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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTTCTTAAAGATCTGGCTCTGTCAGGGTTTGGCCATATCGATGTCATTGATATGGACACCATTGACGTGTCCAACCTCAATCGACAATTCCTTTTCAGgtttgtaccctcatcatgtggactgaaaattctaggtgttgacttgagcattttaggatcagttgcaacttcaatttgaaagcgtatttggttgtgtaat...

Basic information

species Physcomitrella patens
transcript PP1S235_30V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S235_30V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os01g16540.1 (Oryza sativa), 5'ss of exon 2
AGCTTCTTAAAGATCTGGCTCTGTCAGGGTTTGGCCATATCGATGTCATTGATATGGACACCATTGACGTGTCCAACCTCAATCGACAATTCCTTTTCAGgtttgtaccctcatcatgtggactgaaaattctaggtgttgacttgagcattttaggatcagttgcaacttcaatttgaaagcgtatttggttgtgtaat---
|||| || || || ||||| || || || ||     | ||| | ||||| || ||||||||||| ||||| ||||||||||| || || ||||| ||||||||| |       || |     |   |    |      |||   ||  |    |     |   ||       |       ||  | ||  |  |||       
AGCTCCTCAAGGACCTGGCGCTCTCCGGATTCAAGAACATCCACGTCATCGACATGGACACCATCGACGTCTCCAACCTCAACCGCCAGTTCCTCTTCAGgttttttttactctccttccttccacacgcccacctaattg---tgccccccctcccccccactgttgtgcgatgccatcagattgttgcgccgtgagggaaa

upper sequence: PP1S235_30V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G007915_T02 (Zea mays), 5'ss of exon 2
AGCTTCTTAAAGATCTGGCTCTGTCAGGGTTTGGCCATATCGATGTCATTGATATGGACACCATTGACGTGTCCAACCTCAATCGACAATTCCTTTTCAGgtttgtaccctcatcatgtggactgaaaattctaggtgttgacttgagcattttaggatcagttgcaacttcaatttgaaagcgtatttggttgtgtaat
|||| || || || |||||||| || ||||||    |  |  | |||||||||||||||||||| ||||| |||||||||||||| || || || |||||||   |||  || ||                | |   |    |  | |    ||   ||| ||||    |       ||  | |     || |  |   |
AGCTCCTCAAGGACCTGGCTCTCTCCGGGTTTAAGAAACTGCACGTCATTGATATGGACACCATAGACGTCTCCAACCTCAATCGCCAGTTTCTCTTCAGgtccttacggtcgtctctccctacccgttccccattggcctccaagggtggattctcatctgttgattatctggcgagatggagggagaggatagggttt

upper sequence: PP1S235_30V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EDP05391 (Chlamydomonas reinhardtii), 5'ss of exon 1
AGCTTCTTAAAGATCTGGCTCTGTCAGGGTTTGGCCATATCGATGTCATTGATATGGACACCATTGACGTGTCCAACCTCAATCGACAATTCCTTTTCAGgtttgtaccctcatcatgtggactgaaaattctaggtgttg--acttgagcattttaggatcagttgcaacttcaatttgaaagcgtatttggttgtgtaat---
|| | || || || || || || || ||  | |  || ||||| |||||||| |||||||| ||||||||||| ||||| || || |||||||| ||| |||  |   ||||     |  | | ||    ||  ||    |  ||  | |  |   || |   |  ||  |  ||             | || |   |  |    
AGATCCTAAAGGACCTTGCGCTCTCGGGCGTGGTGCACATCGACGTCATTGACATGGACACAATTGACGTGTCGAACCTGAACCGCCAATTCCTATTCCGgtgagcggcctcg----ggcgcccgagccctcagggccccgggacgggggggtcccagcactcgc-gcggccacatcacactcagtcgtgtgctcccgccaccgg

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|100448450|gb|CJ972749.1|CJ972749
EST:     GATATGGACACCATTGACGTGTCCAACCTCAATCGACAATTCCTTTTCAG                         AATGCAAGATGTTGGGAAGCCCAAGGCTGAGGTGGCTGCACAAAGAGTGAT
genomic: GATATGGACACCATTGACGTGTCCAACCTCAATCGACAATTCCTTTTCAGgtttgtaccc ... tcttatgcagAATGCAAGATGTTGGGAAGCCCAAGGCTGAGGTGGCTGCACAAAGAGTGAT
EST: gi|100418521|gb|BY957460.1|BY957460
EST:     GATATGGACACCATTGACGTGTCCAACCTCAATCGACAATTCCTTTTCAG                         AATGCAAGATGTTGGGAAGCCCAAGGCTGAGGTGGCTGCACAAAGAGTGAT
genomic: GATATGGACACCATTGACGTGTCCAACCTCAATCGACAATTCCTTTTCAGgtttgtaccc ... tcttatgcagAATGCAAGATGTTGGGAAGCCCAAGGCTGAGGTGGCTGCACAAAGAGTGAT

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), 30 (downstream exon)
Score: 5

AGCTTCTTAAAGATCTGGCTCTGTCAGGGTTTGGCCATATCGATGTCATTGATATGGACACCATTGACGTGTCCAACCTCAATCGACAATTCCTTTTCAGgtttgtaccc ... tcttatgcagAATGCAAGATGTTGGGAAGCCCAAGGCTGAGGTGGCTGCACAAAGAGTGATGCAAAGAGTGAAGGGTGTCACAGTTGTCCCTCACTTTTGCAGAATAGAG




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