccccctcgcgcagctggggttcttggattgctcgaaacttagggtttttggcacag

upper sequence: PP1S58_148V6.4 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ36878 (Selaginella moellendorffii), 5'ss of exon 1
GCCTCAGAGTGCGGCAATTACCTGCTCCTTCGTCATGAAGATCTCCGTGAAGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgttgccctgtcttggagttggtgttgcttgcgttcgtggtagggtttggtaatttgaacgggcatcattggtatccgcg----tgaacgtttctgta----
                                  |||||||| ||||| |||||||||||||| ||||| |||||||| || ||    || ||||| |||||||  ||    |  |  || |      ||      || |||  | |                | | ||  |  ||||  | | ||    | |  |||| ||      
----------------------------------ATGAAGATTTCCGTCAAGACGCTCAAGGGCAACCACTTCGATCTCGATGTGCAGCCGGCGGACACGgtaag-cgcgctcacgaattcgctgctctgcccggcgctttctcgcttttcgccccctcgcgcagctggggttcttggattgctcgaaacttagggtttttggcacag

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|67718017|gb|BJ968276.1|BJ968276
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|162200956|gb|FC377359.1|FC377359
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTAAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|208368341|gb|DC935682.1|DC935682
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|100371545|gb|BY968032.1|BY968032
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|67718144|gb|BJ968403.1|BJ968403
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|67718550|gb|BJ968809.1|BJ968809
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|67702167|gb|BJ962400.1|BJ962400
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|100369047|gb|BY984997.1|BY984997
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|100439827|gb|BY980259.1|BY980259
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|18342937|gb|BJ174973.1|BJ174973
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|67716636|gb|BJ966896.1|BJ966896
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|67718192|gb|BJ968451.1|BJ968451
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|67702885|gb|BJ963118.1|BJ963118
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|67703409|gb|BJ963642.1|BJ963642
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|67702261|gb|BJ962494.1|BJ962494
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|162261438|gb|FC438274.1|FC438274
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|67717915|gb|BJ968174.1|BJ968174
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|100440952|gb|BY962440.1|BY962440
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|162150756|gb|FC327028.1|FC327028
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTAAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|208390566|gb|DC937498.1|DC937498
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|208389212|gb|DC933240.1|DC933240
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
EST: gi|18367483|gb|BJ199566.1|BJ199566
EST:     AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACG                         GTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT
genomic: AGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTT

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: 26 (upstream exon), 34 (downstream exon)
Score: 13

GCCTCAGAGTGCGGCAATTACCTGCTCCTTCGTCATGAAGATCTCCGTGAAGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgtt ... ggttgtacagGTCTTGAATGTTAAGAGACAGATAGAAGATTCACAGGGCAAGGAATCATTTCCTTGTTCGCAGCAACTCCTTATCCATCAAGGCAAGGTGTTGAAAGATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTCAGAGTGCGGCAATTACCTGCTCCTTCGTCATGAAGATCTCCGTGAAGACGCTCAAGGGGAACCATTTCGATCTGGAAGTTAGTCCCGCGGATACGgtaaatcgttgccctgtcttggagttggtgttgcttgcgttcgtggtagggtttggtaatttgaacgggcatcattggtatccgcgtgaacgtttctgta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG