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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGTGTTTACTGCCCTGGAGGGCCGGACTCTGATTTTGAATACAGTACTCAATCATACACTGGTTACGAACCTACCAGCATGCGAGCCATCCGGGCGAGgtatggatttgtattcgaacctataaccttttcacttttgcagctttttgatttttattctcctatgacgtccacctaatctagtttcattaactgagga...

Basic information

species Physcomitrella patens
transcript PP1S185_41V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S185_41V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 1
TTTGTGTTTACTGCCCTGGAGGGCCGGACTCTGATTTTGAATACAGTACTCAATCATACACTGGTTACGAACCTACCAGCATGCGAGCCATCCGGGCGAGgta------tggatttgtattcgaacctataaccttttcacttttgcagctttttgatttttattctcctatgacgtccacctaatcta-gtttcattaactgagga
| ||||| |||||||| || || || ||||| || || || ||||| || ||||| |||||||| |||||||| ||||||||||| ||||| ||||| |||||        |   || ||| |   | ||      || |  |  ||   | ||| |  |||  | | |   |  || ||   | |    ||||   | ||      
TCTGTGTCTACTGCCCGGGCGGTCCCGACTCCGACTTCGAGTACAGCACGCAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcactggagtgcattggtgtccatgcttcctttaact--gcttttatttaaacttttctgtacctaggagtgcagtgacttcgtgtttgtgttaca-----

upper sequence: PP1S185_41V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA04G36790.1 (Glycine max), 5'ss of exon 1
TTTGTGTTTACTGCCCTGGAGGGCCGGACTCTGATTTTGAATACAGTACTCAATCATACACTGGTTACGAACCTACCAGCATGCGAGCCATCCGGGCGAGgtatggatttgtattcgaacctataaccttttcacttttgcagcttt--ttgatttttattctc--ctatgacgtccacctaatcta---gtttcattaactgagga
| || || |||||||| || || || ||||| ||||| || ||||||||||| || ||||||||||||||||| ||||||||||| || || || |||||||| || ||| | || |    | |  | | |    |   | |  |     ||||||| |   |      |   ||| |  |||||      ||   || | |     
TCTGCGTCTACTGCCCCGGGGGACCTGACTCCGATTTCGAGTACAGTACTCAGTCTTACACTGGTTACGAACCAACCAGCATGCGCGCAATTCGTGCGAGgta-gggtttatgttag---ttttgtcttctgtgttagggtaaatggaactgattttaagagtgaatagttgagtcaaattaatccctatattctgttgatttt---

upper sequence: PP1S185_41V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT5G50320.1 (Arabidopsis thaliana), 5'ss of exon 1
TTTGTGTTTACTGCCCTGGAGGGCCGGACTCTGATTTTGAATACAGTACTCAATCATACACTGGTTACGAACCTACCAGCATGCGAGCCATCCGGGCGAGgtatggatttgtattcgaacctataaccttttcactt---ttgcagctttttgatttttattctcctatgacgtccacctaatctagtttcattaactgagga--
| || ||||| || || || || || |||||||| ||||| || |||||||| || |||||||| || || ||||||||||||||||| || || || ||||   || | || |||     |||    ||   ||||   || |||||| | ||||  | |  |   | |   |     | |  ||||||   |   |||     
TATGCGTTTATTGTCCCGGTGGACCTGACTCTGACTTTGAGTATAGTACTCAGTCTTACACTGGATATGAGCCTACCAGCATGCGAGCTATTCGAGCCAGgtgaagagt-gtcttctgtgttatggaattgaaacttgtattacagcttctggattgatctagtaa-agggtttggggtttaggtagttt---tgggtgaaattt

upper sequence: PP1S185_41V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv17s0000g10190.t01 (Vitis vinifera), 5'ss of exon 1
TTTGTGTTTACTGCCCTGGAGGGCCGGACTCTGATTTTGAATACAGTACTCAATCATACACTGGTTACGAACCTACCAGCATGCGAGCCATCCGGGCGAGgtatggatttgtattcgaacctataaccttttcacttttgcagctttttgatttt-tattctcctatgacgtccacctaatctagtttcattaactgagga-
|||||||||| ||||||||||| || || ||||||||||| |||||||| || || |||||||| ||||| || ||||||||||| || || || || ||||| || ||| | ||      | |||  || |   || |   | | | || ||   |  |     || |     |    | |||  |   || | | | || 
TTTGTGTTTATTGCCCTGGAGGACCTGATTCTGATTTTGAGTACAGTACACAGTCGTACACTGGATACGAGCCCACCAGCATGCGCGCGATTCGTGCTAGgta-gggtttttctttaggttt-taattttatttgttgtattgatctctgtttggatgatgggaaatcataggaaaaggaactaagtcttttcattaatgaa

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|162167941|gb|FC344879.1|FC344879
EST:     CAATCATACACTGGTTACGAACCTACCAGCATGCGAGCCATCCGGGCGAG                         GTACAATCCTTATGTTCAAGCTCGAGGCCGAATCGACCAGTTGAAGAGGCT
genomic: CAATCATACACTGGTTACGAACCTACCAGCATGCGAGCCATCCGGGCGAGgtatggattt ... tgttctacagGTACAATCCTTATGTTCAAGCTCGAGGCCGAATCGACCAGTTGAAGAGGCT
EST: gi|67718674|gb|BJ968933.1|BJ968933
EST:     CAATCATACACTGGTTACGAACCTACCAGCATGCGAGCCATCCGGGCGAG                         GTACAATCCTTATGTTCAAGCTCGAGGCCGAATCGACCAGTTGAAGAGGCT
genomic: CAATCATACACTGGTTACGAACCTACCAGCATGCGAGCCATCCGGGCGAGgtatggattt ... tgttctacagGTACAATCCTTATGTTCAAGCTCGAGGCCGAATCGACCAGTTGAAGAGGCT
EST: gi|162190238|gb|FC366396.1|FC366396
EST:     CAATCATACACTGGTTACGAACCTACCAGCATGCGAGCCATCCGGGCGAG                         GTACAATCCTTATGTTCAAGCTCGAGGCCGAATCGACCAGTTGAAGAGGCT
genomic: CAATCATACACTGGTTACGAACCTACCAGCATGCGAGCCATCCGGGCGAGgtatggattt ... tgttctacagGTACAATCCTTATGTTCAAGCTCGAGGCCGAATCGACCAGTTGAAGAGGCT

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: 29 (upstream exon), 35 (downstream exon)
Score: 14

TTTGTGTTTACTGCCCTGGAGGGCCGGACTCTGATTTTGAATACAGTACTCAATCATACACTGGTTACGAACCTACCAGCATGCGAGCCATCCGGGCGAGgtatggattt ... tgttctacagGTACAATCCTTATGTTCAAGCTCGAGGCCGAATCGACCAGTTGAAGAGGCTAGGTCACAGTGTAGATAAG




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